Daily Papers

Virtual cell modeling represents an emerging frontier at the intersection of artificial intelligence and biology, aiming to predict quantities such as responses to diverse perturbations quantitatively. However, autonomously building computational models for virtual cells is challenging due to the complexity of biological systems, the heterogeneity of data modalities, and the need for domain-specific expertise across multiple disciplines. Here, we introduce CellForge, an agentic system that leverages a multi-agent framework that transforms presented biological datasets and research objectives directly into optimized computational models for virtual cells. More specifically, given only raw single-cell multi-omics data and task descriptions as input, CellForge outputs both an optimized model architecture and executable code for training virtual cell models and inference. The framework integrates three core modules: Task Analysis for presented dataset characterization and relevant literature retrieval, Method Design, where specialized agents collaboratively develop optimized modeling strategies, and Experiment Execution for automated generation of code. The agents in the Design module are separated into experts with differing perspectives and a central moderator, and have to collaboratively exchange solutions until they achieve a reasonable consensus. We demonstrate CellForge's capabilities in single-cell perturbation prediction, using six diverse datasets that encompass gene knockouts, drug treatments, and cytokine stimulations across multiple modalities. CellForge consistently outperforms task-specific state-of-the-art methods. Overall, CellForge demonstrates how iterative interaction between LLM agents with differing perspectives provides better solutions than directly addressing a modeling challenge. Our code is publicly available at https://github.com/gersteinlab/CellForge.

Cell painting is a popular technique for creating human-interpretable, high-contrast images of cell morphology. There are two major issues with cell paint: (1) it is labor-intensive and (2) it requires chemical fixation, making the study of cell dynamics impossible. We train a diffusion model (Morphological Observation Neural Enhancement Tool, or MONET) on a large dataset to predict cell paint channels from brightfield images. We show that model quality improves with scale. The model uses a consistency architecture to generate time-lapse videos, despite the impossibility of obtaining cell paint video training data. In addition, we show that this architecture enables a form of in-context learning, allowing the model to partially transfer to out-of-distribution cell lines and imaging protocols. Virtual cell painting is not intended to replace physical cell painting completely, but to act as a complementary tool enabling novel workflows in biological research.

Virtual cell modeling predicts molecular state changes under genetic perturbations in silico, which is essential for biological mechanism studies. However, existing approaches suffer from unconstrained reasoning, uninterpretable predictions, and retrieval signals that are weakly aligned with regulatory topology. To address these limitations, we propose AROMA, an Augmented Reasoning Over a Multimodal Architecture for virtual cell genetic perturbation modeling. AROMA integrates textual evidence, graph-topology information, and protein sequence features to model perturbation-target dependencies, and is trained with a two-stage optimization strategy to yield predictions that are both accurate and interpretable. We also construct two knowledge graphs and a perturbation reasoning dataset, PerturbReason, containing more than 498k samples, as reusable resources for the virtual cell domain. Experiments show that AROMA outperforms existing methods across multiple cell lines, and remains robust under zero-shot evaluation on an unseen cell line, as well as in knowledge-sparse, long-tail scenarios. Overall, AROMA demonstrates that combining knowledge-driven multimodal modeling with evidence retrieval provides a promising pathway toward more reliable and interpretable virtual cell perturbation prediction. Model weights are available at https://huggingface.co/blazerye/AROMA. Code is available at https://github.com/blazerye/AROMA.

Virtual cell modeling aims to predict cellular responses to perturbations. Existing virtual cell models rely heavily on large-scale single-cell datasets, learning explicit mappings between gene expression and perturbations. Although recent models attempt to incorporate multi-source biological information, their generalization remains constrained by data quality, coverage, and batch effects. More critically, these models often function as black boxes, offering predictions without interpretability or consistency with biological principles, which undermines their credibility in scientific research. To address these challenges, we present VCWorld, a cell-level white-box simulator that integrates structured biological knowledge with the iterative reasoning capabilities of large language models to instantiate a biological world model. VCWorld operates in a data-efficient manner to reproduce perturbation-induced signaling cascades and generates interpretable, stepwise predictions alongside explicit mechanistic hypotheses. In drug perturbation benchmarks, VCWorld achieves state-of-the-art predictive performance, and the inferred mechanistic pathways are consistent with publicly available biological evidence.

Virtual cell (VC) models aim to predict cellular responses to any perturbations in silico and have emerged as a promising approach for drug discovery and precision medicine. Yet, a clear gap still remains: while models routinely reported impressive results on standard benchmarks, it is unclear whether their predictions are truly meaningful in practice. This is mainly due to limitations in current evaluation setups, which are often overly simplified or inconsistent, and do not reflect the complexity and variability of real biological systems. Here, we introduce a standardized and modular benchmarking framework for virtual cell prediction. Our framework evaluates diverse models under in-the-wild challenging scenarios, including unseen cell contexts, unseen perturbations, and cross-dataset generalization, which better reflect practical applications. Our analysis shows that model performance is highly context-dependent and shaped by task design and evaluation criteria. In commonly used setups, performance is often overestimated, and naive dataset aggregation can even reduce performance. When evaluated under more strict conditions, model performance drops markedly, indicating limited robustness to shifts across cellular contexts. In unseen perturbation settings, models including simple linear approaches capture global transcriptional trends but fail to recover fine-grained perturbation-specific effects. In addition, different evaluation metrics focus on different biological properties, leading to substantially different model rankings. Together, our framework provides a more reliable and biologically grounded evaluation, offering clearer guidance for applying virtual cell models in real scenarios.

Virtual-cell models aim to predict how cell populations respond to perturbations, but control and treated cells are measured as unpaired populations, complicating the learning of perturbation-specific effects. We present SCALE, a conditional transport model that represents cells as unordered sets and predicts treated populations without cell-level matching. A shared set-aware encoder and conditional DiT backbone learn latent transport, making endpoint supervision directly delta-aligned without an auxiliary delta objective. Across genetic, chemical, developmental and immune perturbations, SCALE recovered gene-expression changes, response directions and population structure. In CRISPR data with dominant cell-line effects, SCALE outperformed competing methods across seven metrics and maintained separation among gene-target representations rather than collapsing them into a shared region. SCALE further prioritized cytokines predicted to produce distinct immune activation and inflammatory responses. Experiments using matched PBMC samples from three donors confirmed these predicted differences. Together, SCALE enables perturbation-specific prediction from unpaired populations and supports experimental prioritization.

Drug discovery is fundamentally a process of inferring the effects of treatments on patients, and would therefore benefit immensely from computational models that can reliably simulate patient responses, enabling researchers to generate and test large numbers of therapeutic hypotheses safely and economically before initiating costly clinical trials. Even a more specific model that predicts the functional response of cells to a wide range of perturbations would be tremendously valuable for discovering safe and effective treatments that successfully translate to the clinic. Creating such virtual cells has long been a goal of the computational research community that unfortunately remains unachieved given the daunting complexity and scale of cellular biology. Nevertheless, recent advances in AI, computing power, lab automation, and high-throughput cellular profiling provide new opportunities for reaching this goal. In this perspective, we present a vision for developing and evaluating virtual cells that builds on our experience at Recursion. We argue that in order to be a useful tool to discover novel biology, virtual cells must accurately predict the functional response of a cell to perturbations and explain how the predicted response is a consequence of modifications to key biomolecular interactions. We then introduce key principles for designing therapeutically-relevant virtual cells, describe a lab-in-the-loop approach for generating novel insights with them, and advocate for biologically-grounded benchmarks to guide virtual cell development. Finally, we make the case that our approach to virtual cells provides a useful framework for building other models at higher levels of organization, including virtual patients. We hope that these directions prove useful to the research community in developing virtual models optimized for positive impact on drug discovery outcomes.

Virtual cells are evolving from single-task predictive models toward programmable biological simulation systems, yet heterogeneous data, models, and validation evidence still lack a unified organizational framework. Here, we present PRAXIS-VirtualCell, a modular framework that organizes biological data, predictive models, perturbations, adapters, execution environments, and validation evidence to enable reproducible and auditable virtual experiments. The system supports cross-species tasks spanning Escherichia coli, Saccharomyces cerevisiae, and human K562 cells, while using biological contracts and evidence-aware execution to distinguish supported predictions from extrapolation and abstention. By further integrating agentic orchestration, PRAXIS-VirtualCell automatically translates natural-language questions into traceable virtual experiments, providing a unified runtime foundation for trustworthy and scalable Virtual Cell systems.

The challenge of translating vast, multimodal biological data into predictive and mechanistic understanding of cellular function is a central theme in modern biology. Virtual cells, or digital cellular twins, have emerged as a critical paradigm to meet this challenge by creating integrative computational models of cellular processes. This review synthesizes the evolution and current state of the virtual cell, from foundational mechanistic frameworks like the Virtual Cell that employ deterministic and stochastic simulations to the recent transformative impact of artificial intelligence and foundation models. We examine the core technological pillars required to build these models, including the integration of various data types, such as single-cell and spatial omics, the spectrum of modeling approaches, and the bioengineering principles that connect simulation to application. We further discuss key applications, frameworks for model benchmarking and validation, and the significant hurdles that remain, including computational scalability, parameter inference, and ethical considerations, which provides a roadmap for development of predictive virtual cells that promise to revolutionize biomedical research and clinical practice.

Predicting cellular responses to genetic perturbations is a central capability for virtual cells and a key step toward computational modeling of biological interventions. Most existing models directly map an unperturbed molecular profile and perturba- tion to the resulting observation without explicitly representing the latent cellular transition induced by the intervention. We introduce a mechanism-centric virtual cell world model that represents cellular state as a set of Latent Mechanism Units (LMUs) and treats genetic perturbations as actions on these latent states. Each LMU combines a reusable identity grounded in multimodal biological evidence with an observation-specific state, allowing a perturbation to induce mechanism- specific stochastic transitions before decoding the resulting transcriptional response. We train VCLMU through two-stage pretraining, first on around 200K pseudo-bulk perturbation profiles and then on gene-aligned single-cell perturbation data. Across six perturbation-disjoint benchmarks, VCLMU consistently improves perturbation- specific response recovery over strong baselines while maintaining competitive global response accuracy. We further analyze learned LMUs through enrichment between perturbation responses and LMU gene sets and show that they capture structured biological response programs. These results support mechanism-level latent state transition as a useful formulation for virtual cell models that aim to predict and interpret cellular responses to biological interventions.

The cell is arguably the most fundamental unit of life and is central to understanding biology. Accurate modeling of cells is important for this understanding as well as for determining the root causes of disease. Recent advances in artificial intelligence (AI), combined with the ability to generate large-scale experimental data, present novel opportunities to model cells. Here we propose a vision of leveraging advances in AI to construct virtual cells, high-fidelity simulations of cells and cellular systems under different conditions that are directly learned from biological data across measurements and scales. We discuss desired capabilities of such AI Virtual Cells, including generating universal representations of biological entities across scales, and facilitating interpretable in silico experiments to predict and understand their behavior using virtual instruments. We further address the challenges, opportunities and requirements to realize this vision including data needs, evaluation strategies, and community standards and engagement to ensure biological accuracy and broad utility. We envision a future where AI Virtual Cells help identify new drug targets, predict cellular responses to perturbations, as well as scale hypothesis exploration. With open science collaborations across the biomedical ecosystem that includes academia, philanthropy, and the biopharma and AI industries, a comprehensive predictive understanding of cell mechanisms and interactions has come into reach.

Modeling cellular states and predicting their responses to perturbations are central challenges in computational biology and the development of virtual cells. Existing foundation models for single-cell transcriptomics provide powerful static representations, but they do not explicitly model the distribution of cellular states for generative simulation. Here, we introduce Lingshu-Cell, a masked discrete diffusion model that learns transcriptomic state distributions and supports conditional simulation under perturbation. By operating directly in a discrete token space that is compatible with the sparse, non-sequential nature of single-cell transcriptomic data, Lingshu-Cell captures complex transcriptome-wide expression dependencies across approximately 18,000 genes without relying on prior gene selection, such as filtering by high variability or ranking by expression level. Across diverse tissues and species, Lingshu-Cell accurately reproduces transcriptomic distributions, marker-gene expression patterns and cell-subtype proportions, demonstrating its ability to capture complex cellular heterogeneity. Moreover, by jointly embedding cell type or donor identity with perturbation, Lingshu-Cell can predict whole-transcriptome expression changes for novel combinations of identity and perturbation. It achieves leading performance on the Virtual Cell Challenge H1 genetic perturbation benchmark and in predicting cytokine-induced responses in human PBMCs. Together, these results establish Lingshu-Cell as a flexible cellular world model for in silico simulation of cell states and perturbation responses, laying the foundation for a new paradigm in biological discovery and perturbation screening.

Recent advances in machine learning and large-scale biological data collections have revived the prospect of building a virtual cell, a computational model of cellular behavior that could accelerate biological discovery. One of the most compelling promises of this vision is the ability to perform in silico phenotypic screens, in which a model predicts the effects of cellular perturbations in unseen biological contexts. This task combines heterogeneous textual inputs with diverse phenotypic outputs, making it particularly well-suited to LLMs and agentic systems. Yet, no standard benchmark currently exists for this task, as existing efforts focus on narrower molecular readouts that are only indirectly aligned with the phenotypic endpoints driving many real-world drug discovery workflows. In this work, we present AssayBench, a benchmark for phenotypic screen prediction, built from 1,920 publicly available CRISPR screens spanning five broad classes of cellular phenotypes. We formulate the screen prediction task as a gene rank prediction for each screen and introduce the adjusted nDCG, a continuous metric for comparing performance across heterogeneous assays. Our extensive evaluation shows that existing methods remain far from empirically estimated performance ceilings and zero-shot generalist LLMs outperform biology-specific LLMs and trainable baselines. Optimization techniques such as fine-tuning, ensembling, and prompt optimization can further improve LLM performance on this task. Overall, AssayBench offers a practical testbed for measuring progress toward in silico phenotypic screening and, more broadly, virtual cell models.

Predicting single-cell transcriptional responses to genetic, chemical and cytokine perturbations is a fundamental challenge in computational biology and AI Virtual Cell (AIVC) modeling, with direct implications for drug discovery and the elucidation of gene regulatory networks. Existing approaches often rely on auxiliary cell-state encoders, hierarchical variational autoencoders, dedicated Transformer encoder-decoder modules, or gene-interaction priors to compress high-dimensional expression profiles into latent representations. While effective, these designs increase architectural complexity and may limit scalability and generalizability. This paper introduces OCOO-T, a minimalist flow-matching-based AIVC model for transcriptional perturbation response prediction. OCOO-T utilizes a vanilla Transformer stack that operates directly on continuous gene expression profiles and formulates perturbation response prediction as a continuous-time denoising process. Perturbation embeddings, dosage information, and cell-line/cell-type specificity are integrated through adaptive layer normalization and in-context tokens. Comprehensive evaluations on Tahoe100M, Replogle, and PBMC benchmarks demonstrate that OCOO-T achieves state-of-the-art performance across diverse perturbations and cell types while effectively scaling to long transcriptional profiles through patching and depatching of cellular contexts. By leveraging the simplicity of Transformer-based denoising for single-cell omics, OCOO-T provides an effective and scalable framework for in-silico cellular simulation.

Gene perturbation analysis plays a critical role in drug discovery by enabling researchers to investigate how interventions on specific genes influence global gene expression patterns within cells. Recent advances in artificial intelligence-driven virtual cell models have made it possible to predict gene expression outcomes for a wide range of perturbation strategies in silico, substantially reducing reliance on costly and time-consuming biological experiments. However, effectively exploring and interpreting the high-dimensional perturbation spaces produced by these models remains challenging because of the combinatorial nature of perturbations and the complex cell-specific gene expression responses they generate. In this work, we present CellPrism, a visual analytics system designed to support the systematic exploration of gene perturbation strategies for drug discovery. Specifically, CellPrism integrates clustering-based overviews to summarize perturbation outcomes, a glyph-based representation to compactly encode gene expression patterns across cell types, and coordinated views that enable fine-grained comparison and interpretation of perturbation effects. We demonstrate the effectiveness of CellPrism through a real-world case study and expert interviews. This work highlights the value of visual analytics in bridging virtual cell modeling with expert-driven decision making in drug discovery.

