Daily Papers

Complex gene interactions play a significant role in cancer progression, driving cellular behaviors that contribute to tumor growth, invasion, and metastasis. Gene co-expression networks model the functional connectivity between genes under various biological conditions. Understanding the system-level evolution of these networks in cancer is critical for elucidating disease mechanisms and informing the development of targeted therapies. While previous studies have primarily focused on structural differences between cancer and normal cell co-expression networks, this study applies graph frequency analysis to cancer transcriptomic signals defined on gene co-expression networks, highlighting the graph spectral characteristics of cancer systems. Using a range of graph frequency filters, we showed that cancer cells display distinctive patterns in the graph frequency content of their gene transcriptomic signals, effectively distinguishing between cancer types and stages. The transformation of the original gene feature space into the graph spectral space captured more intricate cancer properties, as validated by significantly higher F-statistic scores for graph frequency-filtered gene features compared to those in the original space.

Survival prediction is a complicated ordinal regression task that aims to predict the ranking risk of death, which generally benefits from the integration of histology and genomic data. Despite the progress in joint learning from pathology and genomics, existing methods still suffer from challenging issues: 1) Due to the large size of pathological images, it is difficult to effectively represent the gigapixel whole slide images (WSIs). 2) Interactions within tumor microenvironment (TME) in histology are essential for survival analysis. Although current approaches attempt to model these interactions via co-attention between histology and genomic data, they focus on only dense local similarity across modalities, which fails to capture global consistency between potential structures, i.e. TME-related interactions of histology and co-expression of genomic data. To address these challenges, we propose a Multimodal Optimal Transport-based Co-Attention Transformer framework with global structure consistency, in which optimal transport (OT) is applied to match patches of a WSI and genes embeddings for selecting informative patches to represent the gigapixel WSI. More importantly, OT-based co-attention provides a global awareness to effectively capture structural interactions within TME for survival prediction. To overcome high computational complexity of OT, we propose a robust and efficient implementation over micro-batch of WSI patches by approximating the original OT with unbalanced mini-batch OT. Extensive experiments show the superiority of our method on five benchmark datasets compared to the state-of-the-art methods. The code is released.

Spatial Transcriptomics (ST) offers spatially resolved gene expression but remains costly. Predicting expression directly from widely available Hematoxylin and Eosin (H&E) stained images presents a cost-effective alternative. However, most computational approaches (i) predict each gene independently, overlooking co-expression structure, and (ii) cast the task as continuous regression despite expression being discrete counts. This mismatch can yield biologically implausible outputs and complicate downstream analyses. We introduce GenAR, a multi-scale autoregressive framework that refines predictions from coarse to fine. GenAR clusters genes into hierarchical groups to expose cross-gene dependencies, models expression as codebook-free discrete token generation to directly predict raw counts, and conditions decoding on fused histological and spatial embeddings. From an information-theoretic perspective, the discrete formulation avoids log-induced biases and the coarse-to-fine factorization aligns with a principled conditional decomposition. Extensive experimental results on four Spatial Transcriptomics datasets across different tissue types demonstrate that GenAR achieves state-of-the-art performance, offering potential implications for precision medicine and cost-effective molecular profiling. Code is publicly available at https://github.com/oyjr/genar.

Predicting transcriptional responses to specific perturbations is critical for understanding cellular regulatory mechanisms and accelerating drug discovery. Single-cell RNA sequencing destroys each measured cell, yielding only unpaired populations of control and perturbed cells. However, existing methods typically model perturbation prediction at the single-cell level and assume cell-to-cell correspondence, which conflicts with the unpaired nature of the observed data. To address this challenge, we propose PopPert, a framework that explicitly parameterizes population-level joint gene expression distributions for collective transcriptional state modeling. Given a control population distribution and a perturbation condition, PopPert predicts perturbation-induced changes in distribution parameters, eliminating the need for cell-level correspondence and reducing sensitivity to single-cell noise. To effectively capture gene co-expression patterns, PopPert leverages a low-rank Gaussian Copula to model cross-gene statistical dependencies and construct the joint gene expression distribution, additionally allowing sampling of synthetic perturbed single-cell profiles. Across multiple single-cell benchmarks spanning both genetic and chemical perturbations, PopPert achieves superior overall performance in differential expression recovery, perturbation effect estimation, and population-level distribution matching. These results establish population-level joint distribution learning as an effective paradigm for predicting transcriptional responses from unpaired single-cell populations. Code for PopPert is publicly available at https://github.com/whd1125/PopPert.

Transcriptome foundation models TFMs hold great promises of deciphering the transcriptomic language that dictate diverse cell functions by self-supervised learning on large-scale single-cell gene expression data, and ultimately unraveling the complex mechanisms of human diseases. However, current TFMs treat cells as independent samples and ignore the taxonomic relationships between cell types, which are available in cell ontology graphs. We argue that effectively leveraging this ontology information during the TFM pre-training can improve learning biologically meaningful gene co-expression patterns while preserving TFM as a general purpose foundation model for downstream zero-shot and fine-tuning tasks. To this end, we present single cell, Cell-ontology guided TFM scCello. We introduce cell-type coherence loss and ontology alignment loss, which are minimized along with the masked gene expression prediction loss during the pre-training. The novel loss component guide scCello to learn the cell-type-specific representation and the structural relation between cell types from the cell ontology graph, respectively. We pre-trained scCello on 22 million cells from CellxGene database leveraging their cell-type labels mapped to the cell ontology graph from Open Biological and Biomedical Ontology Foundry. Our TFM demonstrates competitive generalization and transferability performance over the existing TFMs on biologically important tasks including identifying novel cell types of unseen cells, prediction of cell-type-specific marker genes, and cancer drug responses.

