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Deep Learning · Generative Models and Autoencoders

Divyam Madaan, Sumit Chopra, Kyunghyun Cho

Despite the recent success of Multimodal Large Language Models (MLLMs), existing approaches predominantly assume the availability of multiple modalities during training and inference. In practice, multimodal data is often incomplete because modalities may be missing, collected asynchronously, or available only for a subset of examples. In this work, we propose PRIMO, a supervised latent-variable imputation model that quantifies the predictive impact of any missing modality within the multimodal learning setting. PRIMO enables the use of all available training examples, whether modalities are complete or partial. Specifically, it models the missing modality through a latent variable that captures its relationship with the observed modality in the context of prediction. During inference, we draw many samples from the learned distribution over the missing modality to both obtain the marginal predictive distribution (for the purpose of prediction) and analyze the impact of the missing modalities on the prediction for each instance. We evaluate PRIMO on a synthetic XOR dataset, Audio-Vision MNIST, and MIMIC-III for mortality and ICD-9 prediction. Across all datasets, PRIMO obtains performance comparable to unimodal baselines when a modality is fully missing and to multimodal baselines when all modalities are available. PRIMO quantifies the predictive impact of a modality at the instance level using a variance-based metric computed from predictions across latent completions. We visually demonstrate how varying completions of the missing modality result in a set of plausible labels.

Social Aspects · Alignment

Evan Ellis, Vivek Myers, Jens Tuyls, Sergey Levine, Anca Dragan, Benjamin Eysenbach

Assistive agents should not only take actions on behalf of a human, but also step out of the way and cede control when there are important decisions to be made. However, current methods for building assistive agents, whether via mimicking expert humans or via RL finetuning on an inferred reward, often encourage agents to complete tasks on their own rather than truly assisting the human achieve her objectives. We propose a new approach to tuning assistive language models based on maximizing the human's empowerment, their ability to effect desired changes in the environment. Our empowerment-maximizing method, Empower, only requires offline examples of human-written text, providing a self-supervised method for fine-tuning language models to better assist humans. To study the efficacy of our approach, we conducted an 18-person user study comparing our empowerment assistant with a strong baseline. Participants preferred our assistant 78% of the time (p=0.015), with a 31% higher acceptance rate. With this empowerment objective, we provide a framework for useful aligned AI agents without the need for human feedback or verifiable rewards.

Applications · Neuroscience, Cognitive Science

Junfeng Lu, Zijie Yu, SHAOYANG CUI, Gan He, Ruiqin Xiong, Kai Du, Tiejun Huang

Biophysically detailed neural networks represent a promising frontier for brain-inspired AI, offering intrinsic spatio-temporal dynamics to enhance the expressivity and computational density of deep learning systems. However, general-purpose deep learning frameworks suffer from a fundamental mismatch between their dense parallel optimizations and the irregular, tree-structured complexity of biological mechanisms. In this work, we propose **HelioX**, a **GPU-native** framework designed to unify high-performance simulation with scalable training. Unlike approaches that adapt biology to existing deep learning tools, HelioX adopts a "GPU-to-Biophysics" paradigm. We tailor the underlying GPU parallelism to biological structures by implementing custom-fused CUDA kernels for both the Dendritic Hierarchical Scheduling (DHS) algorithm and its gradient propagation. This design eliminates the runtime overhead of generic automatic differentiation and enables multi-stream concurrency for spike generation and equation assembly. Experimental results demonstrate that HelioX outperforms standard simulators (NEURON) by orders of magnitude and surpasses prior GPU-based solvers in both speed and scalability. We successfully train deep biophysical MLPs and organism-scale biophysical neural networks (e.g., the BAAIWorm C. elegans model) on a single consumer-grade GPU. HelioX establishes a new standard for computational efficiency, enabling the training of biophysically detailed models at scales previously unattainable.

