new

Get trending papers in your email inbox!

Subscribe

Daily Papers

byAK and the research community

Nov 4

CacheFlow: Fast Human Motion Prediction by Cached Normalizing Flow

Many density estimation techniques for 3D human motion prediction require a significant amount of inference time, often exceeding the duration of the predicted time horizon. To address the need for faster density estimation for 3D human motion prediction, we introduce a novel flow-based method for human motion prediction called CacheFlow. Unlike previous conditional generative models that suffer from poor time efficiency, CacheFlow takes advantage of an unconditional flow-based generative model that transforms a Gaussian mixture into the density of future motions. The results of the computation of the flow-based generative model can be precomputed and cached. Then, for conditional prediction, we seek a mapping from historical trajectories to samples in the Gaussian mixture. This mapping can be done by a much more lightweight model, thus saving significant computation overhead compared to a typical conditional flow model. In such a two-stage fashion and by caching results from the slow flow model computation, we build our CacheFlow without loss of prediction accuracy and model expressiveness. This inference process is completed in approximately one millisecond, making it 4 times faster than previous VAE methods and 30 times faster than previous diffusion-based methods on standard benchmarks such as Human3.6M and AMASS datasets. Furthermore, our method demonstrates improved density estimation accuracy and comparable prediction accuracy to a SOTA method on Human3.6M. Our code and models are available at https://github.com/meaten/CacheFlow.

  • 4 authors
·
May 19, 2025

Decoupled Predictive Decision Making: A Shared Conditional Predictor for Agents

Agent decisions depend on empirical relationships that deployment observations reveal and task descriptions alone may leave unresolved. We introduce Decoupled Predictive Decision Making (DPDM), an architecture that formulates heterogeneous agent decisions as conditional prediction with a shared pretrained learner. Language models provide semantic representations of current and historical records, while a general-purpose conditional predictor predicts task-defined targets from the represented evidence. Pretraining supplies reusable inference capability; deployment evidence instantiates problem-specific predictions without updating either model's neural parameters. Tool judgments, candidate preferences, and reasoning assessments share an evidence-and-query interface, with predictions mapped to choices by a decision rule. This architecture establishes complementary sources of agent capability: semantic knowledge acquired through language pretraining and empirical inference acquired through structured-data pretraining. A single frozen LimiX-2 predictor serves all five task categories. With Qwen3.5-27B as the semantic encoder, DPDM raises mean accuracy across 50 benchmarks from 78.80% with few-shot prompting to 84.92% under their respective evaluated history budgets, and reaches 82.33% with identical histories and queries. On ToolPRMBench's BFCL and ToolSandbox tasks, absolute accuracy gains are 34.26% and 28.87%, respectively, at the methods' respective evaluated history budgets. Accuracy improves as history grows. With identical imbalanced histories, mean balanced accuracy improves by an absolute 14.51% across five reasoning-step assessment tasks and four encoders. DPDM makes learning from experience an independently improvable foundation-model capability, creating a shared route for advances in conditional prediction to improve decisions across agent tasks.

  • 8 authors
·
Oct 31

LimiX: Unleashing Structured-Data Modeling Capability for Generalist Intelligence

We argue that progress toward general intelligence requires complementary foundation models grounded in language, the physical world, and structured data. This report presents LimiX, the first installment of our large structured-data models (LDMs). LimiX treats structured data as a joint distribution over variables and missingness, thus capable of addressing a wide range of tabular tasks through query-based conditional prediction via a single model. LimiX is pretrained using masked joint-distribution modeling with an episodic, context-conditional objective, where the model predicts for query subsets conditioned on dataset-specific contexts, supporting rapid, training-free adaptation at inference. We evaluate LimiX across 10 large structured-data benchmarks with broad regimes of sample size, feature dimensionality, class number, categorical-to-numerical feature ratio, missingness, and sample-to-feature ratios. With a single model and a unified interface, LimiX consistently surpasses strong baselines including gradient-boosting trees, deep tabular networks, recent tabular foundation models, and automated ensembles, as shown in Figure 1 and Figure 2. The superiority holds across a wide range of tasks, such as classification, regression, missing value imputation, and data generation, often by substantial margins, while avoiding task-specific architectures or bespoke training per task. All LimiX models are publicly accessible under Apache 2.0.

  • 38 authors
·
Sep 3, 2025

MIMIC: A Generative Multimodal Foundation Model for Biomolecules

Biological function emerges from coupled constraints across sequence, structure, regulation, evolution, and cellular context, yet most foundation models in biology are trained within one modality or for a fixed forward task. We present MIMIC, a generative multimodal foundation model trained on our newly curated and aligned dataset, LORE, linking nucleic acid, protein, evolutionary, structural, regulatory, and semantic/contextual modalities within partially observed biomolecular states. MIMIC uses a split-track encoder-decoder architecture to condition on arbitrary subsets of observed modalities and reconstruct or generate missing components of molecular state across the genome, transcriptome, and proteome. Multimodal conditioning consistently improves MIMIC's sequence reconstruction relative to sequence-only inputs, while its learned representations enable state-of-the-art performance on RNA and protein downstream tasks. MIMIC achieves state-of-the-art splicing prediction, and its joint generative formulation enables isoform-aware inference that further improves performance. Beyond prediction, the same generative framework supports constrained design. For RNA, MIMIC identifies corrective edits in a clinically relevant HBB splice-disrupting mutation without reverting it by using evolutionary and structural signals. For proteins, jointly conditioning on shape and surface chemistry of PD-L1 and hACE2 binding sites produces diverse, high-confidence sequences with strong in silico support for target binding. Finally, MIMIC uses experimental context as semantic conditioning to model assay-dependent RNA chemical probing, rather than treating context as a fixed output. Together, these results position MIMIC's aligned multimodal generative modeling as a strong foundation for unifying representation learning, conditional prediction, and constrained biomolecular design within a single model.

  • 31 authors
·
Apr 26

Training and Inference Dynamics of PLDR-LLMs: Row-Map Collapse, Renormalization, and Predictive Reduction

This monograph develops a unified account of training and inference in Power Law Decoder Representation language models (PLDR-LLMs). Exact finite work identities decompose changes in the absolute energy of the row-centered learned map into parameter contributions, signed interactions, and numerical observation defects. Positive affine blocking retains restarts at the row-constant face, while the augmented AdamW state supplies the complete dynamical description. Predictive renormalization acts on the complete conditional training law for a single pass over distinct corpus target blocks, retaining optimizer memory, remaining data, schedule, and numerical policy. Autonomous reductions require closure; approximate reductions carry successor and emission errors. Finite-population covariance, matched physical clocks, matrix fluxes, and signed temporal energy connect row dynamics to model-wide observations. Absolute row collapse, relative row concentration, operator stabilization, and predictive accuracy are distinguished. Experiments reveal observer and optimizer dependence, reject the tested autonomous row-state candidates, and support finite conditional prediction and state-specific operator reduction. Independent single-pass families exhibit moving finite fluctuation regions without establishing a thermodynamic critical class. Conditional symmetry, head limits, covariance flows, and readout error budgets specify assumptions needed to transfer scaling laws to inference. The theory separates exact identities, conditional dynamical claims, and finite empirical findings, with proofs, selected formal checks, and compact numerical evidence.