Foundation models for single-cell RNA sequencing (scRNA-seq) have shown promising capabilities in capturing gene expression patterns. However, current approaches face critical limitations: they ignore biological prior knowledge encoded in gene regulatory relationships and fail to leverage multi-omics signals that could provide complementary regulatory insights. In this paper, we propose GRNFormer, a new framework that systematically integrates multi-scale Gene Regulatory Networks (GRNs) inferred from multi-omics data into RNA foundation model training. Our framework introduces two key innovations. First, we introduce a pipeline for constructing hierarchical GRNs that capture regulatory relationships at both cell-type-specific and cell-specific resolutions. Second, we design a structure-aware integration framework that addresses the information asymmetry in GRNs through two technical advances: (1) A graph topological adapter using multi-head cross-attention to weight regulatory relationships dynamically, and (2) a novel edge perturbation strategy that perturb GRNs with biologically-informed co-expression links to augment graph neural network training. Comprehensive experiments have been conducted on three representative downstream tasks across multiple model architectures to demonstrate the effectiveness of GRNFormer. It achieves consistent improvements over state-of-the-art (SoTA) baselines: 3.6% increase in drug response prediction correlation, 9.6% improvement in single-cell drug classification AUC, and 1.1% average gain in gene perturbation prediction accuracy.

Tabular data in knowledge-rich domains often carries a latent prior in the form of Boolean implication relationships (BIRs) between pairs of features. We mine such relationships with a sparse-exception binomial test. The mined implications form a typed directed graph, equivalent to a propositional rule base of 2-literal clauses. We encode this graph as the connectivity of a layered neural network, called BIRDNet, in which each hidden unit corresponds to one mined rule and binds only to its two features. We show two consequences of this design: First, the architecture is sparse by construction: at most 2/d of the weights in each BIR layer are active, where d is the input dimension. Second, the model is interpretable: every trained unit keeps a stable symbolic identity, so rules can be read off the network without surrogate models. Unlike most neurosymbolic models, BIRDNet does not consume an external rule base; its structural prior is mined from the data. We evaluate BIRDNet on six transcriptomic and proteomic benchmarks. Our results show that BIRDNet stays within 0.02 AUROC of the strongest dense baseline, at a small accuracy cost, while using up to 96times fewer active parameters than an architecture-matched dense MLP. First-layer rules recover known biological signatures across multiple cancer subtypes and tissue types, including canonical amplicons, lineage-defining co-expression modules, and immune-infiltration markers. Data and code are available at: https://github.com/MAHI-Group/BIRDNet.

The rapid growth of single-cell transcriptomic data has enabled the development of foundation models pretrained primarily by reconstructing masked expression values. This objective encourages these models to learn gene dependencies but does not directly optimize whole-cell representations, which are essential for many downstream tasks. To bridge this gap, we propose a contrastive pretraining framework that learns cell representations through complementary transcriptomic views. Since standard contrastive learning is not readily applicable to single-cell pretraining, we introduce specific adaptations along three dimensions --- co-expression-guided gene partitioning, expression-aware contrast-set construction, and competence-gated contrastive onset. Specifically, we first construct two complementary views of each cell by partitioning its genes according to their co-expression structure. Then, to prevent the model from using gene-set identity as a shortcut, we construct hard negatives by permuting expression values while keeping gene identities unchanged. Finally, we introduce a competence-aware controller to determine how the contrastive objective is applied. Experiments on cell-type annotation and gene regulatory network inference demonstrate competitive transfer under the evaluated protocols. In the six-network GRN evaluation, our method records the highest mean AUROC and AUPRC point estimates among the compared variants, while the highest-scoring variant differs across individual networks. These results establish complementary-view contrastive learning as an effective direction for single-cell pretraining beyond gene reconstruction.

Spatial transcriptomics (ST) provides spatially resolved gene expression profiling but remains expensive, motivating the prediction of ST from histology images. Generative models have emerged as a mainstream paradigm for ST prediction due to their ability to model the conditional distribution of gene expression and capture its inherent stochasticity. However, these methods typically treat genes as independent prediction targets and overlook the intrinsic gene-gene interactions in biological systems, which limits their ability to preserve biologically meaningful co-expression patterns. We argue that gene-gene interactions, which reflect shared pathways and regulatory mechanisms, are essential for generating numerically accurate and biologically coherent ST profiles. In this paper, we propose CorrFlow, a correlation-guided flow matching framework for histology-to-ST prediction that explicitly models gene-gene dependencies through two complementary mechanisms. First, we introduce an annealed masked flow matching strategy, where subsets of genes are progressively masked following a timestep-dependent annealing schedule, encouraging the model to infer masked genes conditioned on the remaining genes and promoting joint conditional modeling beyond per-gene marginal estimation. Second, we devise a gene graph-regularized optimization scheme that integrates prior knowledge from the STRING database and data-driven co-expression estimated by WGCNA to construct a gene affinity graph, which enforces both local consistency and global smoothness in the predicted expression. Extensive experiments across 12 datasets show that CorrFlow achieves the best average PCC and HPCC among evaluated methods, leading to more biologically coherent ST predictions.

Text-to-image generation models have grown in popularity due to their ability to produce high-quality images from a text prompt. One use for this technology is to enable the creation of more accessible art creation software. In this paper, we document the development of an alternative user interface that reduces the typing effort needed to enter image prompts by providing suggestions from a large language model, developed through iterative design and testing within the project team. The results of this testing demonstrate how generative text models can support the accessibility of text-to-image models, enabling users with a range of abilities to create visual art.