Artificial Intelligence Virtual Cells (AIVCs) aim to learn executable, decision-relevant models of cell state from multimodal, multiscale measurements. Recent studies have introduced single-cell and spatial foundation models, improved cross-modality alignment, scaled perturbation atlases, and explored pathway-level readouts. Nevertheless, although held-out validation is standard practice, evaluations remain predominantly within single datasets and settings; evidence indicates that transport across laboratories and platforms is often limited, that some data splits are vulnerable to leakage and coverage bias, and that dose, time and combination effects are not yet systematically handled. Cross-scale coupling also remains constrained, as anchors linking molecular, cellular and tissue levels are sparse, and alignment to scientific or clinical readouts varies across studies. We propose a model-agnostic Cell-State Latent (CSL) perspective that organizes learning via an operator grammar: measurement, lift/project for cross-scale coupling, and intervention for dosing and scheduling. This view motivates a decision-aligned evaluation blueprint across modality, scale, context and intervention, and emphasizes function-space readouts such as pathway activity, spatial neighborhoods and clinically relevant endpoints. We recommend operator-aware data design, leakage-resistant partitions, and transparent calibration and reporting to enable reproducible, like-for-like comparisons.

Large language models (LLMs) are transforming cellular biology by enabling the development of "virtual cells"--computational systems that represent, predict, and reason about cellular states and behaviors. This work provides a comprehensive review of LLMs for virtual cell modeling. We propose a unified taxonomy that organizes existing methods into two paradigms: LLMs as Oracles, for direct cellular modeling, and LLMs as Agents, for orchestrating complex scientific tasks. We identify three core tasks--cellular representation, perturbation prediction, and gene regulation inference--and review their associated models, datasets, evaluation benchmarks, as well as the critical challenges in scalability, generalizability, and interpretability.

A central task in virtual cell modeling is predicting single-cell transcriptional responses to unseen genetic perturbations and drug combinations, and biological networks provide valuable priors on gene relationships. Existing graph-based models commonly use the same network to structure gene representations and mediate intergene interactions, thereby implicitly treating stable associations as perturbation-response pathways. Gene Ontology and control-derived coexpression networks encode relatively stable relationships rather than intervention-specific response directions or magnitudes. We therefore propose GeneGeoFlow, which conditions a control-anchored residual flow on gene-wise geometry derived from biological networks to learn intervention-specific transcriptional responses. GeneGeoFlow derives multi-scale spectral coordinates from Gene Ontology and control-derived coexpression networks. A perturbation-conditioned, gene-wise gating module selects relevant structural scales and network sources, yielding intervention-specific gene geometry. The resulting geometry conditions a control-anchored residual flow without explicitly propagating target-derived signals along the graph. Condition-wise optimal transport couples unpaired control and perturbed populations for training, while a Delta-correlation objective aligns the predicted and observed condition-level expression-shift directions. GeneGeoFlow achieves Pearson Delta scores of 0.8979 on the Norman additive benchmark and 0.9088 on five held-out drug combinations in the fixed ComboSciPlex test split. These results support perturbation-conditioned gene geometry as an effective structural prior for intervention-specific response prediction, without conflating stable gene relationships with response propagation.

Artificial Intelligence Virtual Cells (AIVCs) are envisioned as scientific agents that simulate cellular responses, explain underlying mechanisms, and support hypothesis-driven discovery. Existing AIVC benchmarks, however, operate primarily at the simulation layer, motivating complementary evaluation of how models interpret experimental evidence and formulate biological hypotheses. We introduce OmniVCBench, a figure-centric, source-traceable benchmark for the interpretation component of an AIVC. It contains 6,077 curated single- and multi-subfigure question--answer pairs derived from figures and experimental contexts in the scientific literature. Guided by Bloom's taxonomy, we instantiate interpretation-layer counterparts of the AIVC Predict--Explain--Discover agenda through three scientific reasoning tasks. We further introduce AIVC-Judge, a task-conditioned MLLM-as-a-judge framework with category-specific, reference-aware rubrics for evaluating open-ended responses. A complementary Model-Derived Hard-Negative Mining (MDHNM) strategy converts plausible errors observed during model inference into MCQ distractors for lower-cost evaluation. Within the evaluated heterogeneous model pool, MCQ accuracy correlates positively with AIVC-Judge scores, providing a complementary view of performance alongside open-response evaluation. Code and data demo are available at https://anonymous.4open.science/r/OmniVCBench.

Systematic ablations are essential to attribute performance gains in AI Virtual Cells, yet they are rarely performed because biological repositories are under-standardized and tightly coupled to domain-specific data and formats. While recent coding agents can translate ideas into implementations, they typically stop at producing code and lack a verifier that can reproduce strong baselines and rigorously test which components truly matter. We introduce AblateCell, a reproduce-then-ablate agent for virtual cell repositories that closes this verification gap. AblateCell first reproduces reported baselines end-to-end by auto-configuring environments, resolving dependency and data issues, and rerunning official evaluations while emitting verifiable artifacts. It then conducts closed-loop ablation by generating a graph of isolated repository mutations and adaptively selecting experiments under a reward that trades off performance impact and execution cost. Evaluated on three single-cell perturbation prediction repositories (CPA, GEARS, BioLORD), AblateCell achieves 88.9% (+29.9% to human expert) end-to-end workflow success and 93.3% (+53.3% to heuristic) accuracy in recovering ground-truth critical components. These results enable scalable, repository-grounded verification and attribution directly on biological codebases.

Large language models (LLMs) have recently gained significant attention as a promising approach to accelerate scientific discovery. However, their application in open-ended scientific domains such as biology remains limited, primarily due to the lack of factually grounded and actionable explanations. To address this, we introduce a structured explanation formalism for virtual cells that represents biological reasoning as mechanistic action graphs, enabling systematic verification and falsification. Building upon this, we propose VCR-Agent, a multi-agent framework that integrates biologically grounded knowledge retrieval with a verifier-based filtering approach to generate and validate mechanistic reasoning autonomously. Using this framework, we release VC-TRACES dataset, which consists of verified mechanistic explanations derived from the Tahoe-100M atlas. Empirically, we demonstrate that training with these explanations improves factual precision and provides a more effective supervision signal for downstream gene expression prediction. These results underscore the importance of reliable mechanistic reasoning for virtual cells, achieved through the synergy of multi-agent and rigorous verification.

Artificial intelligence holds immense promise for transforming biology, yet a lack of standardized, cross domain, benchmarks undermines our ability to build robust, trustworthy models. Here, we present insights from a recent workshop that convened machine learning and computational biology experts across imaging, transcriptomics, proteomics, and genomics to tackle this gap. We identify major technical and systemic bottlenecks such as data heterogeneity and noise, reproducibility challenges, biases, and the fragmented ecosystem of publicly available resources and propose a set of recommendations for building benchmarking frameworks that can efficiently compare ML models of biological systems across tasks and data modalities. By promoting high quality data curation, standardized tooling, comprehensive evaluation metrics, and open, collaborative platforms, we aim to accelerate the development of robust benchmarks for AI driven Virtual Cells. These benchmarks are crucial for ensuring rigor, reproducibility, and biological relevance, and will ultimately advance the field toward integrated models that drive new discoveries, therapeutic insights, and a deeper understanding of cellular systems.

Virtual cell models should capture phenotypes induced by specific perturbations. However, image-based models are typically trained and evaluated to match real-image distributions, which alone does not explicitly prioritize perturbation-specific biological responses. Recent approaches add biological signals through reinforcement-learning post-training or inference-time steering, raising a central question: where should biological response information enter the generative pipeline? We introduce PerturbBridge, a stochastic data-to-data bridge model that directly supervises perturbation-specific phenotypes in predicted perturbed images during training. PerturbBridge jointly optimizes bridge regression and differentiable biological response losses, with biological gradients passing through a frozen image encoder. We further introduce perturbation-response evaluations based on downstream classification and retrieval. Across three microscopy benchmarks for perturbation profiling and subcellular imaging, PerturbBridge surpasses CellFlux in biological fidelity, image quality, and sampling efficiency. On BBBC021, mechanism-of-action classification improves by 5.66 and 7.5 percentage points with morphological and learned visual features, respectively. On JUMP and AllenCell, retrieval Hit@10 and Hit@1 improve by 1.77 and 7.15 percentage points, respectively. On BBBC021 and JUMP, PerturbBridge achieves lower FID with 80% fewer model evaluations than CellFlux. Overall, these results show that directly supervising perturbation responses during training improves phenotypic fidelity while enabling efficient cellular image generation. Code is available at https://github.com/yyc1215lll-creator/PerturbBridge.

Building Virtual Cells that can accurately simulate cellular responses to perturbations is a long-standing goal in systems biology. A fundamental challenge is that high-throughput single-cell sequencing is destructive: the same cell cannot be observed both before and after a perturbation. Thus, perturbation prediction requires mapping unpaired control and perturbed populations. Existing models address this by learning maps between distributions, but typically assume a single fixed response distribution when conditioned on observed cellular context (e.g., cell type) and the perturbation type. In reality, responses vary systematically due to unobservable latent factors such as microenvironmental fluctuations and complex batch effects, forming a manifold of possible distributions for the same observed conditions. To account for this variability, we introduce PerturbDiff, which shifts modeling from individual cells to entire distributions. By embedding distributions as points in a Hilbert space, we define a diffusion-based generative process operating directly over probability distributions. This allows PerturbDiff to capture population-level response shifts across hidden factors. Benchmarks on established datasets show that PerturbDiff achieves state-of-the-art performance in single-cell response prediction and generalizes substantially better to unseen perturbations. See our project page (https://katarinayuan.github.io/PerturbDiff-ProjectPage/), where code and data will be made publicly available (https://github.com/DeepGraphLearning/PerturbDiff).

AI virtual cells aim to predict cellular responses to specified interventions, yet held-out predictive performance alone does not establish use of the supplied perturbation information. This prediction-claim gap matters in agentic model discovery, where language-model agents generate and revise predictors using score-based feedback. We introduce CELLAUDIT, which audits input-use claims by asking whether an input can enter the cited computation, whether fitted predictions depend on it, and whether that dependence improves prediction of observed response. On a paired morphology-transcriptomics perturbation benchmark (BBBC047), an agent-selected predictor attains a mean held-out Global Pearson correlation coefficient (PCC) of 0.3153 but remains invariant to compound replacement; a control-profile-only predictor reaches 0.3142. Source inspection identifies a compound-query pathway blocked by singleton key-value attention, and the invariance persists after refitting with disjoint control wells. In a stratified audit of 48 candidates across two linked tasks, 47 change predictions under compound replacement on both held-out folds, but only 20 show target-loss gains with intervals above zero on both folds. On BBBC047, falsification-guided revisions recover positive mean compound contributions while retaining gains over the control-profile-only baseline. In matched sci-Plex searches, audit-enriched feedback yields higher held-out performance and larger mean compound and dose contributions across five trajectories, although paired intervals span zero. Refitting fixed designs on an independently acquired cohort shows predictive generalization need not imply generalization of input-use claims: dose contribution persists, whereas support for compound identity does not. CELLAUDIT adds a falsification layer to agentic model discovery, moving from generate-score-revise toward discover-falsify-revise.

Building a virtual cell capable of accurately simulating cellular behaviors in silico has long been a dream in computational biology. We introduce CellFlux, an image-generative model that simulates cellular morphology changes induced by chemical and genetic perturbations using flow matching. Unlike prior methods, CellFlux models distribution-wise transformations from unperturbed to perturbed cell states, effectively distinguishing actual perturbation effects from experimental artifacts such as batch effects -- a major challenge in biological data. Evaluated on chemical (BBBC021), genetic (RxRx1), and combined perturbation (JUMP) datasets, CellFlux generates biologically meaningful cell images that faithfully capture perturbation-specific morphological changes, achieving a 35% improvement in FID scores and a 12% increase in mode-of-action prediction accuracy over existing methods. Additionally, CellFlux enables continuous interpolation between cellular states, providing a potential tool for studying perturbation dynamics. These capabilities mark a significant step toward realizing virtual cell modeling for biomedical research. Project page: https://yuhui-zh15.github.io/CellFlux/.

Large language models (LLMs) are increasingly applied in scientific research, offering new capabilities for knowledge discovery and reasoning. In single-cell biology, however, evaluation practices for both general and specialized LLMs remain inadequate: existing benchmarks are fragmented across tasks, adopt formats such as multiple-choice classification that diverge from real-world usage, and rely on metrics lacking interpretability and biological grounding. We present SC-ARENA, a natural language evaluation framework tailored to single-cell foundation models. SC-ARENA formalizes a virtual cell abstraction that unifies evaluation targets by representing both intrinsic attributes and gene-level interactions. Within this paradigm, we define five natural language tasks (cell type annotation, captioning, generation, perturbation prediction, and scientific QA) that probe core reasoning capabilities in cellular biology. To overcome the limitations of brittle string-matching metrics, we introduce knowledge-augmented evaluation, which incorporates external ontologies, marker databases, and scientific literature to support biologically faithful and interpretable judgments. Experiments and analysis across both general-purpose and domain-specialized LLMs demonstrate that (i) under the Virtual Cell unified evaluation paradigm, current models achieve uneven performance on biologically complex tasks, particularly those demanding mechanistic or causal understanding; and (ii) our knowledge-augmented evaluation framework ensures biological correctness, provides interpretable, evidence-grounded rationales, and achieves high discriminative capacity, overcoming the brittleness and opacity of conventional metrics. SC-Arena thus provides a unified and interpretable framework for assessing LLMs in single-cell biology, pointing toward the development of biology-aligned, generalizable foundation models.

AIVC (AI Virtual Cell) is a learned simulator of cellular behavior across conditions. Predicting how a cell population responds transcriptionally to a genetic perturbation is a core task. Perturb-seq records that response by destructive sequencing, so a control cell and a perturbed cell are never observed as a pair, and cells under one condition remain heterogeneous and noisy. Regression on individual cells absorbs sampling variation into the estimated effect, whereas interpretation requires the reproducible population effect. P2P (Perturbation-to-Perturbation) takes a stochastic cell-set view as its supervision unit. Two views drawn from the same condition share a reproducible population effect and differ by view-specific variation. A permutation-invariant set encoder summarizes the control population, a structured encoder represents perturbation tokens, cellular context, dose, and combination interactions, and a gate blends empirical condition-effect memory with a neural residual. A heteroscedastic head predicts the population mean and gene-wise response variance. Under one protocol and five seeds, P2P attains the lowest expression RMSE and the highest Effect Pearson, DEG F1, and DEG average precision on each of Adamson, Norman, Replogle K562, and Replogle RPE1 relative to GenePert, LinearPert, SLIM, Scouter, and scPILOT. On Replogle K562, Effect Pearson rises from 0.643 to 0.702 and DEG F1 rises from 0.067 to 0.178 relative to Scouter, the strongest baseline on both metrics.

Generative AI foundation models offer transformative potential for processing structured biological data, particularly in single-cell RNA sequencing, where datasets are rapidly scaling toward billions of cells. We propose the use of agentic foundation models with real-time web search to automate the labeling of experimental data, achieving up to 82.5% accuracy. This addresses a key bottleneck in supervised learning for structured omics data by increasing annotation throughput without manual curation and human error. Our approach enables the development of virtual cell foundation models capable of downstream tasks such as cell-typing and perturbation prediction. As data volume grows, these models may surpass human performance in labeling, paving the way for reliable inference in large-scale perturbation screens. This application demonstrates domain-specific innovation in health monitoring and diagnostics, aligned with efforts like the Human Cell Atlas and Human Tumor Atlas Network.

Single-cell perturbation studies face dual heterogeneity bottlenecks: (i) semantic heterogeneity--identical biological concepts encoded under incompatible metadata schemas across datasets; and (ii) statistical heterogeneity--distribution shifts from biological variation demanding dataset-specific inductive biases. We propose HarmonyCell, an end-to-end agent framework resolving each challenge through a dedicated mechanism: an LLM-driven Semantic Unifier autonomously maps disparate metadata into a canonical interface without manual intervention; and an adaptive Monte Carlo Tree Search engine operates over a hierarchical action space to synthesize architectures with optimal statistical inductive biases for distribution shifts. Evaluated across diverse perturbation tasks under both semantic and distribution shifts, HarmonyCell achieves a 95% valid execution rate on heterogeneous input datasets (versus 0% for general agents) while matching or even exceeding expert-designed baselines in rigorous out-of-distribution evaluations. This dual-track orchestration enables scalable automatic virtual cell modeling without dataset-specific engineering.

