OpenRaiser/Intern-Atlas huggingface dataset:
Improving the Generation and Evaluation of Synthetic Data for Downstream Medical Causal Inference
Venue: Conference NeurIPS 2025
Year: 2025

Causal inference is essential for developing and evaluating medical interventions, yet real-world medical datasets are often difficult to access due to regulatory barriers. This makes synthetic data a potentially valuable asset that enables these medical analyses, along with the development of new inference methods themselves. Generative models can produce synthetic data that closely approximate real data distributions, yet existing methods do not consider the unique challenges that downstream causal inference tasks, and specifically those focused on treatments, pose. We establish a set of desiderata that synthetic data containing treatments should satisfy to maximise downstream utility: preservation of (i) the covariate distribution, (ii) the treatment assignment mechanism, and (iii) the outcome generation mechanism. Based on these desiderata, we propose a set of evaluation metrics to assess such synthetic data. Finally, we present STEAM: a novel method for generating Synthetic data for Treatment Effect Analysis in Medicine that mimics the data-generating process of data containing treatments and optimises for our desiderata. We empirically demonstrate that STEAM achieves state-of-the-art performance across our metrics as compared to existing generative models, particularly as the complexity of the true data-generating process increases.
Enhancing Tactile-based Reinforcement Learning for Robotic Control
Venue: Conference NeurIPS 2025
Year: 2025

Achieving safe, reliable real-world robotic manipulation requires agents to evolve beyond vision and incorporate tactile sensing to overcome sensory deficits and reliance on idealised state information. Despite its potential, the efficacy of tactile sensing in reinforcement learning (RL) remains inconsistent. We address this by developing self-supervised learning (SSL) methodologies to more effectively harness tactile observations, focusing on a scalable setup of proprioception and sparse binary contacts. We empirically demonstrate that sparse binary tactile signals are critical for dexterity, particularly for interactions that proprioceptive control errors do not register, such as decoupled robot-object motions. Our agents achieve superhuman dexterity in complex contact tasks (ball bouncing and Baoding ball rotation). Furthermore, we find that decoupling the SSL memory from the on-policy memory can improve performance. We release the Robot Tactile Olympiad (RoTO) benchmark to standardise and promote future research in tactile-based manipulation. Project page: https://elle-miller.github.io/tactile_rl
Gene Regulatory Network Inference in the Presence of Selection Bias and Latent Confounders
Venue: Conference NeurIPS 2025
Year: 2025

Gene regulatory network inference (GRNI) aims to discover how genes causally regulate each other from gene expression data. It is well-known that statistical dependencies in observed data do not necessarily imply causation, as spurious dependencies may arise from latent confounders, such as non-coding RNAs. Numerous GRNI methods have thus been proposed to address this confounding issue. However, dependencies may also result from selection--only cells satisfying certain survival or inclusion criteria are observed--while these selection-induced spurious dependencies are frequently overlooked in gene expression data analyses. In this work, we show that such selection is ubiquitous and, when ignored or conflated with true regulations, can lead to flawed causal interpretation and misguided intervention recommendations. To address this challenge, a fundamental question arises: can we distinguish dependencies due to regulation, confounding, and crucially, selection? We show that gene perturbations offer a simple yet effective answer: selection-induced dependencies are symmetric under perturbation, while those from regulation or confounding are not. Building on this motivation, we propose GISL (Gene regulatory network Inference in the presence of Selection bias and Latent confounders), a principled algorithm that leverages perturbation data to uncover both true gene regulatory relations and non-regulatory mechanisms of selection and confounding up to the equivalence class. Experiments on synthetic and real-world gene expression data demonstrate the effectiveness of our method.
Heterogeneous Swarms: Jointly Optimizing Model Roles and Weights for Multi-LLM Systems
Venue: Conference NeurIPS 2025
Year: 2025