AI Scientists have shown promising progress across multiple stages of the research pipeline, among which automatic scientific paper writing remains a formidable challenge. The Introduction writing is especially challenging, which demands not only linguistic fluency, but logical soundness and verifiable faithfulness. Most AI-assisted methods treat the task as text generation instead of reasoning and structuring, leading to severe drawbacks, e.g., hallucinating citations. To address this, we first formulate the Content-Conditional Introduction Generation (CCIG) task, which requires grounding the Introduction in the paper's core evidence. We then propose LECTOR, a novel Logic-Expression Co-Reinforcement Learning framework that can strictly follow the scientist's logic, add high-quality citations and keep structured expressions. LECTOR first constructs a logic-reasoning graph from the paper's main body to serve as a verifiable logical blueprint. Subsequently, it employs a Logic-Expression Co-Rewarding mechanism to jointly optimize for both the graph's structural fidelity and the final narrative's quality. We conduct a dataset from Nature Communications papers to assess our method. Extensive experiments show consistent improvements in both logic fidelity and Introduction generation quality metrics, e.g., Graph Quality (+26.7%), Citation Quality (+8.6%), and Paper Consistency (+3.3%). Code and data are available at https://github.com/Xiao-Youth/LECTOR.

Immunohistochemistry (IHC) provides information on protein expression in tissue sections and is commonly used to support pathology diagnosis and disease triage. While AI models for H\&E-stained slides show promise, their applicability to IHC is limited due to domain-specific variations. Here we introduce HPA10M, a dataset that contains 10,495,672 IHC images from the Human Protein Atlas with comprehensive metadata included, and encompasses 45 normal tissue types and 20 major cancer types. Based on HPA10M, we trained iSight, a multi-task learning framework for automated IHC staining assessment. iSight combines visual features from whole-slide images with tissue metadata through a token-level attention mechanism, simultaneously predicting staining intensity, location, quantity, tissue type, and malignancy status. On held-out data, iSight achieved 85.5\% accuracy for location, 76.6\% for intensity, and 75.7\% for quantity, outperforming fine-tuned foundation models (PLIP, CONCH) by 2.5--10.2\%. In addition, iSight demonstrates well-calibrated predictions with expected calibration errors of 0.0150-0.0408. Furthermore, in a user study with eight pathologists evaluating 200 images from two datasets, iSight outperformed initial pathologist assessments on the held-out HPA dataset (79\% vs 68\% for location, 70\% vs 57\% for intensity, 68\% vs 52\% for quantity). Inter-pathologist agreement also improved after AI assistance in both held-out HPA (Cohen's κ increased from 0.63 to 0.70) and Stanford TMAD datasets (from 0.74 to 0.76), suggesting expert--AI co-assessment can improve IHC interpretation. This work establishes a foundation for AI systems that can improve IHC diagnostic accuracy and highlights the potential for integrating iSight into clinical workflows to enhance the consistency and reliability of IHC assessment.

The synthesis of 3D facial animations from speech has garnered considerable attention. Due to the scarcity of high-quality 4D facial data and well-annotated abundant multi-modality labels, previous methods often suffer from limited realism and a lack of lexible conditioning. We address this challenge through a trilogy. We first introduce Generalized Neural Parametric Facial Asset (GNPFA), an efficient variational auto-encoder mapping facial geometry and images to a highly generalized expression latent space, decoupling expressions and identities. Then, we utilize GNPFA to extract high-quality expressions and accurate head poses from a large array of videos. This presents the M2F-D dataset, a large, diverse, and scan-level co-speech 3D facial animation dataset with well-annotated emotional and style labels. Finally, we propose Media2Face, a diffusion model in GNPFA latent space for co-speech facial animation generation, accepting rich multi-modality guidances from audio, text, and image. Extensive experiments demonstrate that our model not only achieves high fidelity in facial animation synthesis but also broadens the scope of expressiveness and style adaptability in 3D facial animation.

Generating holistic co-speech gestures that integrate full-body motion with facial expressions suffers from semantically incoherent coordination on body motion and spatially unstable meaningless movements due to existing part-decomposed or frame-level regression methods, We introduce 3DGesPolicy, a novel action-based framework that reformulates holistic gesture generation as a continuous trajectory control problem through diffusion policy from robotics. By modeling frame-to-frame variations as unified holistic actions, our method effectively learns inter-frame holistic gesture motion patterns and ensures both spatially and semantically coherent movement trajectories that adhere to realistic motion manifolds. To further bridge the gap in expressive alignment, we propose a Gesture-Audio-Phoneme (GAP) fusion module that can deeply integrate and refine multi-modal signals, ensuring structured and fine-grained alignment between speech semantics, body motion, and facial expressions. Extensive quantitative and qualitative experiments on the BEAT2 dataset demonstrate the effectiveness of our 3DGesPolicy across other state-of-the-art methods in generating natural, expressive, and highly speech-aligned holistic gestures.

We propose DiffSHEG, a Diffusion-based approach for Speech-driven Holistic 3D Expression and Gesture generation with arbitrary length. While previous works focused on co-speech gesture or expression generation individually, the joint generation of synchronized expressions and gestures remains barely explored. To address this, our diffusion-based co-speech motion generation transformer enables uni-directional information flow from expression to gesture, facilitating improved matching of joint expression-gesture distributions. Furthermore, we introduce an outpainting-based sampling strategy for arbitrary long sequence generation in diffusion models, offering flexibility and computational efficiency. Our method provides a practical solution that produces high-quality synchronized expression and gesture generation driven by speech. Evaluated on two public datasets, our approach achieves state-of-the-art performance both quantitatively and qualitatively. Additionally, a user study confirms the superiority of DiffSHEG over prior approaches. By enabling the real-time generation of expressive and synchronized motions, DiffSHEG showcases its potential for various applications in the development of digital humans and embodied agents.