Reinforcement Learning · Batch/Offline

Tianwei Ni, Esther Derman, Vineet Jain, Vincent Taboga, Siamak Ravanbakhsh, Pierre-Luc Bacon

Popular offline reinforcement learning (RL) methods rely on conservatism, penalizing out-of-dataset actions or restricting rollout horizons. We question the universality of this principle and revisit a complementary Bayesian perspective. By modeling a posterior over plausible world models and training a history-dependent agent to maximize expected return, the Bayesian approach directly addresses epistemic uncertainty and enables test-time generalization, without conservatism. We first illustrate in a bandit setting that Bayesianism excels on low-quality datasets where conservatism fails. Scaling to realistic tasks, we find that long-horizon rollouts are essential to control value overestimation once conservatism is removed. We introduce design choices that enable learning from long-horizon rollouts while mitigating compounding errors, yielding our algorithm, NEUBAY, grounded in the neutral Bayesian principle. On D4RL and NeoRL benchmarks, NEUBAY is competitive with leading conservative algorithms, achieving new state-of-the-art on 7 datasets with rollout horizons of several hundred steps. Finally, we characterize datasets by quality and coverage to identify when NEUBAY is preferable to conservative methods.

Deep Learning · Large Language Models

Zongyue Qin, Raghavv Goel, Risheek Garrepalli, Mukul Gagrani, Mingu Lee, Yizhou Sun

Speculative decoding has emerged as a powerful approach to accelerate large language model (LLM) inference by employing lightweight draft models to propose candidate tokens that are subsequently verified by the target model. The effectiveness of this paradigm critically depends on the quality of the draft model. While recent advances such as the EAGLE series achieve state-of-the-art speedup, existing draft models remain limited by error accumulation: they condition only on the current prefix, causing their predictions to drift from the target model over steps. In this work, we propose ConFu (Contemplate the Future), a novel speculative decoding framework that enables draft models to anticipate the future direction of generation. ConFu introduces (i) contemplate tokens and soft prompts that allow the draft model to leverage future-oriented signals from the target model at negligible cost, (ii) a dynamic contemplate token mechanism with MoE to enable context-aware future prediction, and (iii) a training framework with anchor token sampling and future prediction replication that learns robust future prediction. Experiments demonstrate that ConFu improves token acceptance rates and generation speed over EAGLE-3 by 8-11%, across various downstream tasks with Llama-3 3B and 8B models. We believe our work is the first to bridge speculative decoding with continuous reasoning tokens, offering a new direction for accelerating LLM inference.

Applications · Chemistry, Physics, and Earth Sciences

hao chen, Tao Han, Jie ZHANG, Song Guo, Fenghua Ling, LEI BAI

Long-term weather forecasting is critical for socioeconomic planning and disaster preparedness. While recent approaches employ finetuning to extend prediction horizons, they remain constrained by the issues of catastrophic forgetting, error accumulation, and high training overhead. To address these limitations, we present a novel pipeline across pretraining, finetuning and forecasting to enhance long‑context modeling while reducing computational overhead. First, we introduce an Efficient Multi‑scale Transformer (EMFormer) to extract multi‑scale features through a single convolution in both training and inference. Based on the new architecture, we further employ an accumulative context finetuning to improve temporal consistency without degrading short‑term accuracy. Additionally, we propose a composite loss that dynamically balances different terms via a sinusoidal weighting, thereby adaptively guiding the optimization trajectory throughout pretraining and finetuning. Experiments show that our approach achieves great performance in weather forecasting and extreme event prediction, substantially improving long-term forecast accuracy. Moreover, EMFormer demonstrates strong generalization on vision benchmarks (ImageNet-1K and ADE20K) while delivering a 5.69$\times$ speedup over conventional multi-scale modules.