Kepler: Auditable World Models for ARC-AGI-3

ARC-AGI-3 evaluates agents in interactive environments whose rules and objectives must be inferred from observation. We present Kepler, an open-source harness that represents hypotheses as executable world models and validates them through retrospective transition checks and conditional prediction checks. Under one frozen Claude Opus 5 configuration, Kepler obtained a server-verified 100.00 RHAE on all 25 public games, with no per-game model selection or score-conditioned reruns. On 181 of 183 completed levels, the final Opus attempt used no more actions than the corresponding median-human baseline. The retained board runs used 8,256 environment actions, of which 7,292 occurred in scored levels. Retained local provider-session records yield 858.0 million tokens, 97.37% cache reads, and a \$777.72 cost at September 1, 2026 API list-equivalent rates. We also report three evaluation failures: source-code leakage that produced an invalid perfect run, agents reconstructing a removed harness in a control condition, and autonomous repair masking a broken planner. A single-game observation case study showed that animation frames contained task-relevant information absent from settled text grids. Across the final Claude Opus 5 and GPT-5.6 Sol boards, 48 of 50 game-model cells reached 100. These results indicate that public-set score alone has limited discriminative value and motivate first-attempt, cost-conditioned, and verification-aware reporting.

  • 1 authors
·
Sep 29

Similarity-Distance-Magnitude Universal Verification

We address the neural network robustness problem by adding Similarity (i.e., correctly predicted depth-matches into training)-awareness and Distance-to-training-distribution-awareness to the existing output Magnitude (i.e., decision-boundary)-awareness of the softmax function. The resulting SDM activation function provides strong signals of the relative epistemic (reducible) predictive uncertainty. We use this novel behavior to further address the complementary HCI problem of mapping the output to human-interpretable summary statistics over relevant partitions of a held-out calibration set. Estimates of prediction-conditional uncertainty are obtained via a parsimonious learned transform over the class-conditional empirical CDFs of the output of a final-layer SDM activation function. For decision-making and as an intrinsic model check, estimates of class-conditional accuracy are obtained by further partitioning the high-probability regions of this calibrated output into class-conditional, region-specific CDFs. The uncertainty estimates from SDM calibration are remarkably robust to test-time distribution shifts and out-of-distribution inputs; incorporate awareness of the effective sample size; provide estimates of uncertainty from the learning and data splitting processes; and are well-suited for selective classification and conditional branching for additional test-time compute based on the predictive uncertainty, as for selective LLM generation, routing, and composition over multiple models and retrieval. Finally, we construct SDM networks, LLMs with uncertainty-aware verification and interpretability-by-exemplar as intrinsic properties. We provide open-source software implementing these results.

  • 1 authors
·
Feb 27, 2025

Eliminating Oversaturation and Artifacts of High Guidance Scales in Diffusion Models

Classifier-free guidance (CFG) is crucial for improving both generation quality and alignment between the input condition and final output in diffusion models. While a high guidance scale is generally required to enhance these aspects, it also causes oversaturation and unrealistic artifacts. In this paper, we revisit the CFG update rule and introduce modifications to address this issue. We first decompose the update term in CFG into parallel and orthogonal components with respect to the conditional model prediction and observe that the parallel component primarily causes oversaturation, while the orthogonal component enhances image quality. Accordingly, we propose down-weighting the parallel component to achieve high-quality generations without oversaturation. Additionally, we draw a connection between CFG and gradient ascent and introduce a new rescaling and momentum method for the CFG update rule based on this insight. Our approach, termed adaptive projected guidance (APG), retains the quality-boosting advantages of CFG while enabling the use of higher guidance scales without oversaturation. APG is easy to implement and introduces practically no additional computational overhead to the sampling process. Through extensive experiments, we demonstrate that APG is compatible with various conditional diffusion models and samplers, leading to improved FID, recall, and saturation scores while maintaining precision comparable to CFG, making our method a superior plug-and-play alternative to standard classifier-free guidance.

  • 3 authors
·
Oct 3, 2024 8

Beyond Isolated Entities: Relation-Aware Multi-Entity Modeling for Unsupervised Video Anomaly Detection

Video anomaly detection for patrol robots and surveillance systems must recognize abnormal interactions among familiar entities. Existing pixel-reconstruction and isolated-entity methods may fail when individual entities appear normal but their spatial or motion relations are abnormal. This work presents Interaction-Centric Network for Temporal Entity-Relation Analysis and Consistency Testing (INTERACT), a framework for unsupervised video anomaly detection. Person-Object Appearance-Motion Interaction (POAMI) moves beyond isolated-entity encoding by jointly modeling the appearance, motion, and spatial configurations of persons and objects in each frame. The resulting representations capture both individual entity states and their cross-entity context. Based on these representations, Target Geometry-Guided Relational Interaction Prediction (TGRIP) predicts target entity interaction states from historical relational memory and target-frame geometry without explicit identity tracking. Motion-Interaction Reconstruction and Alignment (MIRA) then evaluates these predictions through conditional flow reconstruction and semantic consistency checking, providing complementary anomaly evidence beyond prediction error alone. INTERACT achieves state-of-the-art performance, obtaining a frame-level AUC of 84.5% on the ShanghaiTech benchmark. Ablation studies show that removing cross-entity attention causes the largest performance drop, demonstrating the necessity of relational modeling. INTERACT is particularly effective for anomalies caused by changes in relations among people and objects, while maintaining competitive performance in general scenarios. The source code will be made publicly available at https://github.com/ppworkhard/INTERACT.

  • 3 authors
·
Sep 22

RAAG: Ratio Aware Adaptive Guidance

Flow-based generative models have achieved remarkable progress, with classifier-free guidance (CFG) becoming the standard for high-fidelity generation. However, the conventional practice of applying a strong, fixed guidance scale throughout inference is poorly suited for the rapid, few-step sampling required by modern applications. In this work, we uncover the root cause of this conflict: a fundamental sampling instability where the earliest steps are acutely sensitive to guidance. We trace this to a significant spike in the ratio of conditional to unconditional predictions--a spike that we prove to be an inherent property of the training data distribution itself, making it a almost inevitable challenge. Applying a high, static guidance value during this volatile initial phase leads to an exponential amplification of error, degrading image quality. To resolve this, we propose a simple, theoretically grounded, adaptive guidance schedule that automatically dampens the guidance scale at early steps based on the evolving ratio. Our method is lightweight, incurs no inference overhead, and is compatible with standard frameworks. Experiments across state-of-the-art image (SD3.5, Qwen-Image) and video (WAN2.1) models show our approach enables up to 3x faster sampling while maintaining or improving quality, robustness, and semantic alignment. Our findings highlight that adapting guidance to the sampling process, rather than fixing it, is critical for unlocking the full potential of fast, flow-based models.

  • 10 authors
·
Aug 5, 2025

WA-JEPA: Rethinking the Video JEPA Paradigm for World-Action Modeling in Autonomous Driving

Video Joint Embedding Predictive Architecture (V-JEPA) learns powerful spatiotemporal representations from video through self-supervised latent feature prediction. However, V-JEPA is built around random-mask completion and deterministic regression, making it fundamentally ill-suited for autonomous driving planning that demands future-directed prediction tightly coupled with action. To address this, we rethink the V-JEPA paradigm and present WA-JEPA, a V-JEPA-native world-action model designed for autonomous driving planning. Instead of random spatiotemporal masking, WA-JEPA employs hybrid future-masked pre-training, where the model infers future latents from observed context. Departing from deterministic regression, we recast future prediction as conditional flow matching over latent futures, which substantially improves the model's ability to generate plausible future latents for downstream planning. Finally, a joint future-action predictor is proposed to denoise future scene tokens and ego trajectories together in a unified spatiotemporal latent space, allowing action supervision to directly shape planning-relevant world representations. Pre-trained on nuPlan videos and fine-tuned on NAVSIM, WA-JEPA reaches 91.7 EPDMS on NAVSIM-v2, surpassing the strongest end-to-end and world-action baselines by 1.6 and 1.3 EPDMS, and, without HUGSIM-specific fine-tuning, attains the best HD-Score of 0.4462 on the closed-loop HUGSIM benchmark under the same evaluation protocol. These results validate V-JEPA-native world-action modeling as a powerful and scalable paradigm for autonomous driving planning. Code is available at https://github.com/AFARI-Research/WA-JEPA.

