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 Deep Learning


CausalDynamics: A large-scale benchmark for structural discovery of dynamical causal models

Neural Information Processing Systems

Causal discovery for dynamical systems poses a major challenge in fields where active interventions are infeasible. Most methods used to investigate these systems and their associated benchmarks are tailored to deterministic, low-dimensional and weakly nonlinear time-series data. To address these limitations, we present CausalDynamics, a large-scale benchmark and extensible data generation framework to advance the structural discovery of dynamical causal models. Our benchmark consists of true causal graphs derived from thousands of both linearly and nonlinearly coupled ordinary and stochastic differential equations as well as two idealized climate models. We perform a comprehensive evaluation of state-of-the-art causal discovery algorithms for graph reconstruction on systems with noisy, confounded, and lagged dynamics. CausalDynamics consists of a plug-and-play, build-yourown coupling workflow that enables the construction of a hierarchy of physical systems. We anticipate that our framework will facilitate the development of robust causal discovery algorithms that are broadly applicable across domains while addressing their unique challenges. We provide a user-friendly implementation and documentation on https://kausable.github.io/CausalDynamics.


SonoGym: High Performance Simulation for Challenging Surgical Tasks with Robotic Ultrasound

Neural Information Processing Systems

Ultrasound (US) is a widely used medical imaging modality due to its real-time capabilities, non-invasive nature, and cost-effectiveness. Robotic ultrasound can further enhance its utility by reducing operator dependence and improving access to complex anatomical regions. For this, while deep reinforcement learning (DRL) and imitation learning (IL) have shown potential for autonomous navigation, their use in complex surgical tasks such as anatomy reconstruction and surgical guidance remains limited -- largely due to the lack of realistic and efficient simulation environments tailored to these tasks. We introduce SonoGym, a scalable simulation platform for complex robotic ultrasound tasks that enables parallel simulation across tens to hundreds of environments. Our framework supports realistic and real-time simulation of US data from CT-derived 3D models of the anatomy through both a physics-based and a generative modeling approach.


MoME: Mixture of Matryoshka Experts for Audio-Visual Speech Recognition

Neural Information Processing Systems

Large language models (LLMs) have recently shown strong potential in audiovisual speech recognition (AVSR), but their high computational demands and sensitivity to token granularity limit their practicality in resource-constrained settings. Token compression methods can reduce inference cost, but they require fixing a compression rate in advance and produce a single fixed-length output, offering no flexibility to balance information density and efficiency at inference time. Matryoshka representation learning (MRL) addresses this by enabling a single model to operate across multiple token granularities, allowing compression rates to be adjusted dynamically. However, current MRL-based methods treat each scale independently during training, limiting cross-scale generalization, robustness at high compression, and interpretability. To overcome these limitations, we propose MoME (Mixture of Matryoshka Experts), a novel framework that integrates sparse Mixture-of-Experts (MoE) into MRL-based LLMs for AVSR. MoME augments a frozen LLM with top-k routed and shared experts, allowing dynamic capacity allocation across scales and modalities. A shared router promotes consistent expert activation across granularities, enabling compressed sequences to benefit from representations learned at lower compression. Experiments on LRS2 and LRS3 demonstrate that MoME achieves state-of-the-art performance across AVSR, ASR, and VSR tasks, while requiring significantly fewer parameters and maintaining robustness under noise.


Context-Aware Hierarchical Learning: ATwo-Step Paradigm towards Safer LLMs

Neural Information Processing Systems

Large Language Models (LLMs) have emerged as powerful tools for diverse applications. However, their uniform token processing paradigm introduces critical vulnerabilities in instruction handling, particularly when exposed to adversarial scenarios. In this work, we identify and propose a novel class of vulnerabilities, termed Tool-Completion Attack (TCA), which exploits function-calling mechanisms to subvert model behavior. To evaluate LLM robustness against such threats, we introduce the Tool-Completion benchmark, a comprehensive security assessment framework, which reveals that even state-of-the-art models remain susceptible to TCA, with surprisingly high attack success rates. To address these vulnerabilities, we introduce Context-Aware Hierarchical Learning (CAHL), a sophisticated mechanism that dynamically balances semantic comprehension with role-specific instruction constraints. CAHL leverages the contextual correlations between different instruction segments to establish a robust, context-aware instruction hierarchy. Extensive experiments demonstrate that CAHL significantly enhances LLM robustness against both conventional attacks and the proposed TCA, exhibiting strong generalization capabilities in zero-shot evaluations while still preserving model performance on generic tasks. Our code is available at https://github.com/S2AILab/CAHL.