Social Aspects · Alignment

Ezgi Korkmaz

Reinforcement learning from human feedback is the leading approach to aligning powerful AI systems so that they can be safe and helpful for humanity. While RLHF is typically modelled as a problem of learning a single preference ranking from noisy feedback, true human preferences are complex and often conflicting, representing substantive disagreements stemming from the diversity of individual human values. With this motivation, a recent line of research has studied RLHF from the perspective of social choice theory, which provides a set of well-established desirable properties for aggregating diverse preferences. Seen through this lens, the standard learning objective in RLHF is equivalent to aggregating diverse human preferences via the Borda count rule. At the same time, several new RLHF algorithms have been proposed, which turn out to be equivalent to the von Neumann winner social choice rule. However, the connection between social choice theory and RLHF has thus far ignored the critical role of regularization to prevent divergence from a reference policy, which is utilized in essentially all practical RLHF algorithms. In this paper, we study how regularization affects the social choice axioms satisfied by different RLHF algorithms, and prove that regularization improves the axiomatic properties of the von Neumann winner rule. In contrast, the Borda count rule still fails to satisfy key social choice axioms even when regularized. These results provide a principled argument grounded in social choice theory for utilizing practical RLHF algorithms that correspond to the von Neumann winner, rather than the standard RLHF objective.

Deep Learning · Sequential Models, Time series

Tian Lan, Hao Le, Jinbo Li, Wenjun He, Meng Wang, Chenghao Liu, Chen Zhang

TSAD is a critical task, but developing models that generalize to unseen data in a zero-shot manner remains a major challenge. Prevailing foundation models for TSAD predominantly rely on reconstruction-based objectives, which suffer from a fundamental objective mismatch and representation conflict: they tend to memorize static patterns from training data, struggling to identify subtle anomalies while often misinterpreting complex normal patterns in unseen domains. To overcome these limitations, we introduce TimeRCD, a novel foundation model for TSAD built upon a new pre-training paradigm: Relative Context Discrepancy (RCD). Instead of reconstructing inputs based on fixed priors, TimeRCD is explicitly trained to adaptively identify anomalies by contrasting the query with its surrounding context. This relational approach, implemented with a standard Transformer architecture, enables the model to infer normality on-the-fly and capture contextual shifts indicative of anomalies that reconstruction-based methods often miss. To empower this paradigm, we develop a large-scale, diverse synthetic corpus with context-dependent anomaly labels, providing the rich supervisory signal necessary for effective pre-training. Extensive experiments demonstrate that TimeRCD significantly outperforms existing general-purpose and anomaly-specific foundation models in zero-shot TSAD across diverse datasets. Our results validate the superiority of the RCD paradigm and establish a new, effective path toward building robust and generalizable foundation models for time series anomaly detection. The code is available in \url{https://anonymous.4open.science/r/TimeRCD-5BE1/}

Applications · Health / Medicine

Zaikang Lin, Sei Chang, Aaron Zweig, Minseo Kang, Fabian Theis, Elham Azizi, David A Knowles

Modern high-throughput biological datasets containing thousands of perturbations enable large-scale discovery of causal graphs that represent regulatory interactions between genes. Differentiable causal graphical models and regression-based methods have been developed to infer gene regulatory networks (GRNs) from interventional datasets. However, existing approaches fail to capture the non-linear dynamics of biological processes such as cellular differentiation. To address this limitation, we propose \textit{PerturbODE}, a novel framework that employs interpretable neural ordinary differential equations (neural ODEs) to model cell state trajectories under perturbations and derive the underlying causal GRN from the neural ODE parameters, enabling downstream simulation of unseen genetic interventions. The GRN is encoded via a single-hidden-layer feedforward network, implicitly grouping genes into interpretable co-regulated modules. We demonstrate PerturbODE's efficacy in GRN inference and extension to perturbation response prediction across both simulated and real overexpression datasets.

Applications · Chemistry, Physics, and Earth Sciences

Kexin Zhang, Weichen Qin, Yue Teng, Jiale Yu, Yuanyuan Ma, jinyu lin, Liping Sun, Jie Zheng, Jingyi Yu

The emergence of Vibe Researching is transforming scientific research into an interactive workflow, where agents orchestrate complex tasks via the Model Context Protocol (MCP). In this ecosystem, scientific tools must evolve from offline simulators into responsive Agent Skills. However, diffusion-based protein docking models—a core component of the current deep learning infrastructure for structural biology—suffer from excessively high latency, rendering them incompatible with real-time agentic interaction. To bridge this gap, we present a compute-efficient vertical foundation model that synergizes architectural optimization with generative consistency. First, we leverage Progressive Consistency Regularization (PCR) to compress complex generative dynamics into a few-step predictor, achieving sub-second latency. Second, we propose Residual Quantization, using mixed-precision on residual streams to alleviate memory bottlenecks while preserving numerical precision. Our approach achieves state-of-the-art (SOTA) docking accuracy while attaining a two-order-of-magnitude speedup ($>300\times$) over AlphaFold3, establishing a new efficiency standard for high-throughput virtual screening. By transforming molecular docking into an interactive, real-time tool, this work establishes a scalable, deep-learning infrastructure for the next generation of AI-driven drug discovery.