Co-speech gesture video generation aims to synthesize realistic, audio-aligned videos of speakers, complete with synchronized facial expressions and body gestures. This task presents challenges due to the significant one-to-many mapping between audio and visual content, further complicated by the scarcity of large-scale public datasets and high computational demands. We propose a lightweight framework that utilizes 2D full-body skeletons as an efficient auxiliary condition to bridge audio signals with visual outputs. Our approach introduces a diffusion model conditioned on fine-grained audio segments and a skeleton extracted from the speaker's reference image, predicting skeletal motions through skeleton-audio feature fusion to ensure strict audio coordination and body shape consistency. The generated skeletons are then fed into an off-the-shelf human video generation model with the speaker's reference image to synthesize high-fidelity videos. To democratize research, we present CSG-405-the first public dataset with 405 hours of high-resolution videos across 71 speech types, annotated with 2D skeletons and diverse speaker demographics. Experiments show that our method exceeds state-of-the-art approaches in visual quality and synchronization while generalizing across speakers and contexts. Code, models, and CSG-405 are publicly released at https://mpi-lab.github.io/Democratizing-CSG/

Referring Expression Segmentation (RES) is a widely explored multi-modal task, which endeavors to segment the pre-existing object within a single image with a given linguistic expression. However, in broader real-world scenarios, it is not always possible to determine if the described object exists in a specific image. Typically, we have a collection of images, some of which may contain the described objects. The current RES setting curbs its practicality in such situations. To overcome this limitation, we propose a more realistic and general setting, named Group-wise Referring Expression Segmentation (GRES), which expands RES to a collection of related images, allowing the described objects to be present in a subset of input images. To support this new setting, we introduce an elaborately compiled dataset named Grouped Referring Dataset (GRD), containing complete group-wise annotations of target objects described by given expressions. We also present a baseline method named Grouped Referring Segmenter (GRSer), which explicitly captures the language-vision and intra-group vision-vision interactions to achieve state-of-the-art results on the proposed GRES and related tasks, such as Co-Salient Object Detection and RES. Our dataset and codes will be publicly released in https://github.com/yixuan730/group-res.

In this paper, we propose a novel framework, Combo, for harmonious co-speech holistic 3D human motion generation and efficient customizable adaption. In particular, we identify that one fundamental challenge as the multiple-input-multiple-output (MIMO) nature of the generative model of interest. More concretely, on the input end, the model typically consumes both speech signals and character guidance (e.g., identity and emotion), which not only poses challenge on learning capacity but also hinders further adaptation to varying guidance; on the output end, holistic human motions mainly consist of facial expressions and body movements, which are inherently correlated but non-trivial to coordinate in current data-driven generation process. In response to the above challenge, we propose tailored designs to both ends. For the former, we propose to pre-train on data regarding a fixed identity with neutral emotion, and defer the incorporation of customizable conditions (identity and emotion) to fine-tuning stage, which is boosted by our novel X-Adapter for parameter-efficient fine-tuning. For the latter, we propose a simple yet effective transformer design, DU-Trans, which first divides into two branches to learn individual features of face expression and body movements, and then unites those to learn a joint bi-directional distribution and directly predicts combined coefficients. Evaluated on BEAT2 and SHOW datasets, Combo is highly effective in generating high-quality motions but also efficient in transferring identity and emotion. Project website: https://xc-csc101.github.io/combo/{Combo}.

Histopathological examination primarily relies on hematoxylin and eosin (H&E) and immunohistochemistry (IHC) staining. Although IHC provides critical molecular information, it is costly and requires specialized expertise. Stain transfer provides an efficient alternative by computationally generating IHC from H&E images, but remains challenged by unified and interpretable modeling for heterogeneous biomarkers under pixel-unaligned supervision. We propose DMCoStain, a novel Data-Model Co-optimization framework for Stain transfer. It iteratively co-refines training data and model capability, improving staining accuracy and interpretability in both pathological and structural consistency. To refine training data in a clinically meaningful manner, it incorporates the Multimodal Expert-Guided Finer Selection (MEGFS) strategy, built upon a pioneering IHC-positive-expression (IPE) vision-language model (VLM) that emulates pathologist reasoning. To support MEGFS, we construct ImmunoInstruction, the first large-scale IPE instruction-following dataset with 150K VQA samples. Extensive experiments on multiple tissues and biomarkers demonstrate that DMCoStain achieves state-of-the-art (SOTA) accuracy. This paradigm offers strong practical value, and MEGFS also functions as a specialized evaluation tool for future model development. Dataset, code, and more details are in https://github.com/SikangSHU/DMCoStain.

Reconstructing 3D human heads in low-view settings presents technical challenges, mainly due to the pronounced risk of overfitting with limited views and high-frequency signals. To address this, we propose geometry decomposition and adopt a two-stage, coarse-to-fine training strategy, allowing for progressively capturing high-frequency geometric details. We represent 3D human heads using the zero level-set of a combined signed distance field, comprising a smooth template, a non-rigid deformation, and a high-frequency displacement field. The template captures features that are independent of both identity and expression and is co-trained with the deformation network across multiple individuals with sparse and randomly selected views. The displacement field, capturing individual-specific details, undergoes separate training for each person. Our network training does not require 3D supervision or object masks. Experimental results demonstrate the effectiveness and robustness of our geometry decomposition and two-stage training strategy. Our method outperforms existing neural rendering approaches in terms of reconstruction accuracy and novel view synthesis under low-view settings. Moreover, the pre-trained template serves a good initialization for our model when encountering unseen individuals.

Vision-langugage models (VLMs) have shown strong performance in computer vision (CV), yet their performance on remote sensing (RS) data remains limited due to the lack of large-scale, multi-sensor RS image-text datasets with diverse textual annotations. Existing datasets predominantly include aerial Red-Green-Blue imagery, with short or weakly grounded captions, and provide limited diversity in annotation types. To address this limitation, we introduce BigEarthNet.txt, a large-scale, multi-sensor image-text dataset designed to advance instruction-driven image-text learning in Earth observation across multiple tasks. BigEarthNet.txt contains 464044 co-registered Sentinel-1 synthetic aperture radar and Sentinel-2 multispectral images with 9.6M text annotations, including: i) geographically anchored captions describing land-use/land-cover (LULC) classes, their spatial relations, and environmental context; ii) visual question answering pairs relevant for different tasks; and iii) referring expression detection instructions for bounding box prediction. Through a comparative statistical analysis, we demonstrate that BigEarthNet.txt surpasses existing RS image-text datasets in textual richness and annotation type variety. We further establish a manually-verified benchmark split to evaluate VLMs in RS and CV. The results show the limitations of these models on tasks that involve complex LULC classes, whereas fine-tuning using BigEarthNet.txt results in consistent performance gains across all considered tasks.