Predicting single-cell transcriptomic responses to genetic perturbations is central to functional genomics and virtual-cell modeling. Existing approaches, however, typically predict an entire expression profile as a whole, leaving the order in which individual gene responses are generated unmodeled. To address this problem, we introduce D^{2R^{2}} (Discrete Diffusion with Regulation Reinforcement), which reformulates perturbation prediction as regulation-guided gene-wise progressive generation. A Masked Discrete Diffusion Model represents expression as ordinal tokens and reconstructs a fully masked profile step by step, allowing generated gene responses to condition those that remain masked. A Regulatory Policy Module initializes the generation policy from a gene regulatory network inferred from control cells and adapts it to the perturbation and current partially generated state. Then, group-relative policy optimization refines only the ordering policy using final perturbation-effect agreement as reward. Across Norman19 and VCC-H1, D^{2}R^{2} achieves the best performance on all five metrics on Norman19 and remains competitive on H1. Controlled ablations holding the generator and generation budget fixed show that biological-prior ordering improves over random ordering and is more reliable than uncertainty-based heuristics, whereas reversing the biological-prior ordering degrades every metric. Biological analyses further show that the refined policy prioritizes regulatory genes early while promoting perturbation-specific transcription factors and responsive genes. These results establish gene generation order as an effective, controllable, and biologically interpretable dimension of single-cell perturbation prediction.

Predicting how a cell will change its transcriptional state under a developmental signal or a genetic perturbation is the computational core of in-silico biology and the AI Virtual Cell program. Existing approaches either fit static control-to-treated maps that discard time, or solve multi-step ODE / Schrödinger-bridge problems on each dataset independently. We introduce Chreode, a one-step cell world model that predicts action-conditioned cell-state transitions through a structured residual transition operator. It shifts distributional evolution from inference time to training time, enabling single-pass generation while preserving a Waddington-inspired decomposition into downhill landscape flow, rotational in-tangent dynamics, and stochastic spread. The model is pretrained with a shared scVI encoder and a DiT-based dynamics backbone on a 2.4M-cell mouse embryonic atlas spanning 7 datasets. As a fine-tuning initialization, Chreode improves per-target Sinkhorn distance on Weinreb hematopoiesis and Veres islet differentiation over matched scratch models, PI-SDE, and PRESCIENT. As a transferable gene-state embedding for GEARS, the pretrained dynamics representation reduces shared-vocabulary DE20 mean squared error on Norman Perturb-seq from 0.2121 to 0.1858, a 12.4% relative improvement, without changing the GEARS training procedure. We interpret this transfer to perturbation prediction as evidence that pretrained developmental-trajectory dynamics encode differentiation primitives transferable to CRISPR-induced state shifts, since both involve cell-state transitions in a shared latent geometry. The pretrained backbone additionally produces zero-shot clonal fate scores on Weinreb that are competitive with strong dynamic-OT baselines.

Understanding cellular mechanisms requires integrating information across DNA, RNA, and protein - the three molecular systems linked by the Central Dogma of molecular biology. While domain-specific foundation models have achieved success for each modality individually, they remain isolated, limiting our ability to model integrated cellular processes. Here we present the Central Dogma Transformer (CDT), an architecture that integrates pre-trained language models for DNA, RNA, and protein following the directional logic of the Central Dogma. CDT employs directional cross-attention mechanisms - DNA-to-RNA attention models transcriptional regulation, while RNA-to-Protein attention models translational relationships - producing a unified Virtual Cell Embedding that integrates all three modalities. We validate CDT v1 - a proof-of-concept implementation using fixed (non-cell-specific) RNA and protein embeddings - on CRISPRi enhancer perturbation data from K562 cells, achieving a Pearson correlation of 0.503, representing 63% of the theoretical ceiling set by cross-experiment variability (r = 0.797). Attention and gradient analyses provide complementary interpretive windows: in detailed case studies, these approaches highlight largely distinct genomic regions, with gradient analysis identifying a CTCF binding site that Hi-C data showed as physically contacting both enhancer and target gene. These results suggest that AI architectures aligned with biological information flow can achieve both predictive accuracy and mechanistic interpretability.

AI evaluation can support the wrong inference when an in-domain benchmark success does not survive distribution shift, or when the benchmark endpoint is entangled with a design factor. We study this problem in CRISPRi perturbation-effect prediction, evaluating a frozen Geneformer representation under a locked, pre-registered protocol: heads and model selection were frozen before test evaluation; the protocol required external outcome labels to remain withheld until final unblinding; and analysis-governing decisions were fixed before the evaluations they govern. In-distribution on the Virtual Cell Challenge (VCC), the frozen representation carries measurable predictive information beyond a dimension-matched random-feature control (Delta R^2 = +0.1645, 95% CI [+0.1375, +0.1920]), satisfying the pre-registered informativeness gate required before interpreting transfer. It then fails zero-shot transfer on both external screens (Spearman rho = -0.139 and -0.267), lying below that control on each. Adding a predefined magnitude block improves the representation externally (Delta rho = +0.032 and +0.143) but, under the frozen primary head, does not rescue transfer: both remain negative. A pre-registered, count-adjusted max-response secondary is positively associated with the outcome on both screens; we report it as correlational and secondary, not as a recovered magnitude signal. Finally, the VCC endpoint is strongly sample-size associated: a count-only linear model reaches R^2 = +0.4325, versus +0.2589 for the four magnitude scalars; adding those scalars to cell count improves R^2 by only +0.0017, so much of the aggregate-magnitude signal overlaps with cell count. This case study shows how locking the evaluation, harmonizing the measured endpoint, and separating primary from secondary evidence can change the inference supported by an AI benchmark.

Predicting the effects of perturbations in-silico on cell state can identify drivers of cell behavior at scale and accelerate drug discovery. However, modeling challenges remain due to the inherent heterogeneity of single cell gene expression and the complex, latent gene dependencies. Here, we present PRiMeFlow, an end-to-end flow matching based approach to directly model the effects of genetic and small molecule perturbations in the gene expression space. The distribution-fitting approach taken by PRiMeFlow enables it to accurately approximate the empirical distribution of single-cell gene expression, which we demonstrate through extensive benchmarking inside PerturBench. Through ablation studies, we also validate important model design choices such as operating in gene expression space and parameterizing the velocity field with a U-Net architecture. Finally, by scaling PRiMeFlow to a broad perturbation data atlas spanning multiple datasets and employing a carefully designed pretraining-finetuning strategy, we demonstrate its outstanding performance on the H1 human embryonic stem cells from the ARC Virtual Cell Challenge benchmark.

The Perturbation Discrimination Score (PDS) is increasingly used to evaluate whether predicted perturbation effects remain distinguishable, including in Systema and the Virtual Cell Challenge. However, its behavior in high-dimensional gene-expression settings has not been examined in detail. We show that PDS is highly sensitive to the choice of similarity or distance measure and to the scale of predicted effects. Analysis of observed perturbation responses reveals that ell_1 and ell_2-based PDS behave very differently from cosine-based measures, even after norm matching. We provide geometric insight and discuss implications for future discrimination-based evaluation metrics.

Understanding cellular machinery requires atomic-scale reconstruction of large biomolecular assemblies. However, predicting the structures of these systems has been constrained by hardware memory requirements of models like AlphaFold 3, imposing a practical ceiling of a few thousand residues that can be processed on a single GPU. Here we present NVIDIA BioNeMo Fold-CP, a context parallelism framework that overcomes this barrier by distributing the inference and training pipelines of co-folding models across multiple GPUs. We use the Boltz models as open source reference architectures and implement custom multidimensional primitives that efficiently parallelize both the dense triangular updates and the irregular, data-dependent pattern of window-batched local attention. Our approach achieves efficient memory scaling; for an N-token input distributed across P GPUs, per-device memory scales as O(N^2/P), enabling the structure prediction of assemblies exceeding 30,000 residues on 64 NVIDIA B300 GPUs. We demonstrate the scientific utility of this approach through successful developer use cases: Fold-CP enabled the scoring of over 90% of Comprehensive Resource of Mammalian protein complexes (CORUM) database, as well as folding of disease-relevant PI4KA lipid kinase complex bound to an intrinsically disordered region without cropping. By providing a scalable pathway for modeling massive systems with full global context, Fold-CP represents a significant step toward the realization of a virtual cell.

A central hypothesis in aging biology proposes that the gradual accumulation of stochastic molecular damage drives transcriptional deregulation (TD), ultimately leading to functional decline. However, existing single-cell analyses largely rely on static expression measurements and provide limited resolution of how regulatory responses change at the level of individual cells. Here, we leverage DKO, a deep learning framework that predicts cell-specific virtual gene perturbation effects from unperturbed transcriptomes, capturing cell-to-cell differences in regulatory context without requiring a reconstructed gene regulatory network or matched perturbation data. Applying DKO to single-cell transcriptomic datasets from humans, mice, Drosophila, and C. elegans revealed that the transcriptional consequences of perturbing the same gene became increasingly heterogeneous across cells with age, indicating that gene regulatory responses become less consistent and more dependent on cellular context. Furthermore, we find that cells with higher somatic mutation burdens have greater knockout-response variability, linking accumulated molecular damage to regulatory inconsistency. Within the same cellular populations, higher impact variability was also associated with higher senescence scores, linking transcriptional dysregulation to senescence-associated states. Our findings identify a progressive loss of regulatory robustness at both the gene and cell levels as a conserved feature of aging, linking stochastic molecular damage to increasing heterogeneity in cellular regulatory responses.

Transportation Cyber-Physical Systems (T-CPS) enhance safety and mobility by integrating cyber and physical transportation systems. A key component of T-CPS is the Digital Twin (DT), a virtual representation that enables simulation, analysis, and optimization through real-time data exchange and communication. Although existing studies have explored DTs for vehicles, communications, pedestrians, and traffic, real-world validations and implementations of DTs that encompass infrastructure, vehicles, signals, communications, and more remain limited due to several challenges. These include accessing real-world connected infrastructure, integrating heterogeneous, multi-sourced data, ensuring real-time data processing, and synchronizing the digital and physical systems. To address these challenges, this study develops a traffic DT based on a real-world connected vehicle corridor. Leveraging the Cellular Vehicle-to-Everything (C-V2X) infrastructure in the corridor, along with communication, computing, and simulation technologies, the proposed DT accurately replicates physical vehicle behaviors, signal timing, communications, and traffic patterns within the virtual environment. Building upon the previous data pipeline, the digital system ensures robust synchronization with the physical environment. Moreover, the DT's scalable and redundant architecture enhances data integrity, making it capable of supporting future large-scale C-V2X deployments. Furthermore, its ability to provide feedback to the physical system is demonstrated through applications such as signal timing adjustments, vehicle advisory messages, and incident notifications. The proposed DT is a vital tool in T-CPS, enabling real-time traffic monitoring, prediction, and optimization to enhance the reliability and safety of transportation systems.

Hybrid language models like Jamba mix attention layers with State Space Models (SSMs), creating two memory cache types with opposite profiles: Key-Value (KV) caches grow linearly with sequence length, while SSM states stay fixed per layer. Current inference engines handle this poorly. Unified pools pad SSM states to attention page sizes, wasting up to 7.3x capacity. Static dual pools cannot adapt when prompt distributions shift between requests. We present Asymmetric Virtual Memory Paging (AVMP). The allocator separates the two cache types into physically distinct pools behind a unified virtual address space, and migrates capacity between pools when one runs out. Migration triggers only on allocation failure, keeping behavior deterministic. We evaluate AVMP across 270 synthetic cells plus 60 cells of ShareGPT trace replay on an RTX 3060 12GB. Out-of-Memory events drop 7.6% and request throughput improves 1.83x to 13.3x across synthetic workloads and 2.36x on ShareGPT. All gains hold under paired-bootstrap 95% confidence intervals. A phase-time breakdown reveals two distinct mechanisms: shorter OOM recovery on capacity-pressured workloads, and faster allocation calls on KV-heavy workloads. Implementation is pure Python; Triton integration is future work.

Texture modeling and synthesis are essential for enhancing the realism of virtual environments. Methods that directly synthesize textures in 3D offer distinct advantages to the UV-mapping-based methods as they can create seamless textures and align more closely with the ways textures form in nature. We propose Mesh Neural Cellular Automata (MeshNCA), a method that directly synthesizes dynamic textures on 3D meshes without requiring any UV maps. MeshNCA is a generalized type of cellular automata that can operate on a set of cells arranged on non-grid structures such as the vertices of a 3D mesh. MeshNCA accommodates multi-modal supervision and can be trained using different targets such as images, text prompts, and motion vector fields. Only trained on an Icosphere mesh, MeshNCA shows remarkable test-time generalization and can synthesize textures on unseen meshes in real time. We conduct qualitative and quantitative comparisons to demonstrate that MeshNCA outperforms other 3D texture synthesis methods in terms of generalization and producing high-quality textures. Moreover, we introduce a way of grafting trained MeshNCA instances, enabling interpolation between textures. MeshNCA allows several user interactions including texture density/orientation controls, grafting/regenerate brushes, and motion speed/direction controls. Finally, we implement the forward pass of our MeshNCA model using the WebGL shading language and showcase our trained models in an online interactive demo, which is accessible on personal computers and smartphones and is available at https://meshnca.github.io.

Hematoxylin and Eosin (H&E) staining is widely regarded as the standard in pathology for diagnosing diseases and tracking tumor recurrence. While H&E staining shows tissue structures, it lacks the ability to reveal specific proteins that are associated with disease severity and treatment response. Immunohistochemical (IHC) stains use antibodies to highlight the expression of these proteins on their respective cell types, improving diagnostic accuracy, and assisting with drug selection for treatment. Despite their value, IHC stains require additional time and resources, limiting their utilization in some clinical settings. Recent advances in deep learning have positioned Image-to-Image (I2I) translation as a computational, cost-effective alternative for IHC. I2I generates high fidelity stain transformations digitally, potentially replacing manual staining in IHC. Diffusion models, the current state of the art in image generation and conditional tasks, are particularly well suited for virtual IHC due to their ability to produce high quality images and resilience to mode collapse. However, these models require extensive and diverse datasets (often millions of samples) to achieve a robust performance, a challenge in virtual staining applications where only thousands of samples are typically available. Inspired by the success of multitask deep learning models in scenarios with limited data, we introduce STAINDIFFUSER, a novel multitask diffusion architecture tailored to virtual staining that achieves convergence with smaller datasets. STAINDIFFUSER simultaneously trains two diffusion processes: (a) generating cell specific IHC stains from H&E images and (b) performing H&E based cell segmentation, utilizing coarse segmentation labels exclusively during training. STAINDIFFUSER generates high-quality virtual stains for two markers, outperforming over twenty I2I baselines.

Spatial transcriptomics (ST) provides unprecedented insights into tumor heterogeneity by capturing spatially resolved gene expression, yet its high experimental cost hinders large-scale adoption. Consequently, computational approaches that predict spatial gene expression directly from hematoxylin and eosin slides, termed virtual ST, have rapidly emerged. Despite this progress, assessing advances in the field remains difficult due to insufficient benchmarking: prior studies rely on small, heterogeneous datasets, inconsistent training and inference pipelines, and limited evaluation of biological interpretability and model robustness. To address these gaps, we present STP-BENCH, a standardized benchmark for virtual ST models. STP-BENCH comprises six cancer types spanning two ST platforms (Visium and Xenium), with each training dataset containing more than 30,000 spots and at least 15 slides to ensure statistical reliability. We evaluate 21 predictive approaches, re-implemented with a unified pathology foundation model as the morphological encoder when architecturally applicable. Beyond conventional benchmarks that report average predictive accuracy on highly variable genes, we systematically examine which genes and gene sets are recoverable from histomorphology. We further evaluate the downstream biological utility of predicted profiles through cell-type deconvolution and spatial domain identification, and assess model reliability under domain shifts and data scaling. Notably, unified morphological encoding substantially re-orders model rankings established in prior studies, indicating that architectural innovations and image encoding have been conflated in previous evaluations. We publicly release STP-BENCH to support reproducibility and serve as a community benchmark at https://github.com/NEXGEM/STP-Bench.