Kexin Zhang, Weichen Qin, Yue Teng, Jiale Yu, Yuanyuan Ma, jinyu lin, Liping Sun, Jie Zheng, Jingyi Yu

The emergence of Vibe Researching is transforming scientific research into an interactive workflow, where agents orchestrate complex tasks via the Model Context Protocol (MCP). In this ecosystem, scientific tools must evolve from offline simulators into responsive Agent Skills. However, diffusion-based protein docking models—a core component of the current deep learning infrastructure for structural biology—suffer from excessively high latency, rendering them incompatible with real-time agentic interaction. To bridge this gap, we present a compute-efficient vertical foundation model that synergizes architectural optimization with generative consistency. First, we leverage Progressive Consistency Regularization (PCR) to compress complex generative dynamics into a few-step predictor, achieving sub-second latency. Second, we propose Residual Quantization, using mixed-precision on residual streams to alleviate memory bottlenecks while preserving numerical precision. Our approach achieves state-of-the-art (SOTA) docking accuracy while attaining a two-order-of-magnitude speedup ($>300\times$) over AlphaFold3, establishing a new efficiency standard for high-throughput virtual screening. By transforming molecular docking into an interactive, real-time tool, this work establishes a scalable, deep-learning infrastructure for the next generation of AI-driven drug discovery.

Probabilistic Methods · Variational Inference

Mathis Chagneux, Mathias Müller, Pierre Gloaguen, Sylvain Le Corff, Jimmy Olsson

This article addresses online variational estimation in parametric state-space models. We propose a new procedure for efficiently computing the evidence lower bound and its gradient in a streaming-data setting, where observations arrive sequentially. The algorithm allows for the simultaneous training of the model parameters and the distribution of the latent states given the observations. It is based on i.i.d. Monte Carlo sampling, coupled with a well-chosen deep architecture, enabling both computational efficiency and flexibility. The performance of the method is illustrated on both synthetic data and real-world air-quality data. The proposed approach is theoretically motivated by the existence of an asymptotic contrast function and the ergodicity of the underlying Markov chain, and applies more generally to the computation of additive expectations under posterior distributions in state-space models.

Applications · Chemistry, Physics, and Earth Sciences

Haokai Hong, Wanyu LIN, KC Tan

Large-scale molecular dynamics simulations are essential in understanding chemical and biological processes, necessitating the accurate and efficient modeling of interatomic interactions. Existing learning-based methods generally are based on message passing mechanisms; they are either not scalable or too coarse to offer accurate modeling. We propose a new message passing framework that can effectively and efficiently model interatomic interactions for simulating large-scale molecular dynamics at full atomic resolution. Specifically, our framework is stacked with a sequence of message passing neural network layers, each realizing the message passing over a distinct and dilated star-structured path. These star-structured paths are constructed progressively along dilated regions to capture the distance-dependent interactions. The crux of our framework is that it resolves the problem of dense interatomic interactions of large-scale atomic systems with sparser and region-based message passing graphs. We evaluate the framework on four benchmarks: MD22 (molecules with 42–370 atoms), Chignolin (a 166-atom protein featuring diverse conformations), the AdK dataset (a protein trajectory with up to 3,000 atoms), and the MISATO dataset (over 10,000 heterogeneous protein-ligand complexes with systems up to 40,000 atoms). Comprehensive evaluations demonstrate that our approach delivers state-of-the-art performance overall across various benchmarks.