PLEIADES: Building Temporal Kernels with Orthogonal Polynomials

Neural Information Processing Systems

We introduce a class of neural networks named PLEIADES (PoLynomial Expansion In Adaptive Distributed Event-based Systems), which contains temporal convolution kernels generated from orthogonal polynomial basis functions. We focus on interfacing these networks with event-based data to perform online spatiotemporal classification and detection with low latency. By virtue of using structured temporal kernels and event-based data, we have the freedom to vary the sample rate of the data along with the discretization step-size of the network without additional finetuning. We experimented with three event-based benchmarks and obtained state-of-the-art results on all three by large margins with significantly smaller memory and compute costs. We achieved: 1) 99.59% accuracy with 192K parameters on the DVS128 hand gesture recognition dataset and 100% with a small additional output filter; 2) 99.58% test accuracy with 277K parameters on the AIS 2024 eye tracking challenge; and 3) 0.556 mAP with 576k parameters on the PROPHESEE 1 Megapixel Automotive Detection Dataset.


Caption This, Reason That: VLMs Caught in the Middle

Neural Information Processing Systems

Vision-Language Models (VLMs) have shown remarkable progress in visual understanding in recent years. Yet, they still lag behind human capabilities in specific visual tasks such as counting or relational reasoning. To understand the underlying limitations, we adopt methodologies from cognitive science, analyzing VLM performance along core cognitive axes: Perception, Attention, and Memory. Using a suite of tasks targeting these abilities, we evaluate state-of-the-art VLMs, including GPT-4o. Our analysis reveals distinct cognitive profiles: while advanced models approach ceiling performance on some tasks (e.g.


Reinforcing Image Generation with Collaborative Semantic level and Token level CoT

Neural Information Processing Systems

Recent advancements in large language models have demonstrated how chain-ofthought (CoT) and reinforcement learning (RL) can improve performance. However, applying such reasoning strategies to the visual generation domain remains largely unexplored. In this paper, we present T2I-R1, a novel reasoning-enhanced text-to-image generation model, powered by RL with a bi-level CoT reasoning process. Specifically, we identify two levels of CoT that can be utilized to enhance different stages of generation: (1) the semantic-level CoT for high-level planning of the prompt and (2) the token-level CoT for low-level pixel processing during patch-by-patch generation. To better coordinate these two levels of CoT, we introduce BiCoT-GRPO with an ensemble of generation rewards, which seamlessly optimizes both generated CoTs within the same training step. By applying our reasoning strategies to the baseline model, Janus-Pro, we achieve superior performance with 13% improvement on T2I-CompBench and 19% improvement on the WISE benchmark, even surpassing the state-of-the-art model FLUX.1. All the training code and data are available at https://github.com/CaraJ7/T2I-R1.


Generalized and Invariant Single-Neuron In-Vivo Activity Representation Learning

Neural Information Processing Systems

In neuroscience, models that learn representations of single-neuron in-vivo activity are essential for understanding the functional identities of individual neurons. The primary goal of these models--spanning Transformer-based, contrastive, and variational autoencoder frameworks, is not to predict neural activity, but to distill it into a stable, low-dimensional embedding that captures a neuron's intrinsic features. These learned identity embeddings should be invariant to changing experimental conditions while reflecting the neuron's molecular type and anatomical location, thus enabling downstream tasks like in-vivo cell type prediction. However, current models suffer from limited generalizability due to batch effects: non-biological variations arising from differences in experimental design, animal subjects, or recording platforms. These batch effects cause overfitting, reducing model robustness and utility.


KnowMol: Advancing Molecular Large Language Models with Multi-Level Chemical Knowledge

Neural Information Processing Systems

Tthesehe challenges, we introduce cKnoarbwMol-100K,oxylate group and the polarizable sulfur atom, methylsulfanyl group attaalarchge-scaed tole tdatasethe sixwithth c100Karbofine-grainedn and molecular annotations Theacross polamriultiplety of the molecule is increased by the polar verum with data available.


Don't Just Chase " Highlighted Tokens " in MLLMs: Revisiting Visual Holistic Context Retention

Neural Information Processing Systems

Despite their powerful capabilities, Multimodal Large Language Models (MLLMs) suffer from considerable computational overhead due to their reliance on massive visual tokens. Recent studies have explored token pruning to alleviate this problem, which typically uses text-vision cross-attention or [CLS] attention to assess and discard redundant visual tokens. In this work, we identify a critical limitation of such attention-first pruning approaches, i.e., they tend to preserve semantically similar tokens, resulting in pronounced performance drops under high pruning ratios. To this end, we propose HoloV, a simple yet effective, plug-and-play visual token pruning framework for efficient inference.