We introduce Biomaker CA: a Biome Maker project using Cellular Automata (CA). In Biomaker CA, morphogenesis is a first class citizen and small seeds need to grow into plant-like organisms to survive in a nutrient starved environment and eventually reproduce with variation so that a biome survives for long timelines. We simulate complex biomes by means of CA rules in 2D grids and parallelize all of its computation on GPUs through the Python JAX framework. We show how this project allows for several different kinds of environments and laws of 'physics', alongside different model architectures and mutation strategies. We further analyze some configurations to show how plant agents can grow, survive, reproduce, and evolve, forming stable and unstable biomes. We then demonstrate how one can meta-evolve models to survive in a harsh environment either through end-to-end meta-evolution or by a more surgical and efficient approach, called Petri dish meta-evolution. Finally, we show how to perform interactive evolution, where the user decides how to evolve a plant model interactively and then deploys it in a larger environment. We open source Biomaker CA at: https://tinyurl.com/2x8yu34s .

While pathology foundation models have transformed cancer image analysis, they often lack integration with molecular data at single-cell resolution, limiting their utility for precision oncology. Here, we present PAST, a pan-cancer single-cell foundation model trained on 20 million paired histopathology images and single-cell transcriptomes spanning multiple tumor types and tissue contexts. By jointly encoding cellular morphology and gene expression, PAST learns unified cross-modal representations that capture both spatial and molecular heterogeneity at the cellular level. This approach enables accurate prediction of single-cell gene expression, virtual molecular staining, and multimodal survival analysis directly from routine pathology slides. Across diverse cancers and downstream tasks, PAST consistently exceeds the performance of existing approaches, demonstrating robust generalizability and scalability. Our work establishes a new paradigm for pathology foundation models, providing a versatile tool for high-resolution spatial omics, mechanistic discovery, and precision cancer research.

Organic crystal structure prediction (CSP) is a requirement for computational modelling of organic solids, but traditionally costs several CPU-years per molecule. Generative models such as OXtal dramatically reduce this cost by sampling stable organic crystal structures directly. However, OXtal forgoes explicit lattice parametrization in favour of modelling large crops of the bulk material with expensive triangle layers, which can incur a computational cost of minutes per molecule. In this paper, we reduce this to seconds with Clari, a large-scale flow matching model that generates redundancy-free unit cells and replaces triangle layers with pure pair-bias attention. Clari requires only atom types and bonds as input and does not need an RDKit-sanitizable input molecule, which expands its applicability to challenging chemistries such as fullerenes, metal complexes, and atom clusters. We further ablate key design choices such as auxiliary losses, timestep distributions, noise priors, and self-conditioning. On OXtal's test sets, we surpass OXtal's solve rate while obtaining a speedup of 15-30times. Because Clari also models explicit hydrogens, it supports inference-time scaling via direct energy ranking, without any decoration or relaxation step. When generating 150 crystals and selecting the top-30 by energy, we further improve solve rate while maintaining a speedup of 5-8times. We also introduce the CSD Teaching Subset as a new test split of diverse and complex molecules for future benchmarking. Our contributions enable CSP within seconds, making large-scale virtual screening of organic solids practical. Code is available at https://github.com/aspuru-guzik-group/clari.

Virtual Screening (VS) of vast compound libraries guided by Artificial Intelligence (AI) models is a highly productive approach to early drug discovery. Data splitting is crucial for better benchmarking of such AI models. Traditional random data splits produce similar molecules between training and test sets, conflicting with the reality of VS libraries which mostly contain structurally distinct compounds. Scaffold split, grouping molecules by shared core structure, is widely considered to reflect this real-world scenario. However, here we show that the scaffold split also overestimates VS performance. The reason is that molecules with different chemical scaffolds are often similar, which hence introduces unrealistically high similarities between training molecules and test molecules following a scaffold split. Our study examined three representative AI models on 60 NCI-60 datasets, each with approximately 30,000 to 50,000 molecules tested on a different cancer cell line. Each dataset was split with three methods: scaffold, Butina clustering and the more accurate Uniform Manifold Approximation and Projection (UMAP) clustering. Regardless of the model, model performance is much worse with UMAP splits from the results of the 2100 models trained and evaluated for each algorithm and split. These robust results demonstrate the need for more realistic data splits to tune, compare, and select models for VS. For the same reason, avoiding the scaffold split is also recommended for other molecular property prediction problems. The code to reproduce these results is available at https://github.com/ScaffoldSplitsOverestimateVS

Spatial proteomics technologies have transformed our understanding of complex tissue architectures by enabling simultaneous analysis of multiple molecular markers and their spatial organization. The high dimensionality of these data, varying marker combinations across experiments and heterogeneous study designs pose unique challenges for computational analysis. Here, we present Virtual Tissues (VirTues), a foundation model framework for biological tissues that operates across the molecular, cellular and tissue scale. VirTues introduces innovations in transformer architecture design, including a novel tokenization scheme that captures both spatial and marker dimensions, and attention mechanisms that scale to high-dimensional multiplex data while maintaining interpretability. Trained on diverse cancer and non-cancer tissue datasets, VirTues demonstrates strong generalization capabilities without task-specific fine-tuning, enabling cross-study analysis and novel marker integration. As a generalist model, VirTues outperforms existing approaches across clinical diagnostics, biological discovery and patient case retrieval tasks, while providing insights into tissue function and disease mechanisms.

The emergence of "vibe coding" platforms, where users describe applications in natural language and AI agents autonomously generate full-stack software, has created a need for rigorous evaluation beyond code-level benchmarks. In order to assess them as virtual software development agencies on understanding business requirements, making architectural decisions, writing production code, handling iterative modifications, and maintaining business readiness, we introduce SWE-WebDev Bench, a 68-metric evaluation framework spanning 25 primary and 43 diagnostic metrics across seven groups, organized along three dimensions: Interaction Mode (App Creation Request (ACR) vs. App Modification Request (AMR)), Agency Angle (Product Manager (PM), Engineering, Ops), and Complexity Tier (T4 multi-role SaaS, T5 AI-native). Our evaluation (six platforms, three domains, 18 evaluation cells) reveals four recurring shortcomings in the current generation of AI app builders: (1) A specification bottleneck, where platforms compress rich business requirements into oversimplified technical plans, (2) A pervasive frontend-backend decoupling, where visually polished UIs mask absent or broken backend infrastructure, (3) A steep production-readiness cliff, where no platform scores above 60% on engineering quality and post-generation human effort varies substantially across platforms and (4) Widespread security and infrastructure failures, with no platform exceeding 65% Security Score against a 90% target and concurrency handling as low as 6%. These observations are descriptive of our sample and require larger-scale replication to establish generality. We release SWE-WebDev Bench as a community benchmark to enable such replication and help platform builders identify and address these gaps. Code and benchmark resources are available at: https://github.com/snowmountainAi/webdevbench and https://webdevbench.com/.

Global placement is a critical step with high computational complexity in VLSI physical design. Modern analytical placers formulate the placement problem as a nonlinear optimization, where initialization strongly affects both convergence behavior and final placement quality. However, existing initialization methods exhibit a trade-off: area-aware initializers account for cell areas but are computationally expensive and can dominate total runtime, while fast point-based initializers ignore cell area, leading to a modeling gap that impairs convergence and solution quality. We propose a lightweight co-optimization framework that bridges this initialization gap through two strategies. First, an area-hint refinement initializer incorporates heuristic cell area information into a signed graph signal by augmenting the netlist graph with virtual nodes and negative-weight edges, yielding an area-aware and spectrally smooth placement initialization. Second, a macro-schedule placement procedure progressively restores area constraints, enabling a smooth transition from the refined initializer to the full area-aware objective and producing high-quality placement results. We evaluate the framework on macro-heavy ISPD2005 academic benchmarks and two real-world industrial designs across two technology nodes (12 cases in total). Experimental results show that our method consistently improves half-perimeter wirelength (HPWL) over point-based initializers in 11 out of 12 cases, achieving up to 2.2% HPWL reduction, while running approximately 100 times faster than the state-of-the-art area-aware initializer.

Holistic 3D modeling of molecularly defined brain structures is crucial for understanding complex brain functions. Emerging tissue profiling technologies enable the construction of a comprehensive atlas of the mammalian brain with sub-cellular resolution and spatially resolved gene expression data. However, such tera-scale volumetric datasets present significant computational challenges in understanding complex brain functions within their native 3D spatial context. Here, we propose the novel generative approach Tera-MIND, which can simulate Tera-scale Mouse braINs in 3D using a patch-based and boundary-aware Diffusion model. Taking spatial transcriptomic data as the conditional input, we generate virtual mouse brains with comprehensive cellular morphological detail at teravoxel scale. Through the lens of 3D gene-gene self-attention, we identify spatial molecular interactions for key transcriptomic pathways in the murine brain, exemplified by glutamatergic and dopaminergic neuronal systems. Importantly, these in-silico biological findings are consistent and reproducible across three tera-scale virtual mouse brains. Therefore, Tera-MIND showcases a promising path toward efficient and generative simulations of whole organ systems for biomedical research. Project website: http://musikisomorphie.github.io/Tera-MIND.html{https}

Cloud computing is an established technology allowing users to share resources on a large scale, never before seen in IT history. A cloud system connects multiple individual servers in order to process related tasks in several environments at the same time. Clouds are typically more cost-effective than single computers of comparable computing performance. The sheer physical size of the system itself means that thousands of machines may be involved. The focus of this research was to design a strategy to dynamically allocate tasks without overloading Cloud nodes which would result in system stability being maintained at minimum cost. This research has added the following new contributions to the state of knowledge: (i) a novel taxonomy and categorisation of three classes of schedulers, namely OS-level, Cluster and Big Data, which highlight their unique evolution and underline their different objectives; (ii) an abstract model of cloud resources utilisation is specified, including multiple types of resources and consideration of task migration costs; (iii) a virtual machine live migration was experimented with in order to create a formula which estimates the network traffic generated by this process; (iv) a high-fidelity Cloud workload simulator, based on a month-long workload traces from Google's computing cells, was created; (v) two possible approaches to resource management were proposed and examined in the practical part of the manuscript: the centralised metaheuristic load balancer and the decentralised agent-based system. The project involved extensive experiments run on the University of Westminster HPC cluster, and the promising results are presented together with detailed discussions and a conclusion.

As large language models (LLMs) continue to improve in reasoning and decision-making, there is a growing need for realistic and interactive environments where their abilities can be rigorously evaluated. We present VirtualEnv, a next-generation simulation platform built on Unreal Engine 5 that enables fine-grained benchmarking of LLMs in embodied and interactive scenarios. VirtualEnv supports rich agent-environment interactions, including object manipulation, navigation, and adaptive multi-agent collaboration, as well as game-inspired mechanics like escape rooms and procedurally generated environments. We provide a user-friendly API built on top of Unreal Engine, allowing researchers to deploy and control LLM-driven agents using natural language instructions. We integrate large-scale LLMs and vision-language models (VLMs), such as GPT-based models, to generate novel environments and structured tasks from multimodal inputs. Our experiments benchmark the performance of several popular LLMs across tasks of increasing complexity, analyzing differences in adaptability, planning, and multi-agent coordination. We also describe our methodology for procedural task generation, task validation, and real-time environment control. VirtualEnv is released as an open-source platform, we aim to advance research at the intersection of AI and gaming, enable standardized evaluation of LLMs in embodied AI settings, and pave the way for future developments in immersive simulations and interactive entertainment.

Structured illumination microscopy (SIM) is an optical super-resolution technique that enables live-cell imaging beyond the diffraction limit. Reconstruction of SIM data is prone to artefacts, which becomes problematic when imaging highly dynamic samples because previous methods rely on the assumption that samples are static. We propose a new transformer-based reconstruction method, VSR-SIM, that uses shifted 3-dimensional window multi-head attention in addition to channel attention mechanism to tackle the problem of video super-resolution (VSR) in SIM. The attention mechanisms are found to capture motion in sequences without the need for common motion estimation techniques such as optical flow. We take an approach to training the network that relies solely on simulated data using videos of natural scenery with a model for SIM image formation. We demonstrate a use case enabled by VSR-SIM referred to as rolling SIM imaging, which increases temporal resolution in SIM by a factor of 9. Our method can be applied to any SIM setup enabling precise recordings of dynamic processes in biomedical research with high temporal resolution.

Virtual Try-On (VTON) is a transformative technology in e-commerce and fashion design, enabling realistic digital visualization of clothing on individuals. In this work, we propose VTON 360, a novel 3D VTON method that addresses the open challenge of achieving high-fidelity VTON that supports any-view rendering. Specifically, we leverage the equivalence between a 3D model and its rendered multi-view 2D images, and reformulate 3D VTON as an extension of 2D VTON that ensures 3D consistent results across multiple views. To achieve this, we extend 2D VTON models to include multi-view garments and clothing-agnostic human body images as input, and propose several novel techniques to enhance them, including: i) a pseudo-3D pose representation using normal maps derived from the SMPL-X 3D human model, ii) a multi-view spatial attention mechanism that models the correlations between features from different viewing angles, and iii) a multi-view CLIP embedding that enhances the garment CLIP features used in 2D VTON with camera information. Extensive experiments on large-scale real datasets and clothing images from e-commerce platforms demonstrate the effectiveness of our approach. Project page: https://scnuhealthy.github.io/VTON360.

Virtual Try-On (trying clothes virtually) is a promising application of the Generative Adversarial Network (GAN). However, it is an arduous task to transfer the desired clothing item onto the corresponding regions of a human body because of varying body size, pose, and occlusions like hair and overlapped clothes. In this paper, we try to produce photo-realistic translated images through semantic segmentation and a generative adversarial architecture-based image translation network. We present a novel image-based Virtual Try-On application VTON-IT that takes an RGB image, segments desired body part, and overlays target cloth over the segmented body region. Most state-of-the-art GAN-based Virtual Try-On applications produce unaligned pixelated synthesis images on real-life test images. However, our approach generates high-resolution natural images with detailed textures on such variant images.

Tactile sensing is one of the modalities humans rely on heavily to perceive the world. Working with vision, this modality refines local geometry structure, measures deformation at the contact area, and indicates the hand-object contact state. With the availability of open-source tactile sensors such as DIGIT, research on visual-tactile learning is becoming more accessible and reproducible. Leveraging this tactile sensor, we propose a novel visual-tactile in-hand object reconstruction framework VTacO, and extend it to VTacOH for hand-object reconstruction. Since our method can support both rigid and deformable object reconstruction, no existing benchmarks are proper for the goal. We propose a simulation environment, VT-Sim, which supports generating hand-object interaction for both rigid and deformable objects. With VT-Sim, we generate a large-scale training dataset and evaluate our method on it. Extensive experiments demonstrate that our proposed method can outperform the previous baseline methods qualitatively and quantitatively. Finally, we directly apply our model trained in simulation to various real-world test cases, which display qualitative results. Codes, models, simulation environment, and datasets are available at https://sites.google.com/view/vtaco/.

Virtual Try-On (VTON) aims to synthesize photorealistic images of garments precisely aligned with a person's body and pose. Current diffusion-based methods, however, face a fundamental trade-off between structural integrity and textural fidelity. In this paper, we formalize this challenge as a consequence of complementary inductive biases inherent in prevailing architectures: models heavily reliant on spatial constraints naturally favor geometric alignment but often suppress textures, whereas models dominated by unconstrained generative priors excel at vibrant detail rendering but are prone to structural drift. Based on this diagnosis, we propose LPH-VTON, a new synergistic framework that resolves this tension within a single, continuous denoising process. LPH-VTON strategically decomposes the generation, leveraging a structure-biased model to establish a geometrically consistent latent scaffold in the early stages, before handing over control to a texture-biased model for high-fidelity detail rendering. Extensive experiments validate our approach. Our model achieves a superior Pareto-optimal balance, establishing new benchmarks in perceptual faithfulness while maintaining highly competitive structural alignment across the standard dataset VITON-HD, proving the efficacy of temporal architectural decoupling.

Virtual try-on has emerged as a pivotal task at the intersection of computer vision and fashion, aimed at digitally simulating how clothing items fit on the human body. Despite notable progress in single-image virtual try-on (VTO), current methodologies often struggle to preserve a consistent and authentic appearance of clothing across extended video sequences. This challenge arises from the complexities of capturing dynamic human pose and maintaining target clothing characteristics. We leverage pre-existing video foundation models to introduce RealVVT, a photoRealistic Video Virtual Try-on framework tailored to bolster stability and realism within dynamic video contexts. Our methodology encompasses a Clothing & Temporal Consistency strategy, an Agnostic-guided Attention Focus Loss mechanism to ensure spatial consistency, and a Pose-guided Long Video VTO technique adept at handling extended video sequences.Extensive experiments across various datasets confirms that our approach outperforms existing state-of-the-art models in both single-image and video VTO tasks, offering a viable solution for practical applications within the realms of fashion e-commerce and virtual fitting environments.