This research offers a unique evaluation of how AI systems interpret the digital language of Generation Alpha (Gen Alpha, born 2010-2024). As the first cohort raised alongside AI, Gen Alpha faces new forms of online risk due to immersive digital engagement and a growing mismatch between their evolving communication and existing safety tools. Their distinct language, shaped by gaming, memes, and AI-driven trends, often conceals harmful interactions from both human moderators and automated systems. We assess four leading AI models (GPT-4, Claude, Gemini, and Llama 3) on their ability to detect masked harassment and manipulation within Gen Alpha discourse. Using a dataset of 100 recent expressions from gaming platforms, social media, and video content, the study reveals critical comprehension failures with direct implications for online safety. This work contributes: (1) a first-of-its-kind dataset capturing Gen Alpha expressions; (2) a framework to improve AI moderation systems for youth protection; (3) a multi-perspective evaluation including AI systems, human moderators, and parents, with direct input from Gen Alpha co-researchers; and (4) an analysis of how linguistic divergence increases youth vulnerability. Findings highlight the urgent need to redesign safety systems attuned to youth communication, especially given Gen Alpha reluctance to seek help when adults fail to understand their digital world. This study combines the insight of a Gen Alpha researcher with systematic academic analysis to address critical digital safety challenges.

Developing Large Language Model (LLM) agents that exhibit human-like behavior, encompassing not only individual heterogeneity rooted in unique user profiles but also adaptive response to socially connected neighbors, is a significant research challenge. Social media platforms, with their diverse user data and explicit social structures, provide an ideal testbed for such investigations. This paper introduces EvoBot, an Evolving LLM-based social Bot that significantly enhances human-like generative capabilities through a novel adversarial learning framework. EvoBot is initialized by Supervised Fine-Tuning (SFT) on representative data from social media and then iteratively refines its generation of sophisticated, human-like content via Direct Preference Optimization (DPO). This refinement is guided by feedback from a co-adapting Detector which concurrently improves its ability to distinguish EvoBot from humans, thereby creating an increasingly challenging learning environment for EvoBot. Experiments demonstrate that EvoBot generates content aligned with diverse user profiles, increasingly bypassing the co-adapting Detector through human-like expression. Moreover, it exhibits strong social responsiveness, more accurately modeling real-world opinion dynamics and information spread in multi-agent simulations. The framework also yields a more robust Detector, underscoring its broader utility for both advanced agent development and related detection tasks. The code is available at https://github.com/kfq20/EvoBot.

Expressive co-speech gestures are crucial for natural human--robot interaction, yet generating them on physical humanoid robots remains challenging because, unlike virtual avatars, robots must synchronize gestures with speech under strict kinematic and actuator constraints. We present WaveSync, a hybrid framework in which a Large Language Model decomposes dialogue responses into structured semantic schemas and assigns per-word importance weights, forming a continuous Semantic Importance Wave. Gesture trajectories are shaped through Dynamic Movement Primitives to ensure kinematic feasibility while enhancing expressiveness. A Wavefront Optimization stage aligns gesture stroke peaks with speech emphasis peaks and resolves residual temporal conflicts through gesture-duration compression and forward propagation. Experimental evaluation across five dialogue scenarios demonstrates effective gesture--speech alignment and favorable performance in both objective and subjective evaluations. The results further show that the key components of WaveSync contribute to producing gestures that are expressive, semantically grounded, and kinematically feasible. The code, resources, and videos are available at https://github.com/pairs-lab/WaveSync{WaveSync}.

The generation of realistic and contextually relevant co-speech gestures is a challenging yet increasingly important task in the creation of multimodal artificial agents. Prior methods focused on learning a direct correspondence between co-speech gesture representations and produced motions, which created seemingly natural but often unconvincing gestures during human assessment. We present an approach to pre-train partial gesture sequences using a generative adversarial network with a quantization pipeline. The resulting codebook vectors serve as both input and output in our framework, forming the basis for the generation and reconstruction of gestures. By learning the mapping of a latent space representation as opposed to directly mapping it to a vector representation, this framework facilitates the generation of highly realistic and expressive gestures that closely replicate human movement and behavior, while simultaneously avoiding artifacts in the generation process. We evaluate our approach by comparing it with established methods for generating co-speech gestures as well as with existing datasets of human behavior. We also perform an ablation study to assess our findings. The results show that our approach outperforms the current state of the art by a clear margin and is partially indistinguishable from human gesturing. We make our data pipeline and the generation framework publicly available.

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.

Along with the explosion of large language models, improvements in speech synthesis, advancements in hardware, and the evolution of computer graphics, the current bottleneck in creating digital humans lies in generating character movements that correspond naturally to text or speech inputs. In this work, we present DeepGesture, a diffusion-based gesture synthesis framework for generating expressive co-speech gestures conditioned on multimodal signals - text, speech, emotion, and seed motion. Built upon the DiffuseStyleGesture model, DeepGesture introduces novel architectural enhancements that improve semantic alignment and emotional expressiveness in generated gestures. Specifically, we integrate fast text transcriptions as semantic conditioning and implement emotion-guided classifier-free diffusion to support controllable gesture generation across affective states. To visualize results, we implement a full rendering pipeline in Unity based on BVH output from the model. Evaluation on the ZeroEGGS dataset shows that DeepGesture produces gestures with improved human-likeness and contextual appropriateness. Our system supports interpolation between emotional states and demonstrates generalization to out-of-distribution speech, including synthetic voices - marking a step forward toward fully multimodal, emotionally aware digital humans. Project page: https://deepgesture.github.io