  • 14 authors
·
Aug 21

VGL-stGen: Learning a shared multimodal model for lung histology and spatial transcriptomics

VGL-stGen is a multimodal large language model adapted from a pretrained medical vision-language model using paired lung H&E and spatial transcriptomics with single-cell references. Training integrates image-expression and expression-cell-type pairs, and gene-conditioned pseudo-labels transfer transcriptomic cell-type supervision to histology images. One deployed checkpoint supports thirteen evaluated tasks spanning tissue and cell-type classification, gene prediction and conditional expression completion from combinations of histology, cell identity and observed gene expression. Task-specific decoding produces categorical labels, gene lists and structured expression levels. For conditional completion, fixing queried gene identities and predicting their levels autoregressively improves structured prediction. Controlled adaptation shows that restricting supervision to requested expression-level tokens can further improve image-conditioned completion. Image-permutation experiments indicate that correctly paired histology adds information beyond observed expression. External classification relies partly on computational references with shared annotation lineage, and some H&E sources were exposed during cancer training or model development. Within these conditions, VGL-stGen demonstrates how a medical vision-language backbone can learn from spatial transcriptomics and histology to connect tissue morphology and molecular states through shared generative modeling.

  • 6 authors
·
Oct 19

UniGenX: Unified Generation of Sequence and Structure with Autoregressive Diffusion

Unified generation of sequence and structure for scientific data (e.g., materials, molecules, proteins) is a critical task. Existing approaches primarily rely on either autoregressive sequence models or diffusion models, each offering distinct advantages and facing notable limitations. Autoregressive models, such as GPT, Llama, and Phi-4, have demonstrated remarkable success in natural language generation and have been extended to multimodal tasks (e.g., image, video, and audio) using advanced encoders like VQ-VAE to represent complex modalities as discrete sequences. However, their direct application to scientific domains is challenging due to the high precision requirements and the diverse nature of scientific data. On the other hand, diffusion models excel at generating high-dimensional scientific data, such as protein, molecule, and material structures, with remarkable accuracy. Yet, their inability to effectively model sequences limits their potential as general-purpose multimodal foundation models. To address these challenges, we propose UniGenX, a unified framework that combines autoregressive next-token prediction with conditional diffusion models. This integration leverages the strengths of autoregressive models to ease the training of conditional diffusion models, while diffusion-based generative heads enhance the precision of autoregressive predictions. We validate the effectiveness of UniGenX on material and small molecule generation tasks, achieving a significant leap in state-of-the-art performance for material crystal structure prediction and establishing new state-of-the-art results for small molecule structure prediction, de novo design, and conditional generation. Notably, UniGenX demonstrates significant improvements, especially in handling long sequences for complex structures, showcasing its efficacy as a versatile tool for scientific data generation.

  • 25 authors
·
Mar 9, 2025

MCVD: Masked Conditional Video Diffusion for Prediction, Generation, and Interpolation

Video prediction is a challenging task. The quality of video frames from current state-of-the-art (SOTA) generative models tends to be poor and generalization beyond the training data is difficult. Furthermore, existing prediction frameworks are typically not capable of simultaneously handling other video-related tasks such as unconditional generation or interpolation. In this work, we devise a general-purpose framework called Masked Conditional Video Diffusion (MCVD) for all of these video synthesis tasks using a probabilistic conditional score-based denoising diffusion model, conditioned on past and/or future frames. We train the model in a manner where we randomly and independently mask all the past frames or all the future frames. This novel but straightforward setup allows us to train a single model that is capable of executing a broad range of video tasks, specifically: future/past prediction -- when only future/past frames are masked; unconditional generation -- when both past and future frames are masked; and interpolation -- when neither past nor future frames are masked. Our experiments show that this approach can generate high-quality frames for diverse types of videos. Our MCVD models are built from simple non-recurrent 2D-convolutional architectures, conditioning on blocks of frames and generating blocks of frames. We generate videos of arbitrary lengths autoregressively in a block-wise manner. Our approach yields SOTA results across standard video prediction and interpolation benchmarks, with computation times for training models measured in 1-12 days using le 4 GPUs. Project page: https://mask-cond-video-diffusion.github.io ; Code : https://github.com/voletiv/mcvd-pytorch

  • 3 authors
·
May 19, 2022

Conditional Coverage Diagnostics for Conformal Prediction

Evaluating conditional coverage remains one of the most persistent challenges in assessing the reliability of predictive systems. Although conformal methods can give guarantees on marginal coverage, no method can guarantee to produce sets with correct conditional coverage, leaving practitioners without a clear way to interpret local deviations. To overcome sample-inefficiency and overfitting issues of existing metrics, we cast conditional coverage estimation as a classification problem. Conditional coverage is violated if and only if some classifier can achieve lower risk than the target coverage. Through the choice of a (proper) loss function, the resulting risk difference gives a conservative estimate of natural miscoverage measures such as L1 and L2 distance, and can even separate the effects of over- and under-coverage, and non-constant target coverages. We call the resulting family of metrics excess risk of the target coverage (ERT). We show experimentally that the use of modern classifiers provides much higher statistical power than simple classifiers underlying established metrics like CovGap. Additionally, we use our metric to benchmark different conformal prediction methods. Finally, we release an open-source package for ERT as well as previous conditional coverage metrics. Together, these contributions provide a new lens for understanding, diagnosing, and improving the conditional reliability of predictive systems.

  • 4 authors
·
May 28

Degradation Prediction of Semiconductor Lasers using Conditional Variational Autoencoder

Semiconductor lasers have been rapidly evolving to meet the demands of next-generation optical networks. This imposes much more stringent requirements on the laser reliability, which are dominated by degradation mechanisms (e.g., sudden degradation) limiting the semiconductor laser lifetime. Physics-based approaches are often used to characterize the degradation behavior analytically, yet explicit domain knowledge and accurate mathematical models are required. Building such models can be very challenging due to a lack of a full understanding of the complex physical processes inducing the degradation under various operating conditions. To overcome the aforementioned limitations, we propose a new data-driven approach, extracting useful insights from the operational monitored data to predict the degradation trend without requiring any specific knowledge or using any physical model. The proposed approach is based on an unsupervised technique, a conditional variational autoencoder, and validated using vertical-cavity surface-emitting laser (VCSEL) and tunable edge emitting laser reliability data. The experimental results confirm that our model (i) achieves a good degradation prediction and generalization performance by yielding an F1 score of 95.3%, (ii) outperforms several baseline ML based anomaly detection techniques, and (iii) helps to shorten the aging tests by early predicting the failed devices before the end of the test and thereby saving costs

  • 5 authors
·
Nov 5, 2022

Learning Perturbation-Specific Representations through Conditional Energy Prior for Cellular Response Prediction