Simulated virtual environments have been widely used to learn robotic agents that perform daily household tasks. These environments encourage research progress by far, but often provide limited object interactability, visual appearance different from real-world environments, or relatively smaller environment sizes. This prevents the learned models in the virtual scenes from being readily deployable. To bridge the gap between these learning environments and deploying (i.e., real) environments, we propose the ReALFRED benchmark that employs real-world scenes, objects, and room layouts to learn agents to complete household tasks by understanding free-form language instructions and interacting with objects in large, multi-room and 3D-captured scenes. Specifically, we extend the ALFRED benchmark with updates for larger environmental spaces with smaller visual domain gaps. With ReALFRED, we analyze previously crafted methods for the ALFRED benchmark and observe that they consistently yield lower performance in all metrics, encouraging the community to develop methods in more realistic environments. Our code and data are publicly available.

Virtual Reality (VR) bares promise of social interactions that can feel more immersive than other media. Key to this is the ability to accurately animate a photorealistic avatar of one's likeness while wearing a VR headset. Although high quality registration of person-specific avatars to headset-mounted camera (HMC) images is possible in an offline setting, the performance of generic realtime models are significantly degraded. Online registration is also challenging due to oblique camera views and differences in modality. In this work, we first show that the domain gap between the avatar and headset-camera images is one of the primary sources of difficulty, where a transformer-based architecture achieves high accuracy on domain-consistent data, but degrades when the domain-gap is re-introduced. Building on this finding, we develop a system design that decouples the problem into two parts: 1) an iterative refinement module that takes in-domain inputs, and 2) a generic avatar-guided image-to-image style transfer module that is conditioned on current estimation of expression and head pose. These two modules reinforce each other, as image style transfer becomes easier when close-to-ground-truth examples are shown, and better domain-gap removal helps registration. Our system produces high-quality results efficiently, obviating the need for costly offline registration to generate personalized labels. We validate the accuracy and efficiency of our approach through extensive experiments on a commodity headset, demonstrating significant improvements over direct regression methods as well as offline registration.

There is a sensory gulf between the Earth that humans inhabit and the digital realms in which modern AI agents are created. To develop AI agents that can sense, think, and act as flexibly as humans in real-world settings, it is imperative to bridge the realism gap between the digital and physical worlds. How can we embody agents in an environment as rich and diverse as the one we inhabit, without the constraints imposed by real hardware and control? Towards this end, we introduce V-IRL: a platform that enables agents to scalably interact with the real world in a virtual yet realistic environment. Our platform serves as a playground for developing agents that can accomplish various practical tasks and as a vast testbed for measuring progress in capabilities spanning perception, decision-making, and interaction with real-world data across the entire globe.

Creating virtual digital replicas from real-world data unlocks significant potential across domains like gaming and robotics. In this paper, we present DRAWER, a novel framework that converts a video of a static indoor scene into a photorealistic and interactive digital environment. Our approach centers on two main contributions: (i) a reconstruction module based on a dual scene representation that reconstructs the scene with fine-grained geometric details, and (ii) an articulation module that identifies articulation types and hinge positions, reconstructs simulatable shapes and appearances and integrates them into the scene. The resulting virtual environment is photorealistic, interactive, and runs in real time, with compatibility for game engines and robotic simulation platforms. We demonstrate the potential of DRAWER by using it to automatically create an interactive game in Unreal Engine and to enable real-to-sim-to-real transfer for robotics applications.

Simulated evaluation is increasingly used alongside real-world evaluation of robot policies because it is cheaper and easier to repeat; however, its value depends on how closely its outcomes track the real robot's. We test whether our reconstruction pipeline, combining metrically scaled object geometry, authored physical parameters and scene reconstruction, reduces disagreement between simulated and real robot scores relative to a default open-source recipe. We constructed two simulated versions of one bimanual robot cell: an authored reconstruction, using object geometry at estimated metric scale, projected textures, authored physics and our own scene splat; and a baseline, referred to as the default reconstruction, using the open-source recipe of a generative single-image mesh, engine-default physics and a Gaussian-splat scene. Both reconstructions use the same object photographs and scene video. Two policies ran five tasks each, giving ten task-policy pairs, which we call cells; each cell was run twenty times in each reconstruction with all other settings held fixed. Both reconstructions were scored against the same real trials, graded by a third-party evaluator. Pearson correlation between the ten simulated and real cell means is r = 0.90 for the authored reconstruction and 0.51 for the default. Mean score error is 6.97 percentage points for the authored reconstruction and 17.54 for the default, a reduction of 10.56 percentage points. These results show that improving the quality of the environment reconstruction through higher visual fidelity, authored physics and metric scale makes the simulation more faithful to the real world and narrows the sim-to-real gap. We release the harness, the per-trial scores, every reported run's configuration, and the assets and scenes of both reconstructions.

While LLM/VLM-powered AI agents have advanced rapidly in math, coding, and computer use, their applications in complex physical and social environments remain challenging. Building agents that can survive and thrive in the real world (for example, by autonomously earning income or running a business) requires massive-scale interaction, reasoning, training, and evaluation across diverse embodied scenarios. However, existing world simulators for such development fall short: they often rely on limited hand-crafted environments, simulate simplified game-like physics and social rules, and lack native support for LLM/VLM agents. We introduce SimWorld, a new simulator built on Unreal Engine 5, designed for developing and evaluating LLM/VLM agents in rich, real-world-like settings. SimWorld offers three core capabilities: (1) realistic, open-ended world simulation, including accurate physical and social dynamics and language-driven procedural environment generation; (2) a rich interface for LLM/VLM agents, with multimodal world inputs and open-vocabulary actions at varying levels of abstraction; and (3) diverse and extensible physical and social reasoning scenarios that are easily customizable by users. We demonstrate SimWorld by deploying frontier LLM agents (e.g., GPT-4o, Gemini-2.5-Flash, Claude-3.5, and DeepSeek-Prover-V2) on long-horizon multi-agent delivery tasks involving strategic cooperation and competition. The results reveal distinct reasoning patterns and limitations across models. We open-source SimWorld and hope it becomes a foundational platform for advancing real-world agent intelligence across disciplines: https://simworld.org.

We introduce a framework that enables both multi-view character consistency and 3D camera control in video diffusion models through a novel customization data pipeline. We train the character consistency component with recorded volumetric capture performances re-rendered with diverse camera trajectories via 4D Gaussian Splatting (4DGS), lighting variability obtained with a video relighting model. We fine-tune state-of-the-art open-source video diffusion models on this data to provide strong multi-view identity preservation, precise camera control, and lighting adaptability. Our framework also supports core capabilities for virtual production, including multi-subject generation using two approaches: joint training and noise blending, the latter enabling efficient composition of independently customized models at inference time; it also achieves scene and real-life video customization as well as control over motion and spatial layout during customization. Extensive experiments show improved video quality, higher personalization accuracy, and enhanced camera control and lighting adaptability, advancing the integration of video generation into virtual production. Our project page is available at: https://eyeline-labs.github.io/Virtually-Being.

The increasing prominence of e-commerce has underscored the importance of Virtual Try-On (VTON). However, previous studies predominantly focus on the 2D realm and rely heavily on extensive data for training. Research on 3D VTON primarily centers on garment-body shape compatibility, a topic extensively covered in 2D VTON. Thanks to advances in 3D scene editing, a 2D diffusion model has now been adapted for 3D editing via multi-viewpoint editing. In this work, we propose GaussianVTON, an innovative 3D VTON pipeline integrating Gaussian Splatting (GS) editing with 2D VTON. To facilitate a seamless transition from 2D to 3D VTON, we propose, for the first time, the use of only images as editing prompts for 3D editing. To further address issues, e.g., face blurring, garment inaccuracy, and degraded viewpoint quality during editing, we devise a three-stage refinement strategy to gradually mitigate potential issues. Furthermore, we introduce a new editing strategy termed Edit Recall Reconstruction (ERR) to tackle the limitations of previous editing strategies in leading to complex geometric changes. Our comprehensive experiments demonstrate the superiority of GaussianVTON, offering a novel perspective on 3D VTON while also establishing a novel starting point for image-prompting 3D scene editing.

Virtual 3D meetings offer the potential to enhance copresence, increase engagement and thus improve effectiveness of remote meetings compared to standard 2D video calls. However, representing people in 3D meetings remains a challenge; existing solutions achieve high quality by using complex hardware, making use of fixed appearance via enrolment, or by inverting a pre-trained generative model. These approaches lead to constraints that are unwelcome and ill-fitting for videoconferencing applications. We present the first method to predict 3D Gaussian reconstructions in real time from a single 2D webcam feed, where the 3D representation is not only live and realistic, but also authentic to the input video. By conditioning the 3D representation on each video frame independently, our reconstruction faithfully recreates the input video from the captured viewpoint (a property we call authenticity), while generalizing realistically to novel viewpoints. Additionally, we introduce a stability loss to obtain reconstructions that are temporally stable on video sequences. We show that our method delivers state-of-the-art accuracy in visual quality and stability metrics compared to existing methods, and demonstrate our approach in live one-to-one 3D meetings using only a standard 2D camera and display. This demonstrates that our approach can allow anyone to communicate volumetrically, via a method for 3D videoconferencing that is not only highly accessible, but also realistic and authentic.

Contouring is an indispensable step in Radiotherapy (RT) treatment planning. However, today's contouring software is constrained to only work with a 2D display, which is less intuitive and requires high task loads. Virtual Reality (VR) has shown great potential in various specialties of healthcare and health sciences education due to the unique advantages of intuitive and natural interactions in immersive spaces. VR-based radiation oncology integration has also been advocated as a target healthcare application, allowing providers to directly interact with 3D medical structures. We present VRContour and investigate how to effectively bring contouring for radiation oncology into VR. Through an autobiographical iterative design, we defined three design spaces focused on contouring in VR with the support of a tracked tablet and VR stylus, and investigating dimensionality for information consumption and input (either 2D or 2D + 3D). Through a within-subject study (n = 8), we found that visualizations of 3D medical structures significantly increase precision, and reduce mental load, frustration, as well as overall contouring effort. Participants also agreed with the benefits of using such metaphors for learning purposes.

Against all attempts that consider virtuality as a substance (a parallel or alternative reality) or as a modality (like potentiality or possibility), we want to defend the pragmatic point of view that it is rather a dynamic cognitive and sensitive interaction with reality. More precisely, we show that the ``virtus'' is an operating capacity that produces simulations of real and fictional contexts to experiment with their effects. Based on Peirce's semiotics, we define virtual reality (VR) and augmented reality (AR) as mixed realities made of ``symbolic assemblies'', that is to say, structures of signs assembled by processes of computation and meaning (semiosis). We show that VR can be defined as a synesthetic experiment that does not reshape reality itself, but rather the senses and understanding we already have about it. In conclusion, we criticize David Chalmer's extended mind theory by distinguishing between knowledge and information, and we try to redefine AR as a hermeneutic device that extends not the mind itself, but the activity of thought by adding symbols to read in the world.

Recent research has been increasingly focusing on developing 3D world models that simulate complex real-world scenarios. World models have found broad applications across various domains, including embodied AI, autonomous driving, entertainment, etc. A more realistic simulation with accurate physics will effectively narrow the sim-to-real gap and allow us to gather rich information about the real world conveniently. While traditional manual modeling has enabled the creation of virtual 3D scenes, modern approaches have leveraged advanced machine learning algorithms for 3D world generation, with most recent advances focusing on generative methods that can create virtual worlds based on user instructions. This work explores such a research direction by proposing LatticeWorld, a simple yet effective 3D world generation framework that streamlines the industrial production pipeline of 3D environments. LatticeWorld leverages lightweight LLMs (LLaMA-2-7B) alongside the industry-grade rendering engine (e.g., Unreal Engine 5) to generate a dynamic environment. Our proposed framework accepts textual descriptions and visual instructions as multimodal inputs and creates large-scale 3D interactive worlds with dynamic agents, featuring competitive multi-agent interaction, high-fidelity physics simulation, and real-time rendering. We conduct comprehensive experiments to evaluate LatticeWorld, showing that it achieves superior accuracy in scene layout generation and visual fidelity. Moreover, LatticeWorld achieves over a 90times increase in industrial production efficiency while maintaining high creative quality compared with traditional manual production methods. Our demo video is available at https://youtu.be/8VWZXpERR18

LLM/VLM-based digital agents have advanced rapidly thanks to scalable sandboxes for coding, web navigation, and computer use, which provide rich interactive training grounds. In contrast, embodied agents still lack abundant, diverse, and automatically generated 3D environments for interactive learning. Existing embodied simulators rely on manually crafted scenes or procedural templates, while recent LLM-based 3D generation systems mainly produce static scenes rather than deployable environments with verifiable tasks and standard learning interfaces. We introduce SimWorld Studio, an open-source platform built on Unreal Engine 5 for generating evolving embodied learning environments. At its core is SimCoder, a tool/skill-augmented coding agent that writes and executes engine-level code to construct physically grounded 3D worlds from language/image instructions. SimCoder self-evolves by using verifier feedback (e.g., compilation errors, physics checks, VLM critiques) to revise environments and autonomously add reusable tools and skills to its library. Generated worlds are exported as Gym-style environments for embodied agent learning. SimWorld Studio further enables co-evolution between environment generation and embodied learning: agent performance feedback guides SimCoder to generate adaptive curricula near the learner's capability frontier, so that environments become increasingly challenging as the embodied agent improves. Three case studies on embodied navigation show that self-evolution improves generation reliability, generated environments substantially improve embodied agent performance that generalizes to unseen benchmarks, and co-evolution yields an 18-point success-rate gain over fixed-environment learning and a 40-point gain over an untrained agent.

The development of embodied Intelligent Virtual Agents (IVAs) that have cognitive capabilities in real-time interactive virtual environments remains a challenge, even with today's advancements in technology. Existing architectures are often focused on either the implementation of low-level reactive control systems that are constrained by commercial game engines, or high-level representations of reasoning models that can be difficult to implement in virtual worlds. This paper builds on that notion and proposes a modular cognitive architecture for deploying embodied IVAs. This architecture builds on existing, pre-established frameworks such as the Sense-Think-Act paradigm and the Belief-Desire-Intention cognitive model, among others, and aims to provide a reusable implementation-oriented framework as a template for deploying IVA "brains" in interactive 3D computing systems. The proposed architecture contributes by providing a modular, implementation-oriented framework for the deployment of embodied, cognitive-capable IVAs and bridges the gap between high-level agent reasoning models with real-time embodied execution, for scalable, adaptive, and explainable agents in complex interactive virtual environments.

The fashion e-commerce industry has witnessed significant growth in recent years, prompting exploring image-based virtual try-on techniques to incorporate Augmented Reality (AR) experiences into online shopping platforms. However, existing research has primarily overlooked a crucial aspect - the runtime of the underlying machine-learning model. While existing methods prioritize enhancing output quality, they often disregard the execution time, which restricts their applications on a limited range of devices. To address this gap, we propose Distilled Mobile Real-time Virtual Try-On (DM-VTON), a novel virtual try-on framework designed to achieve simplicity and efficiency. Our approach is based on a knowledge distillation scheme that leverages a strong Teacher network as supervision to guide a Student network without relying on human parsing. Notably, we introduce an efficient Mobile Generative Module within the Student network, significantly reducing the runtime while ensuring high-quality output. Additionally, we propose Virtual Try-on-guided Pose for Data Synthesis to address the limited pose variation observed in training images. Experimental results show that the proposed method can achieve 40 frames per second on a single Nvidia Tesla T4 GPU and only take up 37 MB of memory while producing almost the same output quality as other state-of-the-art methods. DM-VTON stands poised to facilitate the advancement of real-time AR applications, in addition to the generation of lifelike attired human figures tailored for diverse specialized training tasks. https://sites.google.com/view/ltnghia/research/DMVTON

The advent of immersive Virtual Reality applications has transformed various domains, yet their integration with advanced artificial intelligence technologies like Visual Language Models remains underexplored. This study introduces a pioneering approach utilizing VLMs within VR environments to enhance user interaction and task efficiency. Leveraging the Unity engine and a custom-developed VLM, our system facilitates real-time, intuitive user interactions through natural language processing, without relying on visual text instructions. The incorporation of speech-to-text and text-to-speech technologies allows for seamless communication between the user and the VLM, enabling the system to guide users through complex tasks effectively. Preliminary experimental results indicate that utilizing VLMs not only reduces task completion times but also improves user comfort and task engagement compared to traditional VR interaction methods.

