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 Deep Learning


CRRL: Learning Channel-invariant Neural Representations for High-performance Cross-day Decoding

Neural Information Processing Systems

Brain-computer interfaces have shown great potential in motor and speech rehabilitation, but still suffer from low performance stability across days, mostly due to the instabilities in neural signals. These instabilities, partially caused by neuron deaths and electrode shifts, leading to channel-level variabilities among different recording days. Previous studies mostly focused on aligning multi-day neural signals onto a low-dimensional latent manifold to reduce the variabilities, while faced with difficulties when neural signals exhibit significant drift. Here, we propose to learn a channel-level invariant neural representation to address the variabilities in channels across days. It contains a channel-rearrangement module to learn stable representations against electrode shifts, and a channel reconstruction module to handle the missing neurons. The proposed method achieved the state-of-the-art performance with cross-day decoding tasks over two months, on multiple benchmark BCI datasets. The proposed approach showed good generalization ability that can be incorporated to different neural networks.


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Neural Information Processing Systems

Recent advances in diffusion models have dramatically improved image fidelity and diversity. However, aligning these models with nuanced human preferences -such as aesthetics, engagement, and subjective appeal remains a key challenge due to the scarcity of large-scale human annotations. Collecting such data is both expensive and limited in diversity. To address this, we leverage the reasoning capabilities of vision-language models (VLMs) and propose Self-Play Reward Optimization (SPRO), a scalable, annotation-free training framework based on multimodal self-play. SPRO learns to jointly align prompt and image generation with human preferences by iteratively generating, evaluating, and learning to refine outputs using synthetic reward signals such as aesthetics and human engagement.


eri

Neural Information Processing Systems

There is growing interest in using machine learning (ML) to support clinical diagnosis, but most approaches rely on static, fully observed datasets and fail to reflect the sequential, resource-aware reasoning clinicians use in practice. Diagnosis remains complex and error prone, especially in high-pressure or resource-limited settings, underscoring the need for frameworks that help clinicians make timely and cost-effective decisions. We propose ACTMED(Adaptive Clinical Test selection via Model-based Experimental Design), a diagnostic framework that integrates Bayesian Experimental Design (BED) with large language models (LLMs) to better emulate real-world diagnostic reasoning. At each step, ACTMED selects the test expected to yield the greatest reduction in diagnostic uncertainty for a given patient. LLMs act as flexible simulators, generating plausible patient state distributions and supporting belief updates without requiring structured, task-specific training data. Clinicians can remain in the loop; reviewing test suggestions, interpreting intermediate outputs, and applying clinical judgment throughout. We evaluate ACTMEDon real-world datasets and show it can optimize test selection to improve diagnostic accuracy, interpretability, and resource use. This represents a step toward transparent, adaptive, and clinician-aligned diagnostic systems that generalize across settings with reduced reliance on domain-specific data.


Turning the Tables: Enabling Backward Transfer via Causal-Aware LoRA in Continual Learning

Neural Information Processing Systems

Current parameter-efficient fine-tuning (PEFT) methods have shown superior performance in continual learning. However, most existing PEFT-based methods focus on mitigating catastrophic forgetting by limiting modifications to the old task model caused by new tasks. This hinders backward knowledge transfer, as when new tasks have a strong positive correlation with old tasks, appropriately training on new tasks can transfer beneficial knowledge to old tasks. Critically, achieving backward knowledge transfer faces two fundamental challenges: (1) some parameters may be ineffective on task performance, which constrains the task solution space and model capacity; (2) since old task data are inaccessible, modeling task correlation via shared data is infeasible. To address these challenges, we propose CaLoRA, a novel causal-aware low-rank adaptation framework that is the first PEFT-based continual learning work with backward knowledge transfer. Specifically, we first propose parameter-level counterfactual attribution (PaCA) that estimates the causal effect of LoRA parameters via counterfactual reasoning, identifying effective parameters from a causal view. Second, we propose cross-task gradient adaptation (CaGA) to quantify task correlation by gradient projection and evaluate task affinity based on gradient similarity. By incorporating causal effect, task correlation, and affinity, CaGA adaptively adjusts task gradients, facilitating backward knowledge transfer without relying on data replay. Extensive experiments across multiple benchmarks and continual learning settings show that CaLoRA outperforms stateof-the-art methods.