Single-cell transcriptomes are sparse observations of coordinated biological programmes, yet most self-supervised models learn by reconstructing individual genes. Here we present BioM-JEPA, a joint-embedding predictive architecture that instead predicts aggregate representations of graph-connected gene blocks defined by protein-association and corpus-derived coexpression evidence. A student network infers each target-block representation from the remaining genes in a cell, while a slowly updated teacher supplies the corresponding target from the full observed gene set. Under the reported extraction procedure, block-level prediction produced embeddings with higher effective rank and weaker association with detected-gene depth in the tested diagnostics than token-prediction, random-block and reconstruction controls. Across CellBench tasks, frozen BioM-JEPA embeddings retained expression, pathway and neighbourhood information and achieved the lowest aggregate perturbation-response error among the evaluated models. Representation diagnostics were also consistent with canonical pancreatic programmes and compositional relationships between genetic perturbations. Linear attention avoids constructing a quadratic gene-by-gene attention matrix; in a matched one-epoch hPancreas experiment at batch size 8, BioM-JEPA provided 5.75-fold higher fine-tuning throughput and 3.76-fold higher held-out embedding throughput than scFoundation. Together, these results support graph-connected gene blocks as useful prediction units for JEPA-style representation learning in single-cell biology.

We propose EMAGE, a framework to generate full-body human gestures from audio and masked gestures, encompassing facial, local body, hands, and global movements. To achieve this, we first introduce BEAT2 (BEAT-SMPLX-FLAME), a new mesh-level holistic co-speech dataset. BEAT2 combines MoShed SMPLX body with FLAME head parameters and further refines the modeling of head, neck, and finger movements, offering a community-standardized, high-quality 3D motion captured dataset. EMAGE leverages masked body gesture priors during training to boost inference performance. It involves a Masked Audio Gesture Transformer, facilitating joint training on audio-to-gesture generation and masked gesture reconstruction to effectively encode audio and body gesture hints. Encoded body hints from masked gestures are then separately employed to generate facial and body movements. Moreover, EMAGE adaptively merges speech features from the audio's rhythm and content and utilizes four compositional VQ-VAEs to enhance the results' fidelity and diversity. Experiments demonstrate that EMAGE generates holistic gestures with state-of-the-art performance and is flexible in accepting predefined spatial-temporal gesture inputs, generating complete, audio-synchronized results. Our code and dataset are available at https://pantomatrix.github.io/EMAGE/

Existing image editing methods can be generally categorized into textual instruction-based and visual prompt-based ones. Textual instructions are semantically expressive, but are limited by the coarse granularity of spatial control of the editing results. In contrast, visual prompts such as drag and point can provide precise spatial guidance, but are limited by the inherent ambiguity in semantic intent. To unify the strength of textual and visual prompts, we present Text-Vision Co-Instructed Image Editing, which jointly models textual instructions as semantic intent and sparse visual instructions as spatial guidance, aiming to achieve precise and intent-faithful image manipulation. To this end, we first construct a textual-visual instruction paired dataset with more than 23K samples derived from dynamic videos, enabling aligned supervision for cross-modal instruction. We then propose TV-Edit, a Textual-Visual instruction unified Editing framework to contextualize drag or point-based visual instructions with image-text semantics and lift them into semantic-aware control representations for pretrained editing backbones. By integrating semantic intent and spatial constraints, TV-Edit leads to more precise spatial control, less instruction ambiguity, and stronger structural consistency than text-only or drag-based alternatives. Finally, we establish TV-Edit-Bench, a deliberately designed benchmark to evaluate semantic faithfulness, spatial alignment, and visual consistency with ground-truth references and controlled textual-visual variations for reliable assessment. Our experiments across multiple editing backbones demonstrate that TV-Edit consistently yields more precise and intent-faithful edits, significantly outperforming state-of-the-art instruction-based and drag-based baselines.

Human communication combines speech with expressive nonverbal cues such as hand gestures that serve manifold communicative functions. Yet, current generative gesture generation approaches are restricted to simple, repetitive beat gestures that accompany the rhythm of speaking but do not contribute to communicating semantic meaning. This paper tackles a core challenge in co-speech gesture synthesis: generating iconic or deictic gestures that are semantically coherent with a verbal utterance. Such gestures cannot be derived from language input alone, which inherently lacks the visual meaning that is often carried autonomously by gestures. We therefore introduce a zero-shot system that generates gestures from a given language input and additionally is informed by imagistic input, without manual annotation or human intervention. Our method integrates an image analysis pipeline that extracts key object properties such as shape, symmetry, and alignment, together with a semantic matching module that links these visual details to spoken text. An inverse kinematics engine then synthesizes iconic and deictic gestures and combines them with co-generated natural beat gestures for coherent multimodal communication. A comprehensive user study demonstrates the effectiveness of our approach. In scenarios where speech alone was ambiguous, gestures generated by our system significantly improved participants' ability to identify object properties, confirming their interpretability and communicative value. While challenges remain in representing complex shapes, our results highlight the importance of context-aware semantic gestures for creating expressive and collaborative virtual agents or avatars, marking a substantial step forward towards efficient and robust, embodied human-agent interaction. More information and example videos are available here: https://review-anon-io.github.io/ImaGGen.github.io/

Embodied Conversational Agents (ECAs) aim to emulate human face-to-face interaction through speech, gestures, and facial expressions. Current large language model (LLM)-based conversational agents lack embodiment and the expressive gestures essential for natural interaction. Existing solutions for ECAs often produce rigid, low-diversity motions, that are unsuitable for human-like interaction. Alternatively, generative methods for co-speech gesture synthesis yield natural body gestures but depend on future speech context and require long run-times. To bridge this gap, we present MIBURI, the first online, causal framework for generating expressive full-body gestures and facial expressions synchronized with real-time spoken dialogue. We employ body-part aware gesture codecs that encode hierarchical motion details into multi-level discrete tokens. These tokens are then autoregressively generated by a two-dimensional causal framework conditioned on LLM-based speech-text embeddings, modeling both temporal dynamics and part-level motion hierarchy in real time. Further, we introduce auxiliary objectives to encourage expressive and diverse gestures while preventing convergence to static poses. Comparative evaluations demonstrate that our causal and real-time approach produces natural and contextually aligned gestures against recent baselines. We urge the reader to explore demo videos on https://vcai.mpi-inf.mpg.de/projects/MIBURI/.

