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Enhancing Bioactivity Prediction via Spatial Emptiness Representation of Protein-ligand Complex and Union of Multiple Pockets

Neural Information Processing Systems

Predicting the bioactivity of candidate ligands remains a central challenge in drug discovery. Ligands and endogenous substrates often compete for the same binding sites on target proteins, and the extent to which a ligand can modulate protein function depends not only on its binding but also on how effectively it occupies the relevant pocket. However, most existing methods focus narrowly on local interactions within protein-ligand complexes and neglect spatial emptiness--the unoccupied regions within the binding site that may permit endogenous molecules to engage or interfere. Such unfilled space can diminish the ligand's functional impact, regardless of binding affinity. To overcome this key limitation in protein-ligand modeling, we propose LigoSpace, a novel method integrating three core components. LigoSpace introduces GeoREC (Geometric Representation of Spatial Emptiness in Complexes) to quantify atomic-level empty space and UnionPocket to unify multiple protein pockets, providing a global view of binding sites. Additionally, LigoSpace employs a pairwise loss instead of commonly used MSE loss, to better capture relative relationships critical for drug discovery. Extensive experiments on multiple datasets with diverse bioactivity types demonstrate that LigoSpace significantly improves performance when integrated into state-of-the-art models, highlighting the effectiveness of its novel components. Equal contribution, may cite either first.


HCRMP: ALLM-Hinted Contextual Reinforcement Learning Framework for Autonomous Driving

Neural Information Processing Systems

Integrating the understanding and reasoning capabilities of Large Language Models (LLM) with the self-learning capabilities of Reinforcement Learning (RL) enables more reliable driving performance under complex driving conditions. There has been a lot of work exploring LLM-Dominated RL methods in the field of autonomous driving motion planning. These methods, which utilize LLM to directly generate policies or provide decisive instructions during policy learning of RL agent, are centrally characterized by an over-reliance on LLM outputs. However, LLM outputs are susceptible to hallucinations. Evaluations show that state-of-theart LLM indicates a non-hallucination rate of only approximately 57.95% when assessed on essential driving-related tasks. Thus, in these methods, hallucinations from the LLM can directly jeopardize the performance of driving policies.


Absolute Zero: Reinforced Self-play Reasoning with Zero Data

Neural Information Processing Systems

Reinforcement learning with verifiable rewards (RLVR) has shown promise in enhancing the reasoning capabilities of large language models by learning directly from rule-based outcome rewards. Recent RLVR works that operate under the zero setting avoid supervision in labeling the reasoning process, but still depend on manually curated collections of questions and answers for training. The scarcity of high-quality, human-produced examples raises concerns about the long-term scalability of relying on human supervision, a challenge already evident in the domain of language model pretraining. Furthermore, in a hypothetical future where AI surpasses human intelligence, tasks provided by humans may offer limited learning potential for a superintelligent system. To address these concerns, we propose a new RLVR paradigm called Absolute Zero, in which a single model learns to propose tasks that maximize its own learning progress and improves reasoning by solving them, without relying on any external human or distillation data. Under this paradigm, we introduce the Absolute Zero Reasoner (AZR), a system that self-evolves its training curriculum and reasoning ability. AZR uses a code executor to both validate self-proposed code reasoning tasks and verify answers, serving as an unified source of verifiable feedback to guide open-ended yet grounded learning. Despite being trained entirely without external data, AZR achieves overall SOTA performance on coding and mathematical reasoning tasks, outperforming existing zero-setting models that rely on tens of thousands of in-domain human-curated examples. Furthermore, we demonstrate that AZR can be effectively applied across different model scales and is compatible with various model classes.


SciArena: An Open Evaluation Platform for Non-Verifiable Scientific Literature-Grounded Tasks

Neural Information Processing Systems

Unlike traditional benchmarks for scientific literature understanding and synthesis, SciArena engages the research community directly, following the Chatbot Arena evaluation approach of community voting on model comparisons. By leveraging collective intelligence, SciArena offers a community-driven evaluation of model performance on open-ended scientific tasks that demand literature-grounded, long-form responses. The platform currently supports 47 foundation models and has collected over 20,000 votes from human researchers across diverse scientific domains. Our analysis of the data collected so far confirms its high quality. We discuss the results and insights based on the model ranking leaderboard. To further promote research in building modelbased automated evaluation systems for literature tasks, we release SciArena-Eval, a meta-evaluation benchmark based on collected preference data. It measures the accuracy of models in judging answer quality by comparing their pairwise assessments with human votes. Our experiments highlight the benchmark's challenges and emphasize the need for more reliable automated evaluation methods.