Deep Learning · Large Language Models

Xiaojun Guo, Runyu Zhou, Yifei Wang, Qi Zhang, Chenheng Zhang, Stefanie Jegelka, Xiaohan Wang, Jiajun Chai, Guojun Yin, Wei Lin 等

Vision-language models (VLMs) have shown remarkable abilities by integrating large language models with visual inputs. However, they often fail to utilize visual evidence adequately, either depending on linguistic priors in vision-centric tasks or resorting to textual shortcuts during reasoning. Although reinforcement learning (RL) can align models with desired behaviors, its application to VLMs has been hindered by the lack of scalable and reliable reward mechanisms. To overcome this challenge, we propose **SSL4RL**, a novel framework that leverages self-supervised learning (SSL) tasks as a source of verifiable rewards for RL-based fine-tuning. Our approach reformulates SSL objectives—such as predicting image rotation or reconstructing masked patches—into dense, automatic reward signals, eliminating the need for human preference data or unreliable AI evaluators. Experiments show that SSL4RL substantially improves performance on both vision-centric and vision-language reasoning benchmarks, with encouraging potentials on open-ended image-captioning scenarios and stronger resilience to visual corruptions. Through systematic ablations, we identify key factors—such as data volume, model scale, model choice, task difficulty, and semantic alignment with the target domain—that influence the effectiveness of SSL4RL tasks, offering new design principles for future work. We also demonstrate the framework’s generality by applying it to graph learning, where it yields significant gains. SSL4RL establishes a versatile and effective paradigm for aligning multimodal models using verifiable, self-supervised objectives.

Deep Learning · Foundation Models

Wenhan Ma, Hailin Zhang, Liang Zhao, Yifan Song, Yudong Wang, Fuli Luo, Zhifang Sui

Reinforcement learning (RL) has emerged as a crucial approach for enhancing the capabilities of large language models. However, in Mixture-of-Experts (MoE) models, the routing mechanism often introduces instability, even leading to catastrophic RL training collapse. We analyze the training-inference consistency of MoE models and identify a notable discrepancy in routing behaviors between the two phases. To address this issue, we propose \textbf{Rollout Routing Replay (R3)}, a novel and effective method that records routing distributions from the inference engine and replays them during training. R3 significantly reduces training-inference policy KL divergence and mitigates extreme discrepancies without compromising training speed. Extensive experiments on various settings confirm that R3 succeeds in stabilizing RL training, preventing collapse and outperforming strong baselines. R3 is orthogonal to most policy optimization algorithm improvements, allowing it to be used in conjunction with them. We believe this work can offer a new solution for stabilizing RL in MoE model.

Deep Learning · Large Language Models

Ran Xu, Tianci Liu, Zihan Dong, Tony Yu, Ilgee Hong, Carl Yang, Linjun Zhang, Tuo Zhao, Haoyu Wang

Standard reward models typically predict scalar scores that fail to capture the multifaceted nature of response quality in non-verifiable domains, such as creative writing or open-ended instruction following. To address this limitation, we propose Rubric-ARM, a framework that jointly optimizes a rubric generator and a judge using reinforcement learning from preference feedback. Unlike existing methods that rely on static rubrics or disjoint training pipelines, our approach treats rubric generation as a latent action learned to maximize judgment accuracy. We introduce an alternating optimization strategy to mitigate the non-stationarity of simultaneous updates, providing theoretical analysis that demonstrates how this schedule reduces gradient variance during training. Extensive experiments show that Rubric-ARM achieves state-of-the-art performance among baselines on multiple benchmarks and significantly improves downstream policy alignment in both offline and online reinforcement learning settings.

Probabilistic Methods · Bayesian Models and Methods

Theodore Papamarkou, Pierre Alquier, Matthias Bauer, Wray Buntine, Andrew Davison, Gintare Karolina Dziugaite, Maurizio Filippone, Andrew Y. K. Foong, Vincent Fortuin, Dimitris Fouskakis 等