AI-based cellular perturbation prediction is essential to accelerate drug discovery and therapeutic identification. However, perturbation-specific signals are generally obscured by cellular complexity, making it difficult for existing methods to correctly capture perturbation effects. To address this problem, we propose PerturbEnergy, which introduces a conditional energy-based prior over perturbation representations. It assigns lower energy (higher probability) to representations compatible with the given perturbation and higher energy to others, thereby explicitly tilting the latent space toward perturbation-preferred regions. Besides, PerturbEnergy can be integrated into autoencoder architectures as we find its Evidence Lower Bound (ELBO) is equivalent to the ELBO of the complete autoencoder. We further prove that optimizing PerturbEnergy increases the lower bound on the conditional mutual information between representation and perturbation. Extensive experiments on four benchmark datasets demonstrate the effectiveness of our PerturbEnergy: it improves perturbation recognition especially in latent space with improvement of up to 83.2\%; It also achieves state-of-the-art performance for predicting top-50/100/200 differentially expressed gene(DEG) response and remaining competitive on highly variable gene(HVG) prediction. The code is provided: https://github.com/BlueWhaleLab/PerturbEnergy

  • 2 authors
·
Oct 12

Beyond Aggregate Calibration: Decomposing Income-Conditional Recall Disparities in Automated Credit Default Prediction

Data-centric curation pipelines frequently rely on model confidence scores to flag and filter noisy or mislabeled training instances. Evaluating this filtering convention on a large-scale consumer lending sample (LendingClub, N = 1,344,936) uncovers an underlying demographic asymmetry: high-income defaulters are disproportionately classified as label noise relative to low-income defaulters (Cramer's V approximately 0.03-0.07). Re-examining this behavior through the lens of equal opportunity [Hardt et al., 2016] reveals a far more severe discrepancy: a 16.86 percentage point gap in true positive rate (recall) between high- and low-income borrowers who ultimately defaulted. Implementing a sequential feature-blinding methodology allows us to isolate the drivers of this disparity across three distinct mechanisms: (1) direct reliance on self-reported applicant income; (2) algorithmic absorption of upstream institutional bias encoded within origination interest rates; and (3) a residual disparity (3.55 percentage points in cross-validation; 2.56 percentage points on a held-out test partition, Z = -4.04, p < 0.0001) that remains even after purging both income and interest rates from the model. Out-of-sample signed SHAP valuations demonstrate that this residual gap is maintained by structural proxies, most notably loan amount and home ownership status. These empirical findings show that simply blinding an algorithm to sensitive attributes fails to ensure fairness when institutional pricing decisions and behavioral proxy variables collectively reconstruct the omitted signals. We outline the practical implications of these findings for auditing data-centric AI workflows within regulated financial institutions.

  • 1 authors
·
Aug 7

Conditional Generative Adversarial Networks for Speed Control in Trajectory Simulation

Motion behaviour is driven by several factors -- goals, presence and actions of neighbouring agents, social relations, physical and social norms, the environment with its variable characteristics, and further. Most factors are not directly observable and must be modelled from context. Trajectory prediction, is thus a hard problem, and has seen increasing attention from researchers in the recent years. Prediction of motion, in application, must be realistic, diverse and controllable. In spite of increasing focus on multimodal trajectory generation, most methods still lack means for explicitly controlling different modes of the data generation. Further, most endeavours invest heavily in designing special mechanisms to learn the interactions in latent space. We present Conditional Speed GAN (CSG), that allows controlled generation of diverse and socially acceptable trajectories, based on user controlled speed. During prediction, CSG forecasts future speed from latent space and conditions its generation based on it. CSG is comparable to state-of-the-art GAN methods in terms of the benchmark distance metrics, while being simple and useful for simulation and data augmentation for different contexts such as fast or slow paced environments. Additionally, we compare the effect of different aggregation mechanisms and show that a naive approach of concatenation works comparable to its attention and pooling alternatives.

  • 4 authors
·
Mar 21, 2021

Conditional Neural Optimal Transport for Predicting Cellular Phenotypes from Molecular Structure

High-content microscopy enables systematic profiling of cellular responses to chemical perturbations, but the scale of the chemical space makes exhaustive phenotypic characterization experimentally infeasible. This motivates computational models that can predict image-derived phenotypes without acquiring the corresponding treated cells. We formulate molecule-induced phenotype prediction as an inductive conditional transport problem in image representation space. Given a negative-control phenotype and the structure of a molecule, we aim to predict the phenotype induced by the corresponding molecule. We first evaluate classical optimal transport baselines and show that static couplings do not yield useful predictions on large-scale phenotypic image datasets. We then introduce a molecule-conditioned Neural Optimal Transport (NOT) model with a Monge-Gap regularization training objective that learns to transport negative-control unperturbed phenotypes toward perturbed phenotypes using molecular structure as conditioning information. NOT recovers molecule-specific phenotypic effects while reducing microscopy-associated technical variation, thereby facilitating comparisons across experimental batches. On unseen active molecules, the model outperforms baseline approaches, demonstrating that chemically conditioned transport can generalize beyond the molecules observed during training. We identified the molecular encoder as the main limitation to this generalization, while transport in a compressed representation space improves performance and scalability. These results establish NOT as a promising framework for predicting cellular phenotypes from molecular structure and negative-control phenotypes, while highlighting the development of more informative molecular representations as a key direction for improving out-of-distribution performance.

  • 4 authors
·
Aug 13

Predicting Unseen Scientific Interactions: Conditional Flow Models Hallucinate Non-Additive Effects

Conditional generative models are increasingly used for scientific prediction beyond the direct training support. Yet scientific questions often concern whether one intervention changes the effect of another. Such interactions can be of primary interest while explaining little of the total variation, allowing models to appear accurate overall without recovering the relevant scientific effect. It remains unclear how these models learn interactions and when these successfully extrapolate to unseen conditions. We therefore study interaction recovery in flow-matching models using a physiological time-series simulator, drug dose-response data, combinatorial cell perturbations, and molecular conformer generations, where we separate recovery from hallucinated interaction structure. In the controlled setting, individual effects are learned much earlier than interactions and models hallucinate interactions where none exist. Across settings, we find qualitatively different generalization problems, with successful prediction depending on whether condition structure continues from observed to held-out targets. When it does, interactions are recoverable. If not, models can generate plausible responses while missing the interaction. We furthermore find that hallucinations increase as targets become less identifiable, and that successful interaction recovery in output space can fail under nonlinear readouts. Finally, we show that aggregate fidelity metrics can conceal whether models learn and extrapolate interactions.

  • 3 authors
·
Oct 13

Generative Compositional Augmentations for Scene Graph Prediction

Inferring objects and their relationships from an image in the form of a scene graph is useful in many applications at the intersection of vision and language. We consider a challenging problem of compositional generalization that emerges in this task due to a long tail data distribution. Current scene graph generation models are trained on a tiny fraction of the distribution corresponding to the most frequent compositions, e.g. <cup, on, table>. However, test images might contain zero- and few-shot compositions of objects and relationships, e.g. <cup, on, surfboard>. Despite each of the object categories and the predicate (e.g. 'on') being frequent in the training data, the models often fail to properly understand such unseen or rare compositions. To improve generalization, it is natural to attempt increasing the diversity of the training distribution. However, in the graph domain this is non-trivial. To that end, we propose a method to synthesize rare yet plausible scene graphs by perturbing real ones. We then propose and empirically study a model based on conditional generative adversarial networks (GANs) that allows us to generate visual features of perturbed scene graphs and learn from them in a joint fashion. When evaluated on the Visual Genome dataset, our approach yields marginal, but consistent improvements in zero- and few-shot metrics. We analyze the limitations of our approach indicating promising directions for future research.

