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Identifying interactions across brain areas while accounting for individual-neuron dynamics with a Transformer-based variational autoencoder

Neural Information Processing Systems

Advances in large-scale recording technologies now enable simultaneous measurements from multiple brain areas, offering new opportunities to study signal transmission across interacting components of neural circuits. However, neural responses exhibit substantial trial-to-trial variability, often driven by unobserved factors such as subtle changes in animal behavior or internal states. To prevent evolving background dynamics from contaminating identification of functional coupling, we developed a hybrid neural spike train model, GLM-Transformer, that incorporates flexible, deep latent variable models into a point process generalized linear model (GLM) having an interpretable component for cross-population interactions. ATransformer-based variational autoencoder captures nonstationary individual-neuron dynamics that vary across trials, while standard nonparametric regression GLM coupling terms provide estimates of directed interactions between neural populations. We incorporate a low-rank structure on population-topopulation coupling effects to improve scalability. Across synthetic datasets and mechanistic simulations, GLM-Transformer recovers known coupling structure and remains robust to shared background fluctuations. When applied to the Allen Institute Visual Coding dataset, it identifies feedforward pathways consistent with established visual hierarchy. This work offers a step toward improved identification of neural population interactions, and contributes to ongoing efforts aimed at achieving interpretable results while harvesting the benefits of deep learning.


Training R&DAnalysis Backtest ModelFinancial ModelMarket

Neural Information Processing Systems

Financial markets pose fundamental challenges for asset return prediction due to their high dimensionality, non-stationarity, and persistent volatility. Despite advances in large language models and multi-agent systems, current quantitative research pipelines suffer from limited automation, weak interpretability, and fragmented coordination across key components such as factor mining and model innovation. In this paper, we propose R&D-Agent for Quantitative Finance, in short R&D-Agent(Q), the first data-centric multi-agent framework designed to automate the full-stack research and development of quantitative strategies via coordinated factor-model co-optimization. R&D-Agent(Q)decomposes the quant process into two iterative stages: a Research stage that dynamically sets goal-aligned prompts, formulates hypotheses based on domain priors, and maps them to concrete tasks, and a Development stage that employs a code-generation agent, Co-STEER, to implement task-specific code, which is then executed in real-market backtests. The two stages are connected through a feedback stage that thoroughly evaluates experimental outcomes and informs subsequent iterations, with a multi-armed bandit scheduler for adaptive direction selection. Empirically, R&D-Agent(Q) achieves up to 2 higher annualized returns than classical factor libraries using 70% fewer factors, and outperforms state-of-the-art deep time-series models on real markets. Its joint factor-model optimization delivers a strong balance between predictive accuracy and strategy robustness.


Magical: Medical Lay Language Generation via Semantic Invariance and Layperson-tailored Adaptation

Neural Information Processing Systems

Medical Lay Language Generation (MLLG) plays a vital role in improving the accessibility of complex scientific content for broader audiences. Recent literature to MLLG commonly employ parameter-efficient fine-tuning methods such as LowRank Adaptation (LoRA) to fine-tuning large language models (LLMs) using paired expert-lay language datasets. However, LoRA struggles with the challenges posed by multi-source heterogeneous MLLG datasets. Specifically, through a series of exploratory experiments, we reveal that standard LoRA fail to meet the requirement for semantic fidelity and diverse lay-style generation in MLLG task. To address these limitations, we propose Magical, an asymmetric LoRA architecture tailored for MLLG under heterogeneous data scenarios. Magical employs a shared matrix Afor abstractive summarization, along with multiple isolated matrices B for diverse lay-style generation. To preserve semantic fidelity during the lay language generation process, Magical introduces a Semantic Invariance Constraint to mitigate semantic subspace shifts on matrix A. Furthermore, to better adapt to diverse lay-style generation, Magical incorporates the Recommendation-guided Switch, an externally interface to prompt the LLM to switch between different matrices B. Experimental results on three real-world lay language generation datasets demonstrate that Magical consistently outperforms prompt-based methods, vanilla LoRA, and its recent variants, while also reducing trainable parameters by 31.66%.


BrainODE: Neural Shape Dynamics for Age-and Disease-aware Brain Trajectories

Neural Information Processing Systems

BrainODElearns a deformation space over anatomically meaningful brain regions to facilitate early prediction of neurodegenerative disease progression. Addressing inherent challenges of longitudinal neuroimaging data--such as limited sample sizes, irregular temporal sampling, and substantial inter-subject variability--we propose a conditional neural ODE architecture that models shape dynamics with subject-specific age and cognitive status. To enable autoregressive forecasting of brain morphology from a single observation, we propose a pseudo-cognitive status embedding that allows progressive shape prediction across intermediate time points with predicted cognitive decline. Experiments show that BrainODE outperforms time-aware baselines in predicting future brain shapes, demonstrating strong generalization across longitudinal datasets with both regular and irregular time intervals.