LLMs excel at predictive tasks and complex reasoning tasks, but many high-value deployments rely on decisions under uncertainty, for example, which tool to call, which expert to consult, or how many resources to invest. While the usefulness and feasibility of Bayesian approaches remain unclear for LLM inference, this position paper argues that the control layer of an agentic AI system (that orchestrates LLMs and tools) is a clear case where Bayesian principles should shine. Bayesian decision theory provides a framework for agentic systems that can help to maintain beliefs over task-relevant latent quantities, to update these beliefs from observed agentic and human-AI interactions, and to choose actions. Making LLMs themselves explicitly Bayesian belief-updating engines remains computationally intensive and conceptually nontrivial as a general modeling target. In contrast, this paper argues that coherent decision-making requires Bayesian principles at the level of the agentic system, not necessarily the LLM agent parameters. This paper articulates practical properties for Bayesian control that fit modern agentic AI systems and human-AI collaboration, and provides concrete examples and design patterns to illustrate how calibrated beliefs and utility-aware policies can improve agentic AI orchestration.

Social Aspects · Accountability, Transparency, and Interpretability

Gengrui (Edward) Zhang

GenAI systems, particularly LLMs, rely heavily on vast amounts of publicly available digital content as training data. A significant portion of this content is protected by copyright. While large-scale data scraping may be lawful under certain jurisdictions, the use of copyrighted works to generate outputs that compete with or replicate original creations raises unresolved legal, economic, and ethical concerns. In this position paper, we argue that data providers should be fairly compensated based on their measurable contribution to inference-time outcomes, rather than through coarse, one-time licensing or blanket agreements. We examine alternative perspectives on data ownership, fair use, and model training, and discuss why existing approaches fail to align incentives between GenAI developers and content creators. We then outline concrete roadmaps for developing decentralized systems that enable contribution-aware revenue sharing, including mechanisms for attribution, accounting, and payout at scale. We argue that fair revenue distribution for data providers will not only help resolve ongoing legal disputes surrounding GenAI systems, but also foster a new era of collaboration, rather than competition, between model developers and data creators. By incentivizing the production and sharing of high-quality datasets, such mechanisms can ultimately accelerate the development of more robust, trustworthy, and socially sustainable GenAI systems.

Applications · Time Series

Tong Guan, SHENG PAN, Johan Barthelemy, Zhao Li, Yujun Cai, Cesare Alippi, Ming Jin, Shirui Pan

Recent time series modeling faces a sharp divide between numerical generation and semantic understanding, with research showing that generation models often rely on superficial pattern matching, while understanding-oriented models struggle with high-fidelity numerical output. Although unified multimodal models (UMMs) have bridged this gap in vision, their potential for time series remains untapped. We propose TimeOmni-VL, the first vision-centric framework that unifies time series understanding and generation through two key innovations: (1) Fidelity-preserving bidirectional mapping between time series and images (Bi-TSI), which advances Time Series-to-Image (TS2I) and Image-to-Time Series (I2TS) conversions to ensure near-lossless transformations. (2) Understanding-guided generation. We introduce TSUMM-Suite, a novel dataset consists of six understanding tasks rooted in time series analytics that are coupled with two generation tasks. With a calibrated Chain-of-Thought (CoT), TimeOmni-VL is the first to leverage time series understanding as an explicit control signal for high-fidelity generation. Experiments confirm that this unified approach significantly improves both semantic understanding and numerical precision, establishing a new frontier for multimodal time series modeling.

General Machine Learning · Representation Learning

Ying Tang, Dong Li, Youjia Zhang, Zikai Song, Junqing Yu, Wei Yang

Unifying the complementary strengths of diverse Vision Foundation Models (VFMs) into a single efficient model is highly desirable but challenged by the negative transfer inherent in monolithic distillation. To address these feature conflicts, we introduce \textbf{PRISM}, a novel dual-stream Mixture-of-Experts (MoE) framework that synergizes VFMs via modular specialization. We propose a two-stage paradigm: (1) expertise deconstruction, where a teacher-conditional router guides experts to specialize in distinct representational subspaces to mitigate interference, followed by (2) dynamic recomposition, where the router learns to assemble these experts into tailored computational pathways for downstream tasks. Experiments on PASCAL-Context and NYUD-v2 show that \textbf{PRISM} establishes a new state of the art, validating that sparse, emergent specialization is a scalable approach for integrating diverse visual knowledge.