  • 6 authors
·
Jul 11, 2020

DRIFT: Disentangled Responsive-Invariant Flow Transport for Single-Cell Perturbation Prediction

Predicting cellular responses to perturbations is a central problem in cellular biology, with broad applications in systems biology and drug discovery. This task is challenging because cellular responses can be complex and cell-state dependent, intrinsic cell-to-cell variability can be confounded with perturbation effects, and destructive single-cell RNA sequencing precludes paired measurements of the same cell before and after treatment. Flow matching transports control cells to perturbed states flexibly, but acting on the full cell state can confound perturbation effects with pre-existing cell-to-cell variability. Disentangled approaches separate responsive from invariant components, but model perturbations through prescribed mechanisms, such as latent shifts or graph edits, limiting their flexibility. We address both limitations in a unified framework. A variational encoder disentangles each cell into an invariant block, capturing state unaffected by the perturbation, and a responsive block, capturing state it changes, through conditional priors and an information-theoretic invariance constraint. Conditional flow matching transports only the responsive block, conditioned on the perturbation and invariant state, yielding a flexible, data-driven model of perturbation effects without confounding pre-existing variability. Across several benchmarks, our method outperforms the strongest published method in settings involving combinatorial and unseen perturbation prediction.

  • 3 authors
·
Sep 27

Semantic Sensitivities and Inconsistent Predictions: Measuring the Fragility of NLI Models

Recent studies of the emergent capabilities of transformer-based Natural Language Understanding (NLU) models have indicated that they have an understanding of lexical and compositional semantics. We provide evidence that suggests these claims should be taken with a grain of salt: we find that state-of-the-art Natural Language Inference (NLI) models are sensitive towards minor semantics preserving surface-form variations, which lead to sizable inconsistent model decisions during inference. Notably, this behaviour differs from valid and in-depth comprehension of compositional semantics, however does neither emerge when evaluating model accuracy on standard benchmarks nor when probing for syntactic, monotonic, and logically robust reasoning. We propose a novel framework to measure the extent of semantic sensitivity. To this end, we evaluate NLI models on adversarially generated examples containing minor semantics-preserving surface-form input noise. This is achieved using conditional text generation, with the explicit condition that the NLI model predicts the relationship between the original and adversarial inputs as a symmetric equivalence entailment. We systematically study the effects of the phenomenon across NLI models for in- and out-of- domain settings. Our experiments show that semantic sensitivity causes performance degradations of 12.92% and 23.71% average over in- and out-of- domain settings, respectively. We further perform ablation studies, analysing this phenomenon across models, datasets, and variations in inference and show that semantic sensitivity can lead to major inconsistency within model predictions.

  • 3 authors
·
Jan 25, 2024

Conditional Cross Attention Network for Multi-Space Embedding without Entanglement in Only a SINGLE Network

Many studies in vision tasks have aimed to create effective embedding spaces for single-label object prediction within an image. However, in reality, most objects possess multiple specific attributes, such as shape, color, and length, with each attribute composed of various classes. To apply models in real-world scenarios, it is essential to be able to distinguish between the granular components of an object. Conventional approaches to embedding multiple specific attributes into a single network often result in entanglement, where fine-grained features of each attribute cannot be identified separately. To address this problem, we propose a Conditional Cross-Attention Network that induces disentangled multi-space embeddings for various specific attributes with only a single backbone. Firstly, we employ a cross-attention mechanism to fuse and switch the information of conditions (specific attributes), and we demonstrate its effectiveness through a diverse visualization example. Secondly, we leverage the vision transformer for the first time to a fine-grained image retrieval task and present a simple yet effective framework compared to existing methods. Unlike previous studies where performance varied depending on the benchmark dataset, our proposed method achieved consistent state-of-the-art performance on the FashionAI, DARN, DeepFashion, and Zappos50K benchmark datasets.

  • 5 authors
·
Jul 25, 2023

scDFM: Distributional Flow Matching Model for Robust Single-Cell Perturbation Prediction

A central goal in systems biology and drug discovery is to predict the transcriptional response of cells to perturbations. This task is challenging due to the noisy and sparse nature of single-cell measurements, as well as the fact that perturbations often induce population-level shifts rather than changes in individual cells. Existing deep learning methods typically assume cell-level correspondences, limiting their ability to capture such global effects. We present scDFM, a generative framework based on conditional flow matching that models the full distribution of perturbed cells conditioned on control states. By incorporating a maximum mean discrepancy (MMD) objective, our method aligns perturbed and control populations beyond cell-level correspondences. To further improve robustness to sparsity and noise, we introduce the Perturbation-Aware Differential Transformer (PAD-Transformer), a backbone architecture that leverages gene interaction graphs and differential attention to capture context-specific expression changes. Across multiple genetic and drug perturbation benchmarks, scDFM consistently outperforms prior methods, demonstrating strong generalization in both unseen and combinatorial settings. In the combinatorial setting, it reduces mean squared error by 19.6% relative to the strongest baseline. These results highlight the importance of distribution-level generative modeling for robust in silico perturbation prediction. The code is available at https://github.com/AI4Science-WestlakeU/scDFM

  • 4 authors
·
Feb 5

Let Confidence Change, Not the Prediction: Prediction-Preserving Repair for Post-hoc Calibration

Post-hoc calibration corrects reported confidence, yet a multiclass calibrator can also change the associated top-1 prediction. Accuracy captures only the net effect of these changes on correctness, not how often predictions change; the Top-1 Prediction Change Rate (TPCR) instead measures this frequency. We propose Calibrator-Output Repair for Top-1 Decision Preservation (CORD), the first post-fit adapter to impose exact prediction preservation by repairing the full calibrated probability vector. From the original and calibrated outputs alone, CORD determines the mass assigned to the original top-1. The calibrated conditional distribution allocates the remaining mass over the other classes, yielding a repaired vector whose own argmax recovers the original prediction. On the calibration split, CORD coordinates the repaired masses to retain the calibrated outputs' mean mass on original predictions whenever attainable. The adapter alters neither the fitted calibrator nor its direct output, fits no additional supervised map, and requires no user- or validation-tuned hyperparameter. Across CIFAR-10/100 and ImageNet-1K, CORD attains zero TPCR by construction and lowers mean ECE, NLL, and Brier relative to the corresponding direct outputs in every dataset; paired gains persist under distribution shift and across calibration-set sizes. CORD thus removes the preservation constraint from calibrator fitting and assigns exact recovery of the original decision to subsequent output repair. Our code is available at https://github.com/labhai/CORD.

  • 3 authors
·
Sep 1 2

FlowATC: Aircraft Trajectory Prediction via Flow Matching

Building accurate decision-support tools for next-generation air traffic control requires robust trajectory prediction models. We present a flow-matching architecture trained exclusively on historical aircraft trajectories, with no route labels or chart supervision. Trained on 1.15 million Automatic Dependent Surveillance-Broadcast trajectory windows collected over the San Francisco Bay Area, the model generates aircraft trajectory distributions that closely match historical traffic, reproducing known airspace structure around San Francisco Airport such as the shape of SFO's published NIITE FOUR departure procedure. Our model is trained directly on the native, irregular ADS-B sampling interval. Trajectory prediction is cast as sequence inpainting using a block-causal Transformer that denoises future state tokens conditioned on the observed history using Conditional Flow Matching or Denoising Diffusion Probabilistic Models. We compare our architecture against constant-velocity, deterministic-Long Short Term Memory, and Conditional Variational Autoencoders baselines. At matched parameter count, CFM outperforms DDPM by 11-26% in minADE@20, and both generative objectives surpass the CVAE baseline by 31-41%. We further show that the error degrades gracefully with prediction horizon, and the architecture remains effective when retrained on temporally decimated feeds. Lastly, we sample K independent completions, yielding spatial probabilistic occupancy estimates that can serve as input to downstream conflict-risk estimation.