FIGRDock: Fast Interaction-Guided Regression for Flexible Docking

Neural Information Processing Systems

Flexible docking, which predicts the binding conformations of both proteins and small molecules by modeling their structural flexibility, plays a vital role in structure-based drug design. Although recent generative approaches, particularly diffusion-based models, have shown promising results, they require iterative sampling to generate candidate structures and depend on separate scoring functions for pose selection. This leads to an inefficient pipeline that is difficult to scale in real-world drug discovery workflows. To overcome these challenges, we introduce FIGRDock, a fast and accurate flexible docking framework that understands complicated interactions between molecules and proteins with a regression-based approach. FIGRDock leverages initial docking poses from conventional tools to distill interaction-aware distance patterns, which serve as explicit structural conditions to directly guide the prediction of the final protein-ligand complex via a regression model. This one-shot inference paradigm enables rapid and precise pose prediction without reliance on multi-step sampling or external scoring stages. Experimental results show that FIGRDock achieves up to 100 faster inference than diffusion-based docking methods, while consistently surpassing them in accuracy across standard benchmarks. These results suggest that FIGRDock has the potential to offer a scalable and efficient solution for flexible docking, advancing the pace of structure-based drug discovery.4


Knowledge Distillation of Uncertainty using Deep Latent Factor Model

Neural Information Processing Systems

Deep ensembles deliver state-of-the-art, reliable uncertainty quantification, but their heavy computational and memory requirements hinder their practical deployments to real applications such as on-device AI. Knowledge distillation compresses an ensemble into small student models, but existing techniques struggle to preserve uncertainty partly because reducing the size of DNNs typically results in variation reduction. To resolve this limitation, we introduce a new method of distribution distillation (i.e.


Bilevel Network Learning via Hierarchically Structured Sparsity

Neural Information Processing Systems

Accurate network estimation serves as the cornerstone for understanding complex systems across scientific domains, from decoding gene regulatory networks in systems biology to identifying social relationship patterns in computational sociology. Modern applications demand methods that simultaneously address two critical challenges: capturing nonlinear dependencies between variables and reconstructing inherent hierarchical structures where higher-level entities coordinate lower-level components (e.g., functional pathways organizing gene clusters). Traditional Gaussian graphical models fundamentally fail in these aspects due to their restrictive linear assumptions and flat network representations. We propose NNBLNet, a neural network-based learning framework for bi-level network inference. The core innovation lies in hierarchical selection layers that enforce structural consistency between high-level coordinator groups and their constituent low-level connections via adaptive sparsity constraints. This architecture is integrated with a compositional neural network architecture that learn cross-level association patterns through constrained nonlinear transformations, explicitly preserving hierarchical dependencies while overcoming the representational limitations of linear methods. Crucially, we establish formal theoretical guarantees for the consistent recovery of both high-level connections and their internal low-level structures under general statistical regimes. Extensive validation demonstrates NNBLNet's effectiveness across synthetic and real-world scenarios, achieving superior F1 scores compared to competitive methods and particularly beneficial for complex systems analysis through its interpretable bi-level structure discovery.


DualOptim: Enhancing Efficacy and Stability in Machine Unlearning with Dual Optimizers

Neural Information Processing Systems

In this work, we first empirically demonstrate the instability and suboptimal performance of existing popular MU methods when deployed in different scenarios. To address this issue, we propose Dual Optimizer (DualOptim), which incorporates adaptive learning rate and decoupled momentum factors. Empirical and theoretical evidence demonstrates that DualOptim contributes to effective and stable unlearning. Through extensive experiments, we show that DualOptim can significantly boost MU efficacy and stability across diverse tasks, including image classification, image generation, and large language models, making it a versatile approach to empower existing MU algorithms.


ReSearch: Learning to Reason with Search for LLMs via Reinforcement Learning

Neural Information Processing Systems

Large Language Models (LLMs) have shown remarkable capabilities in reasoning, exemplified by the success of OpenAI-o1 and DeepSeek-R1. However, integrating reasoning with external search processes remains challenging, especially for complex multi-hop questions requiring multiple retrieval steps. We propose ReSearch, a novel framework that trains LLMs to Reason with Search via reinforcement learning without using any supervised data on reasoning steps. Our approach treats search operations as integral components of the reasoning chain, where when and how to perform searches is guided by text-based thinking, and search results subsequently influence further reasoning. We train ReSearch on Qwen2.5-7B(-Instruct) and Qwen2.5-32B(-Instruct)


Generalizable Reasoning through Compositional Energy Minimization

Neural Information Processing Systems

Generalization is a key challenge in machine learning, specifically in reasoning tasks, where models are expected to solve problems more complex than those encountered during training. Existing approaches typically train reasoning models in an end-to-end fashion, directly mapping input instances to solutions. While this allows models to learn useful heuristics from data, it often results in limited generalization beyond the training distribution. In this work, we propose a novel approach to reasoning generalization by learning energy landscapes over the solution spaces of smaller, more tractable subproblems. At test time, we construct a global energy landscape for a given problem by combining the energy functions of multiple subproblems. This compositional approach enables the incorporation of additional constraints during inference, allowing the construction of energy landscapes for problems of increasing difficulty. To improve the sample quality from this newly constructed energy landscape, we introduce Parallel Energy Minimization (PEM). We evaluate our approach on a wide set of reasoning problems. Our method outperforms existing state-of-the-art methods, demonstrating its ability to generalize to larger and more complex problems.