The creation of virtual humans increasingly leverages automated synthesis of speech and gestures, enabling expressive, adaptable agents that effectively engage users. However, the independent development of voice and gesture generation technologies, alongside the growing popularity of virtual reality (VR), presents significant questions about the integration of these signals and their ability to convey emotional detail in immersive environments. In this paper, we evaluate the influence of real and synthetic gestures and speech, alongside varying levels of immersion (VR vs. 2D displays) and emotional contexts (positive, neutral, negative) on user perceptions. We investigate how immersion affects the perceived match between gestures and speech and the impact on key aspects of user experience, including emotional and empathetic responses and the sense of co-presence. Our findings indicate that while VR enhances the perception of natural gesture-voice pairings, it does not similarly improve synthetic ones - amplifying the perceptual gap between them. These results highlight the need to reassess gesture appropriateness and refine AI-driven synthesis for immersive environments. Supplementary video: https://youtu.be/WMfjIB1X-dc

This study explores two frameworks for co-speech gesture generation, AQ-GT and its semantically-augmented variant AQ-GT-a, to evaluate their ability to convey meaning through gestures and how humans perceive the resulting movements. Using sentences from the SAGA spatial communication corpus, contextually similar sentences, and novel movement-focused sentences, we conducted a user-centered evaluation of concept recognition and human-likeness. Results revealed a nuanced relationship between semantic annotations and performance. The original AQ-GT framework, lacking explicit semantic input, was surprisingly more effective at conveying concepts within its training domain. Conversely, the AQ-GT-a framework demonstrated better generalization, particularly for representing shape and size in novel contexts. While participants rated gestures from AQ-GT-a as more expressive and helpful, they did not perceive them as more human-like. These findings suggest that explicit semantic enrichment does not guarantee improved gesture generation and that its effectiveness is highly dependent on the context, indicating a potential trade-off between specialization and generalization.

Attention, as a core layer of the ubiquitous Transformer architecture, is the bottleneck for large language models and long-context applications. While FlashAttention-3 optimized attention for Hopper GPUs through asynchronous execution and warp specialization, it primarily targets the H100 architecture. The AI industry has rapidly transitioned to deploying Blackwell-based systems such as the B200 and GB200, which exhibit fundamentally different performance characteristics due to asymmetric hardware scaling: tensor core throughput doubles while other functional units (shared memory bandwidth, exponential units) scale more slowly or remain unchanged. We develop several techniques to address these shifting bottlenecks on Blackwell GPUs: (1) redesigned pipelines that exploit fully asynchronous MMA operations and larger tile sizes, (2) software-emulated exponential and conditional softmax rescaling that reduces non-matmul operations, and (3) leveraging tensor memory and the 2-CTA MMA mode to reduce shared memory traffic and atomic adds in the backward pass. We demonstrate that our method, FlashAttention-4, achieves up to 1.3times speedup over cuDNN 9.13 and 2.7times over Triton on B200 GPUs with BF16, reaching up to 1613 TFLOPs/s (71% utilization). Beyond algorithmic innovations, we implement FlashAttention-4 entirely in CuTe-DSL embedded in Python, achieving 20-30times faster compile times compared to traditional C++ template-based approaches while maintaining full expressivity.

Large language models (LLMs) face low hardware efficiency during decoding, especially for long-context reasoning tasks. This paper introduces Step-3, a 321B-parameter VLM with hardware-aware model-system co-design optimized for minimizing decoding costs. Step-3 innovates in two key dimensions: (1) A novel Multi-Matrix Factorization Attention (MFA) mechanism that significantly reduces both KV cache size and computation while maintaining high attention expressiveness, and (2) Attention-FFN Disaggregation (AFD), a distributed inference system that decouples attention and Feed-Forward Network (FFN) layers into specialized subsystems. This co-design achieves unprecedented cost efficiency: Step-3 significantly reduces theoretical decoding costs compared with models like DeepSeek-V3 and Qwen3 MoE 235B, with the gains widening at longer context. Step-3 achieves low cost while activating 38B parameters per token (more than DeepSeek-V3 and Qwen3 MoE 235B), demonstrating that hardware-aligned attention arithmetic intensity, MoE sparsity, and AFD are critical to cost-effectiveness. We perform a head-to-head comparison with DeepSeek-V3 in its favorable scenarios. Our implementation on Hopper GPUs achieves a decoding throughput of up to 4,039 tokens per second per GPU under 50ms TPOT SLA (4K context, FP8, no MTP). It is higher than DeepSeek-V3's 2,324 in the same setup and sets a new Pareto frontier for LLM decoding.

Masked modeling framework has shown promise in co-speech motion generation. However, it struggles to identify semantically significant frames for effective motion masking. In this work, we propose a speech-queried attention-based mask modeling framework for co-speech motion generation. Our key insight is to leverage motion-aligned speech features to guide the masked motion modeling process, selectively masking rhythm-related and semantically expressive motion frames. Specifically, we first propose a motion-audio alignment module (MAM) to construct a latent motion-audio joint space. In this space, both low-level and high-level speech features are projected, enabling motion-aligned speech representation using learnable speech queries. Then, a speech-queried attention mechanism (SQA) is introduced to compute frame-level attention scores through interactions between motion keys and speech queries, guiding selective masking toward motion frames with high attention scores. Finally, the motion-aligned speech features are also injected into the generation network to facilitate co-speech motion generation. Qualitative and quantitative evaluations confirm that our method outperforms existing state-of-the-art approaches, successfully producing high-quality co-speech motion.