  • 5 authors
·
Sep 14

PatchCT: Aligning Patch Set and Label Set with Conditional Transport for Multi-Label Image Classification

Multi-label image classification is a prediction task that aims to identify more than one label from a given image. This paper considers the semantic consistency of the latent space between the visual patch and linguistic label domains and introduces the conditional transport (CT) theory to bridge the acknowledged gap. While recent cross-modal attention-based studies have attempted to align such two representations and achieved impressive performance, they required carefully-designed alignment modules and extra complex operations in the attention computation. We find that by formulating the multi-label classification as a CT problem, we can exploit the interactions between the image and label efficiently by minimizing the bidirectional CT cost. Specifically, after feeding the images and textual labels into the modality-specific encoders, we view each image as a mixture of patch embeddings and a mixture of label embeddings, which capture the local region features and the class prototypes, respectively. CT is then employed to learn and align those two semantic sets by defining the forward and backward navigators. Importantly, the defined navigators in CT distance model the similarities between patches and labels, which provides an interpretable tool to visualize the learned prototypes. Extensive experiments on three public image benchmarks show that the proposed model consistently outperforms the previous methods.

  • 7 authors
·
Jul 18, 2023

Meta-DT: Offline Meta-RL as Conditional Sequence Modeling with World Model Disentanglement

A longstanding goal of artificial general intelligence is highly capable generalists that can learn from diverse experiences and generalize to unseen tasks. The language and vision communities have seen remarkable progress toward this trend by scaling up transformer-based models trained on massive datasets, while reinforcement learning (RL) agents still suffer from poor generalization capacity under such paradigms. To tackle this challenge, we propose Meta Decision Transformer (Meta-DT), which leverages the sequential modeling ability of the transformer architecture and robust task representation learning via world model disentanglement to achieve efficient generalization in offline meta-RL. We pretrain a context-aware world model to learn a compact task representation, and inject it as a contextual condition to the causal transformer to guide task-oriented sequence generation. Then, we subtly utilize history trajectories generated by the meta-policy as a self-guided prompt to exploit the architectural inductive bias. We select the trajectory segment that yields the largest prediction error on the pretrained world model to construct the prompt, aiming to encode task-specific information complementary to the world model maximally. Notably, the proposed framework eliminates the requirement of any expert demonstration or domain knowledge at test time. Experimental results on MuJoCo and Meta-World benchmarks across various dataset types show that Meta-DT exhibits superior few and zero-shot generalization capacity compared to strong baselines while being more practical with fewer prerequisites. Our code is available at https://github.com/NJU-RL/Meta-DT.

  • 6 authors
·
Oct 15, 2024

Ctrl-U: Robust Conditional Image Generation via Uncertainty-aware Reward Modeling

In this paper, we focus on the task of conditional image generation, where an image is synthesized according to user instructions. The critical challenge underpinning this task is ensuring both the fidelity of the generated images and their semantic alignment with the provided conditions. To tackle this issue, previous studies have employed supervised perceptual losses derived from pre-trained models, i.e., reward models, to enforce alignment between the condition and the generated result. However, we observe one inherent shortcoming: considering the diversity of synthesized images, the reward model usually provides inaccurate feedback when encountering newly generated data, which can undermine the training process. To address this limitation, we propose an uncertainty-aware reward modeling, called Ctrl-U, including uncertainty estimation and uncertainty-aware regularization, designed to reduce the adverse effects of imprecise feedback from the reward model. Given the inherent cognitive uncertainty within reward models, even images generated under identical conditions often result in a relatively large discrepancy in reward loss. Inspired by the observation, we explicitly leverage such prediction variance as an uncertainty indicator. Based on the uncertainty estimation, we regularize the model training by adaptively rectifying the reward. In particular, rewards with lower uncertainty receive higher loss weights, while those with higher uncertainty are given reduced weights to allow for larger variability. The proposed uncertainty regularization facilitates reward fine-tuning through consistency construction. Extensive experiments validate the effectiveness of our methodology in improving the controllability and generation quality, as well as its scalability across diverse conditional scenarios. Code will soon be available at https://grenoble-zhang.github.io/Ctrl-U-Page/.

  • 5 authors
·
Oct 14, 2024

An Introduction to Artificial Prediction Markets for Classification

Prediction markets are used in real life to predict outcomes of interest such as presidential elections. This paper presents a mathematical theory of artificial prediction markets for supervised learning of conditional probability estimators. The artificial prediction market is a novel method for fusing the prediction information of features or trained classifiers, where the fusion result is the contract price on the possible outcomes. The market can be trained online by updating the participants' budgets using training examples. Inspired by the real prediction markets, the equations that govern the market are derived from simple and reasonable assumptions. Efficient numerical algorithms are presented for solving these equations. The obtained artificial prediction market is shown to be a maximum likelihood estimator. It generalizes linear aggregation, existent in boosting and random forest, as well as logistic regression and some kernel methods. Furthermore, the market mechanism allows the aggregation of specialized classifiers that participate only on specific instances. Experimental comparisons show that the artificial prediction markets often outperform random forest and implicit online learning on synthetic data and real UCI datasets. Moreover, an extensive evaluation for pelvic and abdominal lymph node detection in CT data shows that the prediction market improves adaboost's detection rate from 79.6% to 81.2% at 3 false positives/volume.

  • 2 authors
·
Jul 8, 2012

Conditional Memory Enhanced Item Representation for Generative Recommendation

Generative recommendation (GR) has emerged as a promising paradigm that predicts target items by autoregressively generating their semantic identifiers (SID). Most GR methods follow a quantization-representation-generation pipeline, first assigning each item a SID, then constructing input representations from SID-token embeddings, and finally predicting the target SID through autoregressive generation. Existing item-level representation constructions mainly take two forms: directly merging SID-token embeddings into a compact vector, or enriching item-level representations with external inputs through additional networks. However, these item-level constructors still expose two practical challenges: direct merging may amplify the information loss caused by quantization and ID collision while obscuring SID code relations, whereas external-input-based methods can strengthen item semantics but cannot reliably preserve the SID-structured evidence required for token-level generation. These limitations make representation construction an underexplored bottleneck, leading to two severe problems, the Identity-Structure Preservation Conflict and Input-Output Granularity Mismatch. To this end, we propose ComeIR, a Conditional Memory enhanced Item Representation framework that reconstructs SID-token embeddings into item-aware inputs and restores the token granularity during SID decoding. Specifically, MM-guided token scoring adaptively estimates the contribution of each code within the SID, dual-level Engram memory captures intra-item code composition and inter-item transition patterns, and a memory-restoring prediction head reuses the memories during SID decoding. Extensive experiments demonstrate the effectiveness and flexibility of ComeIR, and further reveal scalable gains from enlarging conditional memory.

  • 5 authors
·
May 11

Beyond the Transcriptome: Chromatin-Informed Prediction of Cell-State-Dependent Perturbation Responses

Predicting transcriptional responses to genetic perturbations is central to understanding gene function. Existing predictors primarily rely on transcriptomic measurements, although chromatin accessibility provides complementary information about the cellular context in which perturbations act. Using this information requires linking chromatin context to specific perturbations and accounting for baseline differences between independently sampled control and perturbed populations. We propose ChromaPert, a chromatin-informed framework for predicting state-dependent perturbation responses. ChromaPert combines molecular and DNA-informed locus priors with paired control RNA--ATAC features to jointly represent target identity and measured cellular context. Its Chromatin-Guided Response Router (CGRR) builds a source bank of control-derived expression offsets and retrieves relevant sources using perturbation/locus or control-ATAC similarity. These offsets account for baseline differences, while conditional transport flow learns the remaining response. Across three unseen-target and held-out-state settings on K562 CAT-ATAC and Perturb-Multiome, ChromaPert achieves the highest all-gene response correlation among evaluated methods. When transferring known perturbations to held-out states, it improves correlation by 23.2% across all genes and 46.2% for the twenty most responsive genes over the strongest respective baselines. Correct RNA--ATAC pairing improves recovery of chromatin-associated response slopes over shuffled pairing, while cross-state predictions retain state-specific responses to the same perturbation.