Single-cell sequencing technologies reveal cellular heterogeneity at high resolution, advancing our understanding of biological complexity. As datasets start to scale to tens of millions of cells, computational workflows face substantial bottlenecks, with CPU-based analytical pipelines requiring hours or days for routine processing steps like filtering, normalization, and clustering. These scalability limitations fundamentally restrict common interactive data exploration and iterative hypothesis testing. Here we introduce rapids-singlecell, a GPU-accelerated framework that integrates natively with the scverse ecosystem and operates directly on the AnnData data structure, which delivers orders-of-magnitude speedups for single-cell workflows. Built on CuPy arrays and the NVIDIA CUDA-X Data Science (RAPIDS) ecosystem, rapids-singlecell provides near drop-in GPU replacements for core scanpy-based analysis steps. Across standard single-cell workflows such as preprocessing, dimensionality reduction, neighborhood graph construction, clustering, and batch correction, rapids-singlecell achieves speedups of up to several hundred-fold compared to optimized CPU baselines. This reduces analysis time from hours to minutes on standard hardware, while maintaining consistent biological interpretations. These performance improvements make it possible to analyze large data sets in close to real time, without the need for data splitting. Together with real-time parameter tuning and iterative workflows, rapids-singlecell makes interactive large-scale single-cell analysis possible.

The teleoperation of robotic systems in medical applications requires stable and convenient visual feedback for the operator. The most accessible approach to delivering visual information from the remote area is using cameras to transmit a video stream from the environment. However, such systems are sensitive to the camera resolution, limited viewpoints, and cluttered environment bringing additional mental demands to the human operator. The paper proposes a novel system of teleoperation based on an augmented virtual environment (VE). The region-based convolutional neural network (R-CNN) is applied to detect the laboratory instrument and estimate its position in the remote environment to display further its digital twin in the VE, which is necessary for dexterous telemanipulation. The experimental results revealed that the developed system allows users to operate the robot smoother, which leads to a decrease in task execution time when manipulating test tubes. In addition, the participants evaluated the developed system as less mentally demanding (by 11%) and requiring less effort (by 16%) to accomplish the task than the camera-based teleoperation approach and highly assessed their performance in the augmented VE. The proposed technology can be potentially applied for conducting laboratory tests in remote areas when operating with infectious and poisonous reagents.

Video Virtual Try-On (VVT) aims to simulate the natural appearance of garments across consecutive video frames, capturing their dynamic variations and interactions with human body motion. However, current VVT methods still face challenges in terms of spatiotemporal consistency and garment content preservation. First, they use diffusion models based on the U-Net, which are limited in their expressive capability and struggle to reconstruct complex details. Second, they adopt a separative modeling approach for spatial and temporal attention, which hinders the effective capture of structural relationships and dynamic consistency across frames. Third, their expression of garment details remains insufficient, affecting the realism and stability of the overall synthesized results, especially during human motion. To address the above challenges, we propose MagicTryOn, a video virtual try-on framework built upon the large-scale video diffusion Transformer. We replace the U-Net architecture with a diffusion Transformer and combine full self-attention to jointly model the spatiotemporal consistency of videos. We design a coarse-to-fine garment preservation strategy. The coarse strategy integrates garment tokens during the embedding stage, while the fine strategy incorporates multiple garment-based conditions, such as semantics, textures, and contour lines during the denoising stage. Moreover, we introduce a mask-aware loss to further optimize garment region fidelity. Extensive experiments on both image and video try-on datasets demonstrate that our method outperforms existing SOTA methods in comprehensive evaluations and generalizes to in-the-wild scenarios.

This paper introduces VIVRA (Voice Interactive Virtual Reality Annotation), a VR application combining multimodal interaction with large language models (LLMs) to transform users' ideas into interactive 3D visualizations. VIVRA converts verbalized thoughts into "idea balloons" that summarize and expand on detected topics by an LLM. VIVRA allows users to verbalize their thoughts in real time or record their ideas to display the topics later. We evaluated the effectiveness of VIVRA in an exploratory study with 29 participants and a user study with 10 participants. Our results show that VIVRA enhanced users' ability to reflect on and develop ideas, achieving high levels of satisfaction, usability, and engagement. Participants valued VIVRA as a reflective tool for exploring personal thoughts and ideas. We discuss the potential advantages and uses of this application, highlighting the potential of combining immersive technologies with LLMs to create powerful ideation and reflection tools.

Vision-language-action (VLA) models have shown promise as generalist robotic policies by jointly leveraging visual, linguistic, and proprioceptive modalities to generate action trajectories. While recent benchmarks have advanced VLA research in domestic tasks, professional science-oriented domains remain underexplored. We introduce AutoBio, a simulation framework and benchmark designed to evaluate robotic automation in biology laboratory environments--an application domain that combines structured protocols with demanding precision and multimodal interaction. AutoBio extends existing simulation capabilities through a pipeline for digitizing real-world laboratory instruments, specialized physics plugins for mechanisms ubiquitous in laboratory workflows, and a rendering stack that support dynamic instrument interfaces and transparent materials through physically based rendering. Our benchmark comprises biologically grounded tasks spanning three difficulty levels, enabling standardized evaluation of language-guided robotic manipulation in experimental protocols. We provide infrastructure for demonstration generation and seamless integration with VLA models. Baseline evaluations with two SOTA VLA models reveal significant gaps in precision manipulation, visual reasoning, and instruction following in scientific workflows. By releasing AutoBio, we aim to catalyze research on generalist robotic systems for complex, high-precision, and multimodal professional environments. The simulator and benchmark are publicly available to facilitate reproducible research.

Cell instance segmentation is a fundamental task in digital pathology with broad clinical applications. Recently, vision foundation models, which are predominantly based on Vision Transformers (ViTs), have achieved remarkable success in pathology image analysis. However, their improvements in cell instance segmentation remain limited. A key challenge arises from the tokenization process in ViTs, which substantially reduces the spatial resolution of input images, leading to suboptimal segmentation quality, especially for small and densely packed cells. To address this problem, we propose CellVTA (Cell Vision Transformer with Adapter), a novel method that improves the performance of vision foundation models for cell instance segmentation by incorporating a CNN-based adapter module. This adapter extracts high-resolution spatial information from input images and injects it into the ViT through a cross-attention mechanism. Our method preserves the core architecture of ViT, ensuring seamless integration with pretrained foundation models. Extensive experiments show that CellVTA achieves 0.538 mPQ on the CoNIC dataset and 0.506 mPQ on the PanNuke dataset, which significantly outperforms the state-of-the-art cell segmentation methods. Ablation studies confirm the superiority of our approach over other fine-tuning strategies, including decoder-only fine-tuning and full fine-tuning. Our code and models are publicly available at https://github.com/JieZheng-ShanghaiTech/CellVTA.

We introduce NeoWorld, a deep learning framework for generating interactive 3D virtual worlds from a single input image. Inspired by the on-demand worldbuilding concept in the science fiction novel Simulacron-3 (1964), our system constructs expansive environments where only the regions actively explored by the user are rendered with high visual realism through object-centric 3D representations. Unlike previous approaches that rely on global world generation or 2D hallucination, NeoWorld models key foreground objects in full 3D, while synthesizing backgrounds and non-interacted regions in 2D to ensure efficiency. This hybrid scene structure, implemented with cutting-edge representation learning and object-to-3D techniques, enables flexible viewpoint manipulation and physically plausible scene animation, allowing users to control object appearance and dynamics using natural language commands. As users interact with the environment, the virtual world progressively unfolds with increasing 3D detail, delivering a dynamic, immersive, and visually coherent exploration experience. NeoWorld significantly outperforms existing 2D and depth-layered 2.5D methods on the WorldScore benchmark.

Bionic vision uses neuroprostheses to restore useful vision to people living with incurable blindness. However, a major outstanding challenge is predicting what people 'see' when they use their devices. The limited field of view of current devices necessitates head movements to scan the scene, which is difficult to simulate on a computer screen. In addition, many computational models of bionic vision lack biological realism. To address these challenges, we present VR-SPV, an open-source virtual reality toolbox for simulated prosthetic vision that uses a psychophysically validated computational model to allow sighted participants to 'see through the eyes' of a bionic eye user. To demonstrate its utility, we systematically evaluated how clinically reported visual distortions affect performance in a letter recognition and an immersive obstacle avoidance task. Our results highlight the importance of using an appropriate phosphene model when predicting visual outcomes for bionic vision.

Virtual try-on has garnered interest as a neural rendering benchmark task to evaluate complex object transfer and scene composition. Recent works in virtual clothing try-on feature a plethora of possible architectural and data representation choices. However, they present little clarity on quantifying the isolated visual effect of each choice, nor do they specify the hyperparameter details that are key to experimental reproduction. Our work, ShineOn, approaches the try-on task from a bottom-up approach and aims to shine light on the visual and quantitative effects of each experiment. We build a series of scientific experiments to isolate effective design choices in video synthesis for virtual clothing try-on. Specifically, we investigate the effect of different pose annotations, self-attention layer placement, and activation functions on the quantitative and qualitative performance of video virtual try-on. We find that DensePose annotations not only enhance face details but also decrease memory usage and training time. Next, we find that attention layers improve face and neck quality. Finally, we show that GELU and ReLU activation functions are the most effective in our experiments despite the appeal of newer activations such as Swish and Sine. We will release a well-organized code base, hyperparameters, and model checkpoints to support the reproducibility of our results. We expect our extensive experiments and code to greatly inform future design choices in video virtual try-on. Our code may be accessed at https://github.com/andrewjong/ShineOn-Virtual-Tryon.

Mobile GUI agents powered by large language models have progressed rapidly, creating urgent needs for realistic and comprehensive evaluation. Existing benchmarks prioritize reproducibility but are often limited to open-source apps or file-operation tasks for the difficulty of constructing rewards on real applications, leaving a gap between benchmark settings and real-world usage. Moreover, most benchmarks focus on basic grounding and navigation, with limited coverage of complex, long-horizon interactions. To address these limitations, we introduce SimuWoB, a fully synthetic benchmark for mobile GUI agents with 120 challenging tasks spanning diverse types and difficulty levels. We build a robust virtual environment generation framework that synthesizes high-fidelity tasks and environments, and automatically provides valid rewards for each task. Each environment is deployed as a backend-free webpage accessible via URL, enabling efficient and reproducible evaluation. We conduct comprehensive experiments on several state-of-the-art mobile GUI agents. The average success rate is only 27.92%, dropping to 17.82% on long-horizon tasks, which reveals substantial weaknesses in current agents under complex scenarios. Evaluation result comparison with real-world sample tasks demonstrate that agent assessments based on our synthetic environment generalize well. We further provide diagnostic insights across key capability dimensions and discuss implications for future mobile GUI agent development.

Large language models (LLMs) and emerging agentic frameworks are beginning to transform single-cell biology by enabling natural-language reasoning, generative annotation, and multimodal data integration. However, progress remains fragmented across data modalities, architectures, and evaluation standards. LLM4Cell presents the first unified survey of 58 foundation and agentic models developed for single-cell research, spanning RNA, ATAC, multi-omic, and spatial modalities. We categorize these methods into five families-foundation, text-bridge, spatial, multimodal, epigenomic, and agentic-and map them to eight key analytical tasks including annotation, trajectory and perturbation modeling, and drug-response prediction. Drawing on over 40 public datasets, we analyze benchmark suitability, data diversity, and ethical or scalability constraints, and evaluate models across 10 domain dimensions covering biological grounding, multi-omics alignment, fairness, privacy, and explainability. By linking datasets, models, and evaluation domains, LLM4Cell provides the first integrated view of language-driven single-cell intelligence and outlines open challenges in interpretability, standardization, and trustworthy model development.

The planning and control of a robot swarm in a complex environment have attracted increasing attention. To this end, the idea of virtual tubes has been taken up in our previous work. Specifically, a virtual tube with varying widths has been planned to avoid collisions with obstacles in a complex environment. Based on the planned virtual tube for a large number of speed-constrained robots, the average forward speed and density along the virtual tube are further planned in this paper to ensure safety and improve efficiency. Compared with the existing methods, the proposed method is based on global information and can be applied to traversing narrow spaces for speed-constrained robot swarms. Numerical simulations and experiments are conducted to show that the safety and efficiency of the passing-through process are improved. A video about simulations and experiments is available on https://youtu.be/lJHdMQMqSpc.

While Video Virtual Try-on (VVT) has achieved remarkable progress in synthesizing realistic garment overlays on dynamic subjects, existing paradigms remains fundamentally constrained by a passive dependency on source camera trajectories, failing to accommodate the requisite interactive freedom for omnidirectional viewpoint exploration. To address this limitation, we define a pioneering research frontier: Camera-controllable Video Virtual Try-on (CaM-VVT). Unlike conventional VVT, CaM-VVT not only necessitates viewpoint-agnostic texture hallucination but also strict structural synchronization between non-rigid human dynamics and background contexts under arbitrary, unconstrained camera movements. To tackle these challenges, we present TryOnCrafter, the first unified DiT-based framework specifically architected for the CaM-VVT task. Departing from implicit pixel-space manipulation, we introduce a Renderable 4D Try-on Proxy that explicitly decouples the human subject from the environment. This is achieved by distilling high-fidelity 2D try-on priors into a clothed 3DGS-based avatar, which is subsequently animated via SMPL-X sequences and metric-aligned into a reconstructed background point cloud. This proxy establishes a robust structural foundation with superior texture density and motion integrity. Our Proxy-Anchored Video DiT leverages this robust structural foundation as a primary geometric anchor, ensuring that the synthesized photorealistic videos are strictly constrained by prescribed trajectories and physically plausible deformations. Benefiting from the inherent editability of the 4D proxy, TryOnCrafter facilitates diverse downstream applications, including human relocalization, ``bullet time'' effects, and 360-degree orbital viewing.

Realistic simulation is critical for applications ranging from robotics to animation. Traditional analytic simulators sometimes struggle to capture sufficiently realistic simulation which can lead to problems including the well known "sim-to-real" gap in robotics. Learned simulators have emerged as an alternative for better capturing real-world physical dynamics, but require access to privileged ground truth physics information such as precise object geometry or particle tracks. Here we propose a method for learning simulators directly from observations. Visual Particle Dynamics (VPD) jointly learns a latent particle-based representation of 3D scenes, a neural simulator of the latent particle dynamics, and a renderer that can produce images of the scene from arbitrary views. VPD learns end to end from posed RGB-D videos and does not require access to privileged information. Unlike existing 2D video prediction models, we show that VPD's 3D structure enables scene editing and long-term predictions. These results pave the way for downstream applications ranging from video editing to robotic planning.

Recent advances in microscopy have enabled the rapid generation of terabytes of image data in cell biology and biomedical research. Vision-language models (VLMs) offer a promising solution for large-scale biological image analysis, enhancing researchers' efficiency, identifying new image biomarkers, and accelerating hypothesis generation and scientific discovery. However, there is a lack of standardized, diverse, and large-scale vision-language benchmarks to evaluate VLMs' perception and cognition capabilities in biological image understanding. To address this gap, we introduce {\mu}-Bench, an expert-curated benchmark encompassing 22 biomedical tasks across various scientific disciplines (biology, pathology), microscopy modalities (electron, fluorescence, light), scales (subcellular, cellular, tissue), and organisms in both normal and abnormal states. We evaluate state-of-the-art biomedical, pathology, and general VLMs on {\mu}-Bench and find that: i) current models struggle on all categories, even for basic tasks such as distinguishing microscopy modalities; ii) current specialist models fine-tuned on biomedical data often perform worse than generalist models; iii) fine-tuning in specific microscopy domains can cause catastrophic forgetting, eroding prior biomedical knowledge encoded in their base model. iv) weight interpolation between fine-tuned and pre-trained models offers one solution to forgetting and improves general performance across biomedical tasks. We release {\mu}-Bench under a permissive license to accelerate the research and development of microscopy foundation models.