EDELINE: Enhancing Memory in Diffusion-based World Models via Linear-Time Sequence Modeling

Neural Information Processing Systems

World models represent a promising approach for training reinforcement learning agents with significantly improved sample efficiency. While most world model methods primarily rely on sequences of discrete latent variables to model environment dynamics, this compression often neglects critical visual details essential for reinforcement learning. Recent diffusion-based world models condition generation on a fixed context length of frames to predict the next observation, using separate recurrent neural networks to model rewards and termination signals. Although this architecture effectively enhances visual fidelity, the fixed context length approach inherently limits memory capacity. In this paper, we introduce EDELINE, a unified world model architecture that integrates state space models with diffusion models. Our approach outperforms existing baselines across visually challenging Atari 100k tasks, memory-demanding Crafter benchmark, and 3D first-person ViZDoom environments, demonstrating superior performance in all these diverse challenges.


ToolRL: Reward is All Tool Learning Needs

Neural Information Processing Systems

Current Large Language Models (LLMs) often undergo supervised fine-tuning (SFT) to acquire tool use capabilities. However, SFT struggles to generalize to unfamiliar or complex tool use scenarios. Recent advancements in reinforcement learning (RL), particularly with R1-like models, have demonstrated promising reasoning and generalization abilities. Yet, reward design for tool use presents unique challenges: multiple tools may be invoked with diverse parameters, and coarse-grained reward signals, such as answer matching, fail to offer the finegrained feedback required for effective learning. In this work, we present the first comprehensive study on reward design for tool selection and application tasks within the RL paradigm. We systematically explore a wide range of reward strategies, analyzing their types, scales, granularity, and temporal dynamics. Building on these insights, we propose a principled reward design tailored for tool use tasks and apply it to train LLMs using RL methods. Empirical evaluations across diverse benchmarks demonstrate that our approach yields robust, scalable, and stable training, achieving a 17% improvement over base models and a 15% gain over SFT models.


Vicinal Label Supervision for Reliable Aleatoric and Epistemic Uncertainty Estimation

Neural Information Processing Systems

Uncertainty estimation is crucial for ensuring the reliability of machine learning models in safety-critical applications. Evidential Deep Learning (EDL) offers a principled framework by modeling predictive uncertainty through Dirichlet distributions over class probabilities. However, existing EDL methods predominantly rely on level-0 hard labels, which supervise an uncertainty-aware model with full certainty. We argue that hard labels not only fail to capture epistemic uncertainty but also obscure the aleatoric uncertainty arising from inherent data noise and label ambiguity. As a result, EDL models often produce degenerate Dirichlet distributions that collapse to near-deterministic outputs. To overcome these limitations, we propose a vicinal risk minimization paradigm for EDL by incorporating level-1 supervision in the form of vicinally smoothed conditional label distributions.


Analog In-memory Training on General Non-ideal Resistive Elements: The Impact of Response Functions

Neural Information Processing Systems

As the economic and environmental costs of training and deploying large vision or language models increase dramatically, analog in-memory computing (AIMC) emerges as a promising energy-efficient solution. However, the training perspective, especially its training dynamics, is underexplored. In AIMC hardware, the trainable weights are represented by the conductance of resistive elements and updated using consecutive electrical pulses. While the conductance changes by a constant in response to each pulse, in reality, the change is scaled by asymmetric and non-linear response functions, leading to a non-ideal training dynamics. This paper provides a theoretical foundation for gradient-based training on AIMC hardware with nonideal response functions.


Measuring and Controlling Solution Degeneracy across Task-Trained Recurrent Neural Networks

Neural Information Processing Systems

Task-trained recurrent neural networks (RNNs) are widely used in neuroscience and machine learning to model dynamical computations. To gain mechanistic insight into how neural systems solve tasks, prior work often reverse-engineers individual trained networks. However, different RNNs trained on the same task and achieving similar performance can exhibit strikingly different internal solutions, a phenomenon known as solution degeneracy. Here, we develop a unified framework to systematically quantify and control solution degeneracy across three levels: behavior, neural dynamics, and weight space. We apply this framework to 3,400 RNNs trained on four neuroscience-relevant tasks: flip-flop memory, sine wave generation, delayed discrimination, and path integration, while systematically varying task complexity, learning regime, network size, and regularization. We find that higher task complexity and stronger feature learning reduce degeneracy in neural dynamics but increase it in weight space, with mixed effects on behavior. In contrast, larger networks and structural regularization reduce degeneracy at all three levels. These findings empirically validate the Contravariance Principle and provide practical guidance for researchers seeking to tune the variability of RNN solutions, either to uncover shared neural mechanisms or to model the individual variability observed in biological systems. This work provides a principled framework for quantifying and controlling solution degeneracy in task-trained RNNs, offering new tools for building more interpretable and biologically grounded models of neural computation.


LaViDa: ALarge Diffusion Language Model for Multimodal Understanding

Neural Information Processing Systems

Modern Vision-Language Models (VLMs) can solve a wide range of tasks requiring visual reasoning. In real-world scenarios, desirable properties for VLMs include fast inference and controllable generation (e.g., constraining outputs to adhere to a desired format).