MLR-Bench: Evaluating AIAgents on Open-Ended Machine Learning Research Hui Chen Miao Xiong Yujie Lu Wei Han Ailin Deng Yufei He Jiaying Wu Yibo Li

Neural Information Processing Systems

Recent advancements in AI agents have demonstrated their growing potential to drive and support scientific discovery. In this work, we introduce MLR-Bench, a comprehensive benchmark for evaluating AI agents on open-ended machine learning research. MLR-Bench includes three key components: (1) 201 research tasks sourced from NeurIPS, ICLR, and ICML workshops covering diverse ML topics; (2) MLR-Judge, an automated evaluation framework combining LLMbased reviewers with carefully designed review rubrics to assess research quality; and (3) MLR-Agent, a modular agent scaffold capable of completing research tasks through four stages: idea generation, proposal formulation, experimentation, and paper writing. Our framework supports both stepwise assessment across these distinct research stages, and end-to-end evaluation of the final research paper. We then use MLR-Bench to evaluate six frontier LLMs and an advanced coding agent, finding that while LLMs are effective at generating coherent ideas and well-structured papers, current coding agents frequently (e.g., in 80% of the cases) produce fabricated or invalidated experimental results--posing a major barrier to scientific reliability.


The Atlas of In-Context Learning: How Attention Heads Shape In-Context Retrieval Augmentation

Neural Information Processing Systems

Large language models are able to exploit in-context learning to access external knowledge beyond their training data through retrieval-augmentation. While promising, its inner workings remain unclear. In this work, we shed light on the mechanism of in-context retrieval augmentation for question answering by viewing a prompt as a composition of informational components. We propose an attributionbased method to identify specialized attention heads, revealing in-context heads that comprehend instructions and retrieve relevant contextual information, and parametric heads that store entities' relational knowledge. To better understand their roles, we extract function vectors and modify their attention weights to show how they can influence the answer generation process. Finally, we leverage the gained insights to trace the sources of knowledge used during inference, paving the way towards more safe and transparent language models.



Antidistillation Sampling

Neural Information Processing Systems

Frontier models that generate extended reasoning traces inadvertently produce token sequences that can facilitate model distillation. Recognizing this vulnerability, model owners may seek sampling strategies that limit the effectiveness of distillation without compromising model performance. Antidistillation sampling provides exactly this capability.


Learning to Reason under Off-Policy Guidance

Neural Information Processing Systems

Recent advances in large reasoning models (LRMs) demonstrate that sophisticated behaviors such as multi-step reasoning and self-reflection can emerge via reinforcement learning with verifiable rewards (RLVR). However, existing RLVR approaches are inherently "on-policy", limiting learning to a model's own outputs and failing to acquire reasoning abilities beyond its initial capabilities. To address this issue, we introduce LUFFY (Learning to reason Under oFF-policY guidance), a framework that augments RLVR with off-policy reasoning traces. LUFFY dynamically balances imitation and exploration by combining off-policy demonstrations with on-policy rollouts during training. Specifically, LUFFY combines the MixedPolicy GRPO framework, which has a theoretically guaranteed convergence rate, alongside policy shaping via regularized importance sampling to avoid superficial and rigid imitation during mixed-policy training. Compared with previous RLVR methods, LUFFY achieves an over +6.4 average gain across six math benchmarks and an advantage of over +6.2 points in out-of-distribution tasks. Most significantly, we show that LUFFY successfully trains weak models in scenarios where on-policy RLVR completely fails. These results provide compelling evidence that LUFFY transcends the fundamental limitations of on-policy RLVR and demonstrates the great potential of utilizing off-policy guidance in RLVR.


Pairwise Optimal Transports for Training All-to-All Flow-Based Condition Transfer Model

Neural Information Processing Systems

In this paper, we propose a flow-based method for learning all-to-all transfer maps among conditional distributions that approximates pairwise optimal transport. The proposed method addresses the challenge of handling the case of continuous conditions, which often involve a large set of conditions with sparse empirical observations per condition. We introduce a novel cost function that enables simultaneous learning of optimal transports for all pairs of conditional distributions. Our method is supported by a theoretical guarantee that, in the limit, it converges to the pairwise optimal transports among infinite pairs of conditional distributions. The learned transport maps are subsequently used to couple data points in conditional flow matching. We demonstrate the effectiveness of this method on synthetic and benchmark datasets, as well as on chemical datasets in which continuous physical properties are defined as conditions.