Video virtual try-on (VVT) technology has garnered considerable academic interest owing to its promising applications in e-commerce advertising and entertainment. However, most existing end-to-end methods rely heavily on scarce paired garment-centric datasets and fail to effectively leverage priors of advanced visual models and test-time inputs, making it challenging to accurately preserve fine-grained garment details and maintain temporal consistency in unconstrained scenarios. To address these challenges, we propose DreamVVT, a carefully designed two-stage framework built upon Diffusion Transformers (DiTs), which is inherently capable of leveraging diverse unpaired human-centric data to enhance adaptability in real-world scenarios. To further leverage prior knowledge from pretrained models and test-time inputs, in the first stage, we sample representative frames from the input video and utilize a multi-frame try-on model integrated with a vision-language model (VLM), to synthesize high-fidelity and semantically consistent keyframe try-on images. These images serve as complementary appearance guidance for subsequent video generation. In the second stage, skeleton maps together with fine-grained motion and appearance descriptions are extracted from the input content, and these along with the keyframe try-on images are then fed into a pretrained video generation model enhanced with LoRA adapters. This ensures long-term temporal coherence for unseen regions and enables highly plausible dynamic motions. Extensive quantitative and qualitative experiments demonstrate that DreamVVT surpasses existing methods in preserving detailed garment content and temporal stability in real-world scenarios. Our project page https://virtu-lab.github.io/

This work addresses the problem of real-time rendering of photorealistic human body avatars learned from multi-view videos. While the classical approaches to model and render virtual humans generally use a textured mesh, recent research has developed neural body representations that achieve impressive visual quality. However, these models are difficult to render in real-time and their quality degrades when the character is animated with body poses different than the training observations. We propose an animatable human model based on 3D Gaussian Splatting, that has recently emerged as a very efficient alternative to neural radiance fields. The body is represented by a set of gaussian primitives in a canonical space which is deformed with a coarse to fine approach that combines forward skinning and local non-rigid refinement. We describe how to learn our Human Gaussian Splatting (HuGS) model in an end-to-end fashion from multi-view observations, and evaluate it against the state-of-the-art approaches for novel pose synthesis of clothed body. Our method achieves 1.5 dB PSNR improvement over the state-of-the-art on THuman4 dataset while being able to render in real-time (80 fps for 512x512 resolution).

Large-scale, diverse datasets have driven the success of LLMs and VLMs. But VLAs for robotics remain limited by the cost and complexity of real-world data collection. While simulation offers a scalable alternative, its potential for sim-to-real VLA learning in mobile manipulation remains largely underexplored. We introduce SimVLA, an end-to-end framework that trains VLAs entirely on synthetic simulation data without teleoperation for mobile manipulation. SimVLA is first pre-trained on two complementary simulation-derived datasets: SimAction, a large-scale robot action dataset spanning 35 diverse mobile manipulation tasks, generated by composing atomic skills, and SimVQA, which leverages privileged simulator state to provide spatial, geometric, and subtask-level visual-language supervision. We further post-train SimVLA on a mixture of SimAction and SimDeploy, a dataset collected from policy rollouts across diverse simulated environments. We evaluate SimVLA on tasks including restocking, pouring, and cleaning, and show zero-shot transfer to real-world mobile manipulation, including real home environments. SimVLA outperforms policies trained on 50 in-domain real-world demonstrations, suggesting that simulation can enable scalable sim-to-real mobile manipulation. We further demonstrate the value of multiple complementary forms of supervision for effectively leveraging simulation in VLA training.

Generative modeling of single-cell RNA-seq data has shown invaluable potential in community-driven tasks such as trajectory inference, batch effect removal and gene expression generation. However, most recent deep models generating synthetic single cells from noise operate on pre-processed continuous gene expression approximations, ignoring the inherently discrete and over-dispersed nature of single-cell data, which limits downstream applications and hinders the incorporation of robust noise models. Moreover, crucial aspects of deep-learning-based synthetic single-cell generation remain underexplored, such as controllable multi-modal and multi-label generation and its role in the performance enhancement of downstream tasks. This work presents Cell Flow for Generation (CFGen), a flow-based conditional generative model for multi-modal single-cell counts, which explicitly accounts for the discrete nature of the data. Our results suggest improved recovery of crucial biological data characteristics while accounting for novel generative tasks such as conditioning on multiple attributes and boosting rare cell type classification via data augmentation. By showcasing CFGen on a diverse set of biological datasets and settings, we provide evidence of its value to the fields of computational biology and deep generative models.

Recent advancements in single-cell multi-omics, particularly RNA-seq, have provided profound insights into cellular heterogeneity and gene regulation. While pre-trained language model (PLM) paradigm based single-cell foundation models have shown promise, they remain constrained by insufficient integration of in-depth individual profiles and neglecting the influence of noise within multi-modal data. To address both issues, we propose an Open-world Language Knowledge-Aided Robust Single-Cell Foundation Model (OKR-CELL). It is built based on a cross-modal Cell-Language pre-training framework, which comprises two key innovations: (1) leveraging Large Language Models (LLMs) based workflow with retrieval-augmented generation (RAG) enriches cell textual descriptions using open-world knowledge; (2) devising a Cross-modal Robust Alignment (CRA) objective that incorporates sample reliability assessment, curriculum learning, and coupled momentum contrastive learning to strengthen the model's resistance to noisy data. After pretraining on 32M cell-text pairs, OKR-CELL obtains cutting-edge results across 6 evaluation tasks. Beyond standard benchmarks such as cell clustering, cell-type annotation, batch-effect correction, and few-shot annotation, the model also demonstrates superior performance in broader multi-modal applications, including zero-shot cell-type annotation and bidirectional cell-text retrieval.

With the rapid advance of computer graphics and artificial intelligence technologies, the ways we interact with the world have undergone a transformative shift. Virtual Reality (VR) technology, aided by artificial intelligence (AI), has emerged as a dominant interaction media in multiple application areas, thanks to its advantage of providing users with immersive experiences. Among those applications, medicine is considered one of the most promising areas. In this paper, we present a comprehensive examination of the burgeoning field of AI-enhanced VR applications in medical care and services. By introducing a systematic taxonomy, we meticulously classify the pertinent techniques and applications into three well-defined categories based on different phases of medical diagnosis and treatment: Visualization Enhancement, VR-related Medical Data Processing, and VR-assisted Intervention. This categorization enables a structured exploration of the diverse roles that AI-powered VR plays in the medical domain, providing a framework for a more comprehensive understanding and evaluation of these technologies. To our best knowledge, this is the first systematic survey of AI-powered VR systems in medical settings, laying a foundation for future research in this interdisciplinary domain.

Video game engines have been an important source for generating large volumes of visual synthetic datasets for training and evaluating computer vision algorithms that are to be deployed in the real world. While the visual fidelity of modern game engines has been significantly improved with technologies such as ray-tracing, a notable sim2real appearance gap between the synthetic and the real-world images still remains, which limits the utilization of synthetic datasets in real-world applications. In this letter, we investigate the ability of a state-of-the-art image generation and editing diffusion model (FLUX.2-4B Klein) to enhance the photorealism of synthetic datasets and compare its performance against a traditional image-to-image translation model (REGEN). Furthermore, we propose a hybrid approach that combines the strong geometry and material transformations of diffusion-based methods with the distribution-matching capabilities of image-to-image translation techniques. Through experiments, it is demonstrated that REGEN outperforms FLUX.2-4B Klein and that by combining both FLUX.2-4B Klein and REGEN models, better visual realism can be achieved compared to using each model individually, while maintaining semantic consistency. The code is available at: https://github.com/stefanos50/Hybrid-Sim2Real

We present Programmable-Room, a framework which interactively generates and edits a 3D room mesh, given natural language instructions. For precise control of a room's each attribute, we decompose the challenging task into simpler steps such as creating plausible 3D coordinates for room meshes, generating panorama images for the texture, constructing 3D meshes by integrating the coordinates and panorama texture images, and arranging furniture. To support the various decomposed tasks with a unified framework, we incorporate visual programming (VP). VP is a method that utilizes a large language model (LLM) to write a Python-like program which is an ordered list of necessary modules for the various tasks given in natural language. We develop most of the modules. Especially, for the texture generating module, we utilize a pretrained large-scale diffusion model to generate panorama images conditioned on text and visual prompts (i.e., layout, depth, and semantic map) simultaneously. Specifically, we enhance the panorama image generation quality by optimizing the training objective with a 1D representation of a panorama scene obtained from bidirectional LSTM. We demonstrate Programmable-Room's flexibility in generating and editing 3D room meshes, and prove our framework's superiority to an existing model quantitatively and qualitatively. Project page is available in https://jihyun0510.github.io/Programmable_Room_Page/.

Pre-trained language models (PLMs) have revolutionized scientific research, yet their application to single-cell analysis remains limited. Text PLMs cannot process single-cell RNA sequencing data, while cell PLMs lack the ability to handle free text, restricting their use in multimodal tasks. Existing efforts to bridge these modalities often suffer from information loss or inadequate single-modal pre-training, leading to suboptimal performances. To address these challenges, we propose Single-Cell MultiModal Generative Pre-trained Transformer (scMMGPT), a unified PLM for joint cell and text modeling. scMMGPT effectively integrates the state-of-the-art cell and text PLMs, facilitating cross-modal knowledge sharing for improved performance. To bridge the text-cell modality gap, scMMGPT leverages dedicated cross-modal projectors, and undergoes extensive pre-training on 27 million cells -- the largest dataset for multimodal cell-text PLMs to date. This large-scale pre-training enables scMMGPT to excel in joint cell-text tasks, achieving an 84\% relative improvement of textual discrepancy for cell description generation, 20.5\% higher accuracy for cell type annotation, and 4\% improvement in k-NN accuracy for text-conditioned pseudo-cell generation, outperforming baselines.

Structured illumination microscopy (SIM) has become an important technique for optical super-resolution imaging because it allows a doubling of image resolution at speeds compatible for live-cell imaging. However, the reconstruction of SIM images is often slow and prone to artefacts. Here we propose a versatile reconstruction method, ML-SIM, which makes use of machine learning. The model is an end-to-end deep residual neural network that is trained on a simulated data set to be free of common SIM artefacts. ML-SIM is thus robust to noise and irregularities in the illumination patterns of the raw SIM input frames. The reconstruction method is widely applicable and does not require the acquisition of experimental training data. Since the training data are generated from simulations of the SIM process on images from generic libraries the method can be efficiently adapted to specific experimental SIM implementations. The reconstruction quality enabled by our method is compared with traditional SIM reconstruction methods, and we demonstrate advantages in terms of noise, reconstruction fidelity and contrast for both simulated and experimental inputs. In addition, reconstruction of one SIM frame typically only takes ~100ms to perform on PCs with modern Nvidia graphics cards, making the technique compatible with real-time imaging. The full implementation and the trained networks are available at http://ML-SIM.com.

Virtual Try-On (VTON) is the task of synthesizing an image of a person wearing a target garment, conditioned on a person image and a garment image. While diffusion-based VTON models featuring a Dual UNet architecture demonstrate superior fidelity compared to single UNet models, they incur substantial computational and memory overhead due to their heavy structure. In this study, through visualization analysis and theoretical analysis, we derived three hypotheses regarding the learning of context features to condition the denoising process. Based on these hypotheses, we developed Re-CatVTON, an efficient single UNet model that achieves high performance. We further enhance the model by introducing a modified classifier-free guidance strategy tailored for VTON's spatial concatenation conditioning, and by directly injecting the ground-truth garment latent derived from the clean garment latent to prevent the accumulation of prediction error. The proposed Re-CatVTON significantly improves performance compared to its predecessor (CatVTON) and requires less computation and memory than the high-performance Dual UNet model, Leffa. Our results demonstrate improved FID, KID, and LPIPS scores, with only a marginal decrease in SSIM, establishing a new efficiency-performance trade-off for single UNet VTON models.

Reconstructing personalized animatable head avatars has significant implications in the fields of AR/VR. Existing methods for achieving explicit face control of 3D Morphable Models (3DMM) typically rely on multi-view images or videos of a single subject, making the reconstruction process complex. Additionally, the traditional rendering pipeline is time-consuming, limiting real-time animation possibilities. In this paper, we introduce CVTHead, a novel approach that generates controllable neural head avatars from a single reference image using point-based neural rendering. CVTHead considers the sparse vertices of mesh as the point set and employs the proposed Vertex-feature Transformer to learn local feature descriptors for each vertex. This enables the modeling of long-range dependencies among all the vertices. Experimental results on the VoxCeleb dataset demonstrate that CVTHead achieves comparable performance to state-of-the-art graphics-based methods. Moreover, it enables efficient rendering of novel human heads with various expressions, head poses, and camera views. These attributes can be explicitly controlled using the coefficients of 3DMMs, facilitating versatile and realistic animation in real-time scenarios.

The current work addresses a virtual environment with self-replicating agents whose decisions are based on a form of "somatic computation" (soma - body) in which basic emotional responses, taken in parallelism to actual living organisms, are introduced as a way to provide the agents with greater reflexive abilities. The work provides a contribution to the field of Artificial Intelligence (AI) and Artificial Life (ALife) in connection to a neurobiology-based cognitive framework for artificial systems and virtual environments' simulations. The performance of the agents capable of emotional responses is compared with that of self-replicating automata, and the implications of research on emotions and AI, in connection to both virtual agents as well as robots, is addressed regarding possible future directions and applications.

We present Habitat, a platform for research in embodied artificial intelligence (AI). Habitat enables training embodied agents (virtual robots) in highly efficient photorealistic 3D simulation. Specifically, Habitat consists of: (i) Habitat-Sim: a flexible, high-performance 3D simulator with configurable agents, sensors, and generic 3D dataset handling. Habitat-Sim is fast -- when rendering a scene from Matterport3D, it achieves several thousand frames per second (fps) running single-threaded, and can reach over 10,000 fps multi-process on a single GPU. (ii) Habitat-API: a modular high-level library for end-to-end development of embodied AI algorithms -- defining tasks (e.g., navigation, instruction following, question answering), configuring, training, and benchmarking embodied agents. These large-scale engineering contributions enable us to answer scientific questions requiring experiments that were till now impracticable or 'merely' impractical. Specifically, in the context of point-goal navigation: (1) we revisit the comparison between learning and SLAM approaches from two recent works and find evidence for the opposite conclusion -- that learning outperforms SLAM if scaled to an order of magnitude more experience than previous investigations, and (2) we conduct the first cross-dataset generalization experiments {train, test} x {Matterport3D, Gibson} for multiple sensors {blind, RGB, RGBD, D} and find that only agents with depth (D) sensors generalize across datasets. We hope that our open-source platform and these findings will advance research in embodied AI.

Our goal is to create a realistic 3D facial avatar with hair and accessories using only a text description. While this challenge has attracted significant recent interest, existing methods either lack realism, produce unrealistic shapes, or do not support editing, such as modifications to the hairstyle. We argue that existing methods are limited because they employ a monolithic modeling approach, using a single representation for the head, face, hair, and accessories. Our observation is that the hair and face, for example, have very different structural qualities that benefit from different representations. Building on this insight, we generate avatars with a compositional model, in which the head, face, and upper body are represented with traditional 3D meshes, and the hair, clothing, and accessories with neural radiance fields (NeRF). The model-based mesh representation provides a strong geometric prior for the face region, improving realism while enabling editing of the person's appearance. By using NeRFs to represent the remaining components, our method is able to model and synthesize parts with complex geometry and appearance, such as curly hair and fluffy scarves. Our novel system synthesizes these high-quality compositional avatars from text descriptions. The experimental results demonstrate that our method, Text-guided generation and Editing of Compositional Avatars (TECA), produces avatars that are more realistic than those of recent methods while being editable because of their compositional nature. For example, our TECA enables the seamless transfer of compositional features like hairstyles, scarves, and other accessories between avatars. This capability supports applications such as virtual try-on.