We introduce EmbeddingGemma, a new lightweight, open text embedding model based on the Gemma 3 language model family. Our innovative training recipe strategically captures knowledge from larger models via encoder-decoder initialization and geometric embedding distillation. We improve model robustness and expressiveness with a spread-out regularizer, and ensure generalizability by merging checkpoints from varied, optimized mixtures. Evaluated on the Massive Text Embedding Benchmark (MTEB) across multilingual, English, and code domains, EmbeddingGemma (300M) achieves state-of-the-art results. Notably, it outperforms prior top models, both proprietary and open, with fewer than 500M parameters, and provides performance comparable to models double its size, offering an exceptional performance-to-cost ratio. Remarkably, this lead persists when quantizing model weights or truncating embedding outputs. This makes EmbeddingGemma particularly well-suited for low-latency and high-throughput use cases such as on-device applications. We provide ablation studies exploring our key design choices. We release EmbeddingGemma to the community to promote further research.

LLM agents increasingly modify their own prompts, tools, middleware, resources, and execution harnesses at runtime. Such self-evolution can improve capability, but a successful mutation may leave persistent effects that cannot be safely reversed in states different from the one in which it was created. We introduce EvoUndo, a framework for representing, synthesizing, diagnosing, and independently verifying recoverability of model-generated self-modifications across counterfactual states. Across 600 unseen one-shot self-evolution tasks, we identify 197 capability-improving mutations that fail recoverability verification. Under the original recovery representation, conventional repair strategies recover 0/197 of these natural failures. Deterministic oracle analysis recovers 48/197 under the original recovery language L0, while the extended recovery calculus increases empirical oracle recovery to 191/197. A protocol-locked 2x2 grounding-by-expressivity intervention then separates two bottlenecks: exact state-address grounding increases successful recovery from 0/48 to 38/48 (79.2%) when the original language is sufficient, while extending the recovery language enables recovery on 142/143 (99.3%) failures in the oracle-defined S1 stratum. On the primary gpt-oss-120b backbone, adding exact-address diagnostics to the richer language reduces recovery to 133/143 (93.0%); a Qwen3.8-27B replication preserves the grounding and expressivity effects but not this negative interaction, indicating that the latter is model-dependent. These results indicate that reliable agent self-evolution requires co-designing verification, state grounding, witness semantics, and recovery-language expressivity rather than relying on iterative prompting alone.

Understanding pain-related facial behaviors is essential for digital healthcare in terms of effective monitoring, assisted diagnostics, and treatment planning, particularly for patients unable to communicate verbally. Existing data-driven methods of detecting pain from facial expressions are limited due to interpretability and severity quantification. To this end, we propose GraphAU-Pain, leveraging a graph-based framework to model facial Action Units (AUs) and their interrelationships for pain intensity estimation. AUs are represented as graph nodes, with co-occurrence relationships as edges, enabling a more expressive depiction of pain-related facial behaviors. By utilizing a relational graph neural network, our framework offers improved interpretability and significant performance gains. Experiments conducted on the publicly available UNBC dataset demonstrate the effectiveness of the GraphAU-Pain, achieving an F1-score of 66.21% and accuracy of 87.61% in pain intensity estimation.

Sequence models based on linear state spaces (SSMs) have recently emerged as a promising choice of architecture for modeling long range dependencies across various modalities. However, they invariably rely on discretization of a continuous state space, which complicates their presentation and understanding. In this work, we dispose of the discretization step, and propose a model based on vanilla Diagonal Linear RNNs (DLR). We empirically show that, despite being conceptually much simpler, DLR is as performant as previously-proposed SSMs on a variety of tasks and benchmarks including Long Range Arena and raw speech classification. Moreover, we characterize the expressivity of SSMs (including DLR) and attention-based models via a suite of 13 synthetic sequence-to-sequence tasks involving interactions over tens of thousands of tokens, ranging from simple operations, such as shifting an input sequence, to detecting co-dependent visual features over long spatial ranges in flattened images. We find that while SSMs report near-perfect performance on tasks that can be modeled via few convolutional kernels, they struggle on tasks requiring many such kernels and especially when the desired sequence manipulation is context-dependent. Despite these limitations, DLR reaches high performance on two higher-order reasoning tasks ListOpsSubTrees and PathfinderSegmentation-256 with input lengths 8K and 65K respectively, and gives encouraging performance on PathfinderSegmentation-512 with input length 262K for which attention is not a viable choice.

We propose to compose dynamic tree structures that place the objects in an image into a visual context, helping visual reasoning tasks such as scene graph generation and visual Q&A. Our visual context tree model, dubbed VCTree, has two key advantages over existing structured object representations including chains and fully-connected graphs: 1) The efficient and expressive binary tree encodes the inherent parallel/hierarchical relationships among objects, e.g., "clothes" and "pants" are usually co-occur and belong to "person"; 2) the dynamic structure varies from image to image and task to task, allowing more content-/task-specific message passing among objects. To construct a VCTree, we design a score function that calculates the task-dependent validity between each object pair, and the tree is the binary version of the maximum spanning tree from the score matrix. Then, visual contexts are encoded by bidirectional TreeLSTM and decoded by task-specific models. We develop a hybrid learning procedure which integrates end-task supervised learning and the tree structure reinforcement learning, where the former's evaluation result serves as a self-critic for the latter's structure exploration. Experimental results on two benchmarks, which require reasoning over contexts: Visual Genome for scene graph generation and VQA2.0 for visual Q&A, show that VCTree outperforms state-of-the-art results while discovering interpretable visual context structures.