  • 6 authors
·
Oct 5

Generalizable single-cell perturbation response prediction using energy-guided flow matching

Predicting phenotypic and transcriptional responses to perturbations at single-cell resolution provides a powerful tool for probing biological systems. However, existing methods typically rely on fixed mappings learned during training, making it challenging to calibrate distribution shifts or adapt to novel perturbation conditions during inference. Here, we present scEGFlow, an energy-guided flow matching framework that dynamically bridges control and perturbed cellular states. scEGFlow models continuous transitions from control cell populations to perturbed states using conditional flow matching. It then applies condition-specific energy gradients to correct and steer these predictions, enabling flexible adjustments without retraining the flow model. Evaluations across benchmarks spanning imaging phenotypes and transcriptomic profiles show that scEGFlow outperforms existing methods in reconstructing response distributions under both seen and unseen perturbation conditions, faithfully preserving cellular manifold geometry and population heterogeneity. This advantage is notable when adapting to new conditions with only a few measured cells, consistently improving prediction accuracy. Furthermore, scEGFlow accurately recapitulates perturbation-induced up- and down-regulation patterns across consensus gene expression signatures, where energy guidance improves the agreement between predicted and observed regulatory directions. Ultimately, these findings demonstrate that scEGFlow provides a modular, generalizable, and steerable solution for single-cell perturbation modeling. By grounding generative flows in learned biological landscapes, this architecture establishes a new computational paradigm for navigating and manipulating cellular behavior in silico.

  • 6 authors
·
Sep 26

Conditional Data Synthesis Augmentation

Reliable machine learning and statistical analysis rely on diverse, well-distributed training data. However, real-world datasets are often limited in size and exhibit underrepresentation across key subpopulations, leading to biased predictions and reduced performance, particularly in supervised tasks such as classification. To address these challenges, we propose Conditional Data Synthesis Augmentation (CoDSA), a novel framework that leverages generative models, such as diffusion models, to synthesize high-fidelity data for improving model performance across multimodal domains including tabular, textual, and image data. CoDSA generates synthetic samples that faithfully capture the conditional distributions of the original data, with a focus on under-sampled or high-interest regions. Through transfer learning, CoDSA fine-tunes pre-trained generative models to enhance the realism of synthetic data and increase sample density in sparse areas. This process preserves inter-modal relationships, mitigates data imbalance, improves domain adaptation, and boosts generalization. We also introduce a theoretical framework that quantifies the statistical accuracy improvements enabled by CoDSA as a function of synthetic sample volume and targeted region allocation, providing formal guarantees of its effectiveness. Extensive experiments demonstrate that CoDSA consistently outperforms non-adaptive augmentation strategies and state-of-the-art baselines in both supervised and unsupervised settings.

  • 2 authors
·
Apr 9, 2025

Conditional Attention Networks for Distilling Knowledge Graphs in Recommendation

Knowledge graph is generally incorporated into recommender systems to improve overall performance. Due to the generalization and scale of the knowledge graph, most knowledge relationships are not helpful for a target user-item prediction. To exploit the knowledge graph to capture target-specific knowledge relationships in recommender systems, we need to distill the knowledge graph to reserve the useful information and refine the knowledge to capture the users' preferences. To address the issues, we propose Knowledge-aware Conditional Attention Networks (KCAN), which is an end-to-end model to incorporate knowledge graph into a recommender system. Specifically, we use a knowledge-aware attention propagation manner to obtain the node representation first, which captures the global semantic similarity on the user-item network and the knowledge graph. Then given a target, i.e., a user-item pair, we automatically distill the knowledge graph into the target-specific subgraph based on the knowledge-aware attention. Afterward, by applying a conditional attention aggregation on the subgraph, we refine the knowledge graph to obtain target-specific node representations. Therefore, we can gain both representability and personalization to achieve overall performance. Experimental results on real-world datasets demonstrate the effectiveness of our framework over the state-of-the-art algorithms.

  • 7 authors
·
Nov 3, 2021

FlowDock: Geometric Flow Matching for Generative Protein-Ligand Docking and Affinity Prediction

Powerful generative AI models of protein-ligand structure have recently been proposed, but few of these methods support both flexible protein-ligand docking and affinity estimation. Of those that do, none can directly model multiple binding ligands concurrently or have been rigorously benchmarked on pharmacologically relevant drug targets, hindering their widespread adoption in drug discovery efforts. In this work, we propose FlowDock, the first deep geometric generative model based on conditional flow matching that learns to directly map unbound (apo) structures to their bound (holo) counterparts for an arbitrary number of binding ligands. Furthermore, FlowDock provides predicted structural confidence scores and binding affinity values with each of its generated protein-ligand complex structures, enabling fast virtual screening of new (multi-ligand) drug targets. For the well-known PoseBusters Benchmark dataset, FlowDock outperforms single-sequence AlphaFold 3 with a 51% blind docking success rate using unbound (apo) protein input structures and without any information derived from multiple sequence alignments, and for the challenging new DockGen-E dataset, FlowDock outperforms single-sequence AlphaFold 3 and matches single-sequence Chai-1 for binding pocket generalization. Additionally, in the ligand category of the 16th community-wide Critical Assessment of Techniques for Structure Prediction (CASP16), FlowDock ranked among the top-5 methods for pharmacological binding affinity estimation across 140 protein-ligand complexes, demonstrating the efficacy of its learned representations in virtual screening. Source code, data, and pre-trained models are available at https://github.com/BioinfoMachineLearning/FlowDock.

  • 2 authors
·
Dec 14, 2024

GIF: A Conditional Multimodal Generative Framework for IR Drop Imaging in Chip Layouts

IR drop analysis is essential in physical chip design to ensure the power integrity of on-chip power delivery networks. Traditional Electronic Design Automation (EDA) tools have become slow and expensive as transistor density scales. Recent works have introduced machine learning (ML)-based methods that formulate IR drop analysis as an image prediction problem. These existing ML approaches fail to capture both local and long-range dependencies and ignore crucial geometrical and topological information from physical layouts and logical connectivity. To address these limitations, we propose GIF, a Generative IR drop Framework that uses both geometrical and topological information to generate IR drop images. GIF fuses image and graph features to guide a conditional diffusion process, producing high-quality IR drop images. For instance, On the CircuitNet-N28 dataset, GIF achieves 0.78 SSIM, 0.95 Pearson correlation, 21.77 PSNR, and 0.026 NMAE, outperforming prior methods. These results demonstrate that our framework, using diffusion based multimodal conditioning, reliably generates high quality IR drop images. This shows that IR drop analysis can effectively leverage recent advances in generative modeling when geometric layout features and logical circuit topology are jointly modeled. By combining geometry aware spatial features with logical graph representations, GIF enables IR drop analysis to benefit from recent advances in generative modeling for structured image generation.