Recent advances in video generation have opened new avenues for macroscopic simulation of complex dynamic systems, but their application to microscopic phenomena remains largely unexplored. Microscale simulation holds great promise for biomedical applications such as drug discovery, organ-on-chip systems, and disease mechanism studies, while also showing potential in education and interactive visualization. In this work, we introduce MicroWorldBench, a multi-level rubric-based benchmark for microscale simulation tasks. MicroWorldBench enables systematic, rubric-based evaluation through 459 unique expert-annotated criteria spanning multiple microscale simulation task (e.g., organ-level processes, cellular dynamics, and subcellular molecular interactions) and evaluation dimensions (e.g., scientific fidelity, visual quality, instruction following). MicroWorldBench reveals that current SOTA video generation models fail in microscale simulation, showing violations of physical laws, temporal inconsistency, and misalignment with expert criteria. To address these limitations, we construct MicroSim-10K, a high-quality, expert-verified simulation dataset. Leveraging this dataset, we train MicroVerse, a video generation model tailored for microscale simulation. MicroVerse can accurately reproduce complex microscale mechanism. Our work first introduce the concept of Micro-World Simulation and present a proof of concept, paving the way for applications in biology, education, and scientific visualization. Our work demonstrates the potential of educational microscale simulations of biological mechanisms. Our data and code are publicly available at https://github.com/FreedomIntelligence/MicroVerse

As consumer Virtual Reality (VR) and Mixed Reality (MR) technologies gain momentum, there's a growing focus on the development of engagements with 3D virtual content. Unfortunately, traditional techniques for content creation, editing, and interaction within these virtual spaces are fraught with difficulties. They tend to be not only engineering-intensive but also require extensive expertise, which adds to the frustration and inefficiency in virtual object manipulation. Our proposed VR-GS system represents a leap forward in human-centered 3D content interaction, offering a seamless and intuitive user experience. By developing a physical dynamics-aware interactive Gaussian Splatting in a Virtual Reality setting, and constructing a highly efficient two-level embedding strategy alongside deformable body simulations, VR-GS ensures real-time execution with highly realistic dynamic responses. The components of our Virtual Reality system are designed for high efficiency and effectiveness, starting from detailed scene reconstruction and object segmentation, advancing through multi-view image in-painting, and extending to interactive physics-based editing. The system also incorporates real-time deformation embedding and dynamic shadow casting, ensuring a comprehensive and engaging virtual experience.Our project page is available at: https://yingjiang96.github.io/VR-GS/.

Video Virtual Try-On (VVT) aims to seamlessly replace a garment on a person in a video with a new one. While existing methods have made significant strides in maintaining temporal consistency, they are predominantly confined to non-interactive scenarios where models merely showcase garments. This limitation overlooks a crucial aspect of real-world apparel presentation: active human-garment interaction. To bridge this gap, we introduce and formalize a new challenging task: Interactive Video Virtual Try-On (Interactive VVT), where subjects in the video actively engage with their clothing. This task introduces unique challenges beyond simple texture preservation, including: (1) resolving the semantic ambiguity of interactions from standard pose information, and (2) learning complex garment deformations from video where interactive moments are sparse and brief. To address these challenges, we propose iTryOn, a novel framework built upon a large-scale video diffusion Transformer. iTryOn pioneers a multi-level interaction injection mechanism to guide the generation of complex dynamics. At the spatial level, we introduce a garment-agnostic 3D hand prior to provide fine-grained guidance for precise hand-garment contact, effectively resolving spatial ambiguity. At the semantic level, iTryOn leverages global captions for overall context and time-stamped action captions for localized interactions, synchronized via our novel Action-aware Rotational Position Embedding (A-RoPE). Extensive experiments demonstrate that iTryOn not only achieves state-of-the-art performance on traditional VVT benchmarks but also establishes a commanding lead in the new interactive setting, marking a significant step towards more dynamic and controllable virtual try-on experiences.

Powered by large-scale text-to-image generation models, text-to-3D avatar generation has made promising progress. However, most methods fail to produce photorealistic results, limited by imprecise geometry and low-quality appearance. Towards more practical avatar generation, we present SEEAvatar, a method for generating photorealistic 3D avatars from text with SElf-Evolving constraints for decoupled geometry and appearance. For geometry, we propose to constrain the optimized avatar in a decent global shape with a template avatar. The template avatar is initialized with human prior and can be updated by the optimized avatar periodically as an evolving template, which enables more flexible shape generation. Besides, the geometry is also constrained by the static human prior in local parts like face and hands to maintain the delicate structures. For appearance generation, we use diffusion model enhanced by prompt engineering to guide a physically based rendering pipeline to generate realistic textures. The lightness constraint is applied on the albedo texture to suppress incorrect lighting effect. Experiments show that our method outperforms previous methods on both global and local geometry and appearance quality by a large margin. Since our method can produce high-quality meshes and textures, such assets can be directly applied in classic graphics pipeline for realistic rendering under any lighting condition. Project page at: https://seeavatar3d.github.io.

Driving a high-quality and photorealistic full-body virtual human from a few RGB cameras is a challenging problem that has become increasingly relevant with emerging virtual reality technologies. A promising solution to democratize such technology would be a generalizable method that takes sparse multi-view images of any person and then generates photoreal free-view renderings of them. However, the state-of-the-art approaches are not scalable to very large datasets and, thus, lack diversity and photorealism. To address this problem, we propose GIGA, a novel, generalizable full-body model for rendering photoreal humans in free viewpoint, driven by a single-view or sparse multi-view video. Notably, GIGA can scale training to a few thousand subjects while maintaining high photorealism and synthesizing dynamic appearance. At the core, we introduce a MultiHeadUNet architecture, which takes an approximate RGB texture accumulated from a single or multiple sparse views and predicts 3D Gaussian primitives represented as 2D texels on top of a human body mesh. At test time, our method performs novel view synthesis of a virtual 3D Gaussian-based human from 1 to 4 input views and a tracked body template for unseen identities. Our method excels over prior works by a significant margin in terms of identity generalization capability and photorealism.

As Large Language Models (LLMs) rapidly evolve, their influence in science is becoming increasingly prominent. The emerging capabilities of LLMs in task generalization and free-form dialogue can significantly advance fields like chemistry and biology. However, the field of single-cell biology, which forms the foundational building blocks of living organisms, still faces several challenges. High knowledge barriers and limited scalability in current methods restrict the full exploitation of LLMs in mastering single-cell data, impeding direct accessibility and rapid iteration. To this end, we introduce ChatCell, which signifies a paradigm shift by facilitating single-cell analysis with natural language. Leveraging vocabulary adaptation and unified sequence generation, ChatCell has acquired profound expertise in single-cell biology and the capability to accommodate a diverse range of analysis tasks. Extensive experiments further demonstrate ChatCell's robust performance and potential to deepen single-cell insights, paving the way for more accessible and intuitive exploration in this pivotal field. Our project homepage is available at https://zjunlp.github.io/project/ChatCell.

Computational pathology has made significant progress in recent years, fueling advances in both fundamental disease understanding and clinically ready tools. This evolution is driven by the availability of large amounts of digitized slides and specialized deep learning methods and models. Multiple self-supervised foundation feature extractors have been developed, enabling downstream predictive applications from cell segmentation to tumor sub-typing and survival analysis. In contrast, generative foundation models designed specifically for histopathology remain scarce. Such models could address tasks that are beyond the capabilities of feature extractors, such as virtual staining. In this paper, we introduce CytoSyn, a state-of-the-art foundation latent diffusion model that enables the guided generation of highly realistic and diverse histopathology H&E-stained images, as shown in an extensive benchmark. We explored methodological improvements, training set scaling, sampling strategies and slide-level overfitting, culminating in the improved CytoSyn-v2, and compared our work to PixCell, a state-of-the-art model, in an in-depth manner. This comparison highlighted the strong sensitivity of both diffusion models and performance metrics to preprocessing-specific details such as JPEG compression. Our model has been trained on a dataset obtained from more than 10,000 TCGA diagnostic whole-slide images of 32 different cancer types. Despite being trained only on oncology slides, it maintains state-of-the-art performance generating inflammatory bowel disease images. To support the research community, we publicly release CytoSyn's weights, its training and validation datasets, and a sample of synthetic images in this repository: https://huggingface.co/Owkin-Bioptimus/CytoSyn.

In this demo paper, we introduce SAPIEN, a platform for high-fidelity virtual agents driven by large language models that can hold open domain conversations with users in 13 different languages, and display emotions through facial expressions and voice. The platform allows users to customize their virtual agent's personality, background, and conversation premise, thus providing a rich, immersive interaction experience. Furthermore, after the virtual meeting, the user can choose to get the conversation analyzed and receive actionable feedback on their communication skills. This paper illustrates an overview of the platform and discusses the various application domains of this technology, ranging from entertainment to mental health, communication training, language learning, education, healthcare, and beyond. Additionally, we consider the ethical implications of such realistic virtual agent representations and the potential challenges in ensuring responsible use.

Generating high-fidelity upper-body 3D avatars from one-shot input image remains a significant challenge. Current 3D avatar generation methods, which rely on large reconstruction models, are fast and capable of producing stable body structures, but they often suffer from artifacts such as blurry textures and stiff, unnatural motion. In contrast, generative video models show promising performance by synthesizing photorealistic and dynamic results, but they frequently struggle with unstable behavior, including body structural errors and identity drift. To address these limitations, we propose a novel approach that combines the strengths of both paradigms. Our framework employs a 3D reconstruction model to provide robust structural and appearance priors, which in turn guides a real-time autoregressive video diffusion model for rendering. This process enables the model to synthesize high-frequency, photorealistic details and fluid dynamics in real time, effectively reducing texture blur and motion stiffness while preventing the structural inconsistencies common in video generation methods. By uniting the geometric stability of 3D reconstruction with the generative capabilities of video models, our method produces high-fidelity digital avatars with realistic appearance and dynamic, temporally coherent motion. Experiments demonstrate that our approach significantly reduces artifacts and achieves substantial improvements in visual quality over leading methods, providing a robust and efficient solution for real-time applications such as gaming and virtual reality. Project page: https://lhyfst.github.io/visa

Despite their success, modern convolutional neural networks (CNNs) exhibit fundamental limitations, including data inefficiency, poor out-of-distribution generalization, and vulnerability to adversarial perturbations. These shortcomings can be traced to a lack of inductive biases that reflect the inherent geometric structure of the visual world. The primate visual system, in contrast, demonstrates superior efficiency and robustness, suggesting that its architectural and computational principles,which evolved to internalize these structures,may offer a blueprint for more capable artificial vision. This paper introduces Visual Cortex Network (VCNet), a novel neural network architecture whose design is informed by the macro-scale organization of the primate visual cortex. VCNet is framed as a geometric framework that emulates key biological mechanisms, including hierarchical processing across distinct cortical areas, dual-stream information segregation for learning disentangled representations, and top-down predictive feedback for representation refinement. We interpret these mechanisms through the lens of geometry and dynamical systems, positing that they guide the learning of structured, low-dimensional neural manifolds. We evaluate VCNet on two specialized benchmarks: the Spots-10 animal pattern dataset, which probes sensitivity to natural textures, and a light field image classification task, which requires processing higher-dimensional visual data. Our results show that VCNet achieves state-of-the-art accuracy of 92.1\% on Spots-10 and 74.4\% on the light field dataset, surpassing contemporary models of comparable size. This work demonstrates that integrating high-level neuroscientific principles, viewed through a geometric lens, can lead to more efficient and robust models, providing a promising direction for addressing long-standing challenges in machine learning.

Image-based 3D Virtual Try-ON (VTON) aims to sculpt the 3D human according to person and clothes images, which is data-efficient (i.e., getting rid of expensive 3D data) but challenging. Recent text-to-3D methods achieve remarkable improvement in high-fidelity 3D human generation, demonstrating its potential for 3D virtual try-on. Inspired by the impressive success of personalized diffusion models (e.g., Dreambooth and LoRA) for 2D VTON, it is straightforward to achieve 3D VTON by integrating the personalization technique into the diffusion-based text-to-3D framework. However, employing the personalized module in a pre-trained diffusion model (e.g., StableDiffusion (SD)) would degrade the model's capability for multi-view or multi-domain synthesis, which is detrimental to the geometry and texture optimization guided by Score Distillation Sampling (SDS) loss. In this work, we propose a novel customizing 3D human try-on model, named DreamVTON, to separately optimize the geometry and texture of the 3D human. Specifically, a personalized SD with multi-concept LoRA is proposed to provide the generative prior about the specific person and clothes, while a Densepose-guided ControlNet is exploited to guarantee consistent prior about body pose across various camera views. Besides, to avoid the inconsistent multi-view priors from the personalized SD dominating the optimization, DreamVTON introduces a template-based optimization mechanism, which employs mask templates for geometry shape learning and normal/RGB templates for geometry/texture details learning. Furthermore, for the geometry optimization phase, DreamVTON integrates a normal-style LoRA into personalized SD to enhance normal map generative prior, facilitating smooth geometry modeling.

Realistic virtual humans play a crucial role in numerous industries, such as metaverse, intelligent healthcare, and self-driving simulation. But creating them on a large scale with high levels of realism remains a challenge. The utilization of deep implicit function sparks a new era of image-based 3D clothed human reconstruction, enabling pixel-aligned shape recovery with fine details. Subsequently, the vast majority of works locate the surface by regressing the deterministic implicit value for each point. However, should all points be treated equally regardless of their proximity to the surface? In this paper, we propose replacing the implicit value with an adaptive uncertainty distribution, to differentiate between points based on their distance to the surface. This simple ``value to distribution'' transition yields significant improvements on nearly all the baselines. Furthermore, qualitative results demonstrate that the models trained using our uncertainty distribution loss, can capture more intricate wrinkles, and realistic limbs. Code and models are available for research purposes at https://github.com/psyai-net/D-IF_release.

Diffusion-based Video Virtual Try-On (VVT) achieves high visual fidelity through bidirectional spatio-temporal modeling, but complete-clip dependence incurs prohibitive latency and computational overhead in practical continuous deployment. Naively enforcing causality disrupts pretrained bidirectional priors and substantially degrades synthesis quality. We introduce LiveVVT, a rolling streaming diffusion framework that preserves bounded bidirectional modeling within causal recurrent generation. Within a fixed-size window, LiveVVT jointly denoises multiple video chunks under bounded look-ahead, preserving local bidirectional interactions while emitting one clean chunk per iteration. Beyond the window, two complementary memories sustain long-term consistency: a bounded temporal memory propagates recent dynamics and occlusion context, whereas a persistent global appearance memory, constructed once from the target garment and a frontal try-on keyframe, anchors garment details and dressed appearance throughout the stream. We further introduce a progressive distillation framework integrating bidirectional VVT learning, teacher-trajectory regression for causal few-step adaptation, and Collaborative Matching Distillation, which couples teacher-distribution matching with rolling flow matching on real videos to align optimization with recurrent inference. Experiments on paired and unpaired long-sequence benchmarks demonstrate superior generation quality over similarly sized models, with 26times lower latency and 11times higher throughput, enabling high-fidelity real-time streaming VVT.

Scientific user facilities, such as synchrotron beamlines, are equipped with a wide array of hardware and software tools that require a codebase for human-computer-interaction. This often necessitates developers to be involved to establish connection between users/researchers and the complex instrumentation. The advent of generative AI presents an opportunity to bridge this knowledge gap, enabling seamless communication and efficient experimental workflows. Here we present a modular architecture for the Virtual Scientific Companion (VISION) by assembling multiple AI-enabled cognitive blocks that each scaffolds large language models (LLMs) for a specialized task. With VISION, we performed LLM-based operation on the beamline workstation with low latency and demonstrated the first voice-controlled experiment at an X-ray scattering beamline. The modular and scalable architecture allows for easy adaptation to new instrument and capabilities. Development on natural language-based scientific experimentation is a building block for an impending future where a science exocortex -- a synthetic extension to the cognition of scientists -- may radically transform scientific practice and discovery.

We report DynaCLR, a self-supervised method for embedding cell and organelle Dynamics via Contrastive Learning of Representations of time-lapse images. DynaCLR integrates single-cell tracking and time-aware contrastive sampling to learn robust, temporally regularized representations of cell dynamics. DynaCLR embeddings generalize effectively to in-distribution and out-of-distribution datasets, and can be used for several downstream tasks with sparse human annotations. We demonstrate efficient annotations of cell states with a human-in-the-loop using fluorescence and label-free imaging channels. DynaCLR method enables diverse downstream biological analyses: classification of cell division and infection, clustering heterogeneous cell migration patterns, cross-modal distillation of cell states from fluorescence to label-free channel, alignment of asynchronous cellular responses and broken cell tracks, and discovering organelle response due to infection. DynaCLR is a flexible method for comparative analyses of dynamic cellular responses to pharmacological, microbial, and genetic perturbations. We provide PyTorch-based implementations of the model training and inference pipeline (https://github.com/mehta-lab/viscy) and a GUI (https://github.com/czbiohub-sf/napari-iohub) for the visualization and annotation of trajectories of cells in the real space and the embedding space.