  • 6 authors
·
Apr 10

C3LLM: Conditional Multimodal Content Generation Using Large Language Models

We introduce C3LLM (Conditioned-on-Three-Modalities Large Language Models), a novel framework combining three tasks of video-to-audio, audio-to-text, and text-to-audio together. C3LLM adapts the Large Language Model (LLM) structure as a bridge for aligning different modalities, synthesizing the given conditional information, and making multimodal generation in a discrete manner. Our contributions are as follows. First, we adapt a hierarchical structure for audio generation tasks with pre-trained audio codebooks. Specifically, we train the LLM to generate audio semantic tokens from the given conditions, and further use a non-autoregressive transformer to generate different levels of acoustic tokens in layers to better enhance the fidelity of the generated audio. Second, based on the intuition that LLMs were originally designed for discrete tasks with the next-word prediction method, we use the discrete representation for audio generation and compress their semantic meanings into acoustic tokens, similar to adding "acoustic vocabulary" to LLM. Third, our method combines the previous tasks of audio understanding, video-to-audio generation, and text-to-audio generation together into one unified model, providing more versatility in an end-to-end fashion. Our C3LLM achieves improved results through various automated evaluation metrics, providing better semantic alignment compared to previous methods.

  • 4 authors
·
May 24, 2024

Radiomap Blind Prediction under Incomplete Observation: Error Characterization and Correctable Propagation-Prior Learning

Radiomap blind prediction aims to infer radiomaps from observable representations of the propagation environment and base station configuration without field measurements. In practice, the observable representations are inherently incomplete. Thus, the target radiomap is not fully determined by the inputs when generalizing to unseen configurations or environments. Under incomplete observation, we establish a population-level theory of deterministic radiomap blind prediction that identifies the conditional mean as its optimal target and separates prediction error into reducible predictor approximation and irreducible uncertainty caused by missing physical information. The framework further characterizes the train-test risk gap and the uncertainty reduction enabled by observation enrichment. Building on it, we reveal the dual role of propagation priors: they provide physically grounded guidance, yet their implementable forms may bias the attainable predictor. This motivates RadioDecomp, which treats a prior-guided predictor as a correctable base and learns its remaining predictable discrepancy through residual refinement. To evaluate RadioDecomp across distinct propagation-prior designs, we instantiate it with a feature-guided monolithic base and a LoS-Shadow structured base, yielding RadioFR and RadioLSR, respectively. Across random, cross-configuration, and cross-environment settings, experiments confirm the benefit of propagation-related representations and show that both instantiations improve upon their respective bases. Further controlled studies on base capacity, training-support coverage, and observation coarsening corroborate the proposed analysis.

  • 7 authors
·
Sep 25

Deep Neural Networks for Rank-Consistent Ordinal Regression Based On Conditional Probabilities

In recent times, deep neural networks achieved outstanding predictive performance on various classification and pattern recognition tasks. However, many real-world prediction problems have ordinal response variables, and this ordering information is ignored by conventional classification losses such as the multi-category cross-entropy. Ordinal regression methods for deep neural networks address this. One such method is the CORAL method, which is based on an earlier binary label extension framework and achieves rank consistency among its output layer tasks by imposing a weight-sharing constraint. However, while earlier experiments showed that CORAL's rank consistency is beneficial for performance, it is limited by a weight-sharing constraint in a neural network's fully connected output layer, which may restrict the expressiveness and capacity of a network trained using CORAL. We propose a new method for rank-consistent ordinal regression without this limitation. Our rank-consistent ordinal regression framework (CORN) achieves rank consistency by a novel training scheme. This training scheme uses conditional training sets to obtain the unconditional rank probabilities through applying the chain rule for conditional probability distributions. Experiments on various datasets demonstrate the efficacy of the proposed method to utilize the ordinal target information, and the absence of the weight-sharing restriction improves the performance substantially compared to the CORAL reference approach. Additionally, the suggested CORN method is not tied to any specific architecture and can be utilized with any deep neural network classifier to train it for ordinal regression tasks.

  • 3 authors
·
May 31, 2023

Towards generalizable single-cell perturbation modeling via the Conditional Monge Gap

Learning the response of single-cells to various treatments offers great potential to enable targeted therapies. In this context, neural optimal transport (OT) has emerged as a principled methodological framework because it inherently accommodates the challenges of unpaired data induced by cell destruction during data acquisition. However, most existing OT approaches are incapable of conditioning on different treatment contexts (e.g., time, drug treatment, drug dosage, or cell type) and we still lack methods that unanimously show promising generalization performance to unseen treatments. Here, we propose the Conditional Monge Gap which learns OT maps conditionally on arbitrary covariates. We demonstrate its value in predicting single-cell perturbation responses conditional to one or multiple drugs, a drug dosage, or combinations thereof. We find that our conditional models achieve results comparable and sometimes even superior to the condition-specific state-of-the-art on scRNA-seq as well as multiplexed protein imaging data. Notably, by aggregating data across conditions we perform cross-task learning which unlocks remarkable generalization abilities to unseen drugs or drug dosages, widely outperforming other conditional models in capturing heterogeneity (i.e., higher moments) in the perturbed population. Finally, by scaling to hundreds of conditions and testing on unseen drugs, we narrow the gap between structure-based and effect-based drug representations, suggesting a promising path to the successful prediction of perturbation effects for unseen treatments.

  • 4 authors
·
Apr 11, 2025

Criterion-Conditional In-Context Learning: Evaluating Criterion-Shift Adaptation in Vision-Language Models

Vision-language models can perform new tasks without parameter updates through in-context learning (ICL), whose core mechanism is utilizing the support set for task induction. In the standard ICL setting, once the task is induced, its decision criterion remains fixed. However, in real-world applications, many tasks exhibit a stable high-level intent, while their decision criteria shift according to specific requirements. Thus, we introduce a new setting, denoted as Criterion-Conditional In-Context Learning (CC-ICL), where models must infer the latent criterion from context and adjust predictions accordingly under fixed task semantics. To evaluate this capability, we propose two complementary metrics, Criterion Invariance and Criterion Sensitivity, capturing the model's robustness and adaptability under criterion shifts. We further construct CC-Bench, a multi-domain benchmark that supports evaluation under the CC-ICL setting. By employing a dual-level data hierarchy, CC-Bench enables legitimate ground-truth variation conditioned on the active criterion even when the task remains fixed. Experiments on CC-Bench reveal that most models exhibit a rigid boundary bias, struggling to align their decisions with the latent criterion. We also find that even a simple multi-criterion training strategy can significantly reduce this bias, improving Criterion Sensitivity and enabling 7B-scale models to surpass proprietary models without degrading general multimodal performance.

Category-Agnostic 6D Pose Estimation with Conditional Neural Processes

We present a novel meta-learning approach for 6D pose estimation on unknown objects. In contrast to ``instance-level" and ``category-level" pose estimation methods, our algorithm learns object representation in a category-agnostic way, which endows it with strong generalization capabilities across object categories. Specifically, we employ a neural process-based meta-learning approach to train an encoder to capture texture and geometry of an object in a latent representation, based on very few RGB-D images and ground-truth keypoints. The latent representation is then used by a simultaneously meta-trained decoder to predict the 6D pose of the object in new images. Furthermore, we propose a novel geometry-aware decoder for the keypoint prediction using a Graph Neural Network (GNN), which explicitly takes geometric constraints specific to each object into consideration. To evaluate our algorithm, extensive experiments are conducted on the \linemod dataset, and on our new fully-annotated synthetic datasets generated from Multiple Categories in Multiple Scenes (MCMS). Experimental results demonstrate that our model performs well on unseen objects with very different shapes and appearances. Remarkably, our model also shows robust performance on occluded scenes although trained fully on data without occlusion. To our knowledge, this is the first work exploring cross-category level 6D pose estimation.

  • 4 authors
·
Jun 14, 2022