We propose Heterogeneous Swarms, an algorithm to design multi-LLM systems by jointly optimizing model roles and weights. We represent multi-LLM systems as directed acyclic graphs (DAGs) of LLMs with topological message passing for collaborative generation. Given a pool of LLM experts and a utility function, Heterogeneous Swarms employs two iterative steps: role-step and weight-step. For role-step, we interpret model roles as learning a DAG that specifies the flow of inputs and outputs between LLMs. Starting from a swarm of random continuous adjacency matrices, we decode them into discrete DAGs, call the LLMs in topological order, evaluate on the utility function (e.g. accuracy on a task), and optimize the adjacency matrices with particle swarm optimization based on the utility score. For weight-step, we assess the contribution of individual LLMs in the multi-LLM systems and optimize model weights with swarm intelligence. We propose JFK-score to quantify the individual contribution of each LLM in the best-found DAG of the role-step, then optimize model weights with particle swarm optimization based on the JFK-score. Experiments demonstrate that Heterogeneous Swarms outperforms 15 role- and/or weight-based baselines by 18.5% on average across 12 tasks. Further analysis reveals that Heterogeneous Swarms discovers multi-LLM systems with heterogeneous model roles and substantial collaborative gains, and benefits from the diversity of language models.
Hankel Singular Value Regularization for Highly Compressible State Space Models
Venue: Conference NeurIPS 2025
Year: 2025

Deep neural networks using state space models as layers are well suited for long-range sequence tasks but can be challenging to compress after training. We use that regularizing the sum of Hankel singular values of state space models leads to a fast decay of these singular values and thus to compressible models. To make the proposed Hankel singular value regularization scalable, we develop an algorithm to efficiently compute the Hankel singular values during training iterations by exploiting the specific block-diagonal structure of the system matrices that we use in our state space model parametrization. Experiments on Long Range Arena benchmarks demonstrate that the regularized state space layers are up to 10$\times$ more compressible than standard state space layers while maintaining high accuracy.
Calibrating Translation Decoding with Quality Estimation on LLMs
Venue: Conference NeurIPS 2025
Year: 2025

Neural machine translation (NMT) systems typically employ maximum a posteriori (MAP) decoding to select the highest-scoring translation from the distribution mass. However, recent evidence highlights the inadequacy of MAP decoding, often resulting in low-quality or even pathological hypotheses -- the decoding objective is not aligned with real-world translation quality. This paper proposes calibrating hypothesis likelihoods with translation quality from a distribution view by directly optimizing their Pearson correlation -- thereby enhancing the effectiveness of translation decoding. With our method, translation on large language models (LLMs) improves substantially after limited training (2K instances per direction). This improvement is orthogonal to those achieved through supervised fine-tuning, leading to substantial gains across a broad range of metrics and human evaluations -- even when applied to top-performing translation-specialized LLMs fine-tuned on high-quality translation data, such as Tower, or when compared to recent preference optimization methods, like CPO. Moreover, the calibrated translation likelihood can directly serve as a strong proxy for translation quality, closely approximating or even surpassing some state-of-the-art translation quality estimation models, like CometKiwi. Lastly, our in-depth analysis demonstrates that calibration enhances the effectiveness of MAP decoding, thereby enabling greater efficiency in real-world deployment. The resulting state-of-the-art translation model, which covers 10 languages, along with the accompanying code and human evaluation data, has been released to the community: https://github.com/moore3930/calibrating-llm-mt.
Structure-Aware Fusion with Progressive Injection for Multimodal Molecular Representation Learning
Venue: Conference NeurIPS 2025
Year: 2025

Multimodal molecular models often suffer from 3D conformer unreliability and modality collapse, limiting their robustness and generalization. We propose MuMo, a structured multimodal fusion framework that addresses these challenges in molecular representation through two key strategies. To reduce the instability of conformer-dependent fusion, we design a Structured Fusion Pipeline (SFP) that combines 2D topology and 3D geometry into a unified and stable structural prior. To mitigate modality collapse caused by naive fusion, we introduce a Progressive Injection (PI) mechanism that asymmetrically integrates this prior into the sequence stream, preserving modality-specific modeling while enabling cross-modal enrichment. Built on a state space backbone, MuMo supports long-range dependency modeling and robust information propagation. Across 29 benchmark tasks from Therapeutics Data Commons (TDC) and MoleculeNet, MuMo achieves an average improvement of 2.7% over the best-performing baseline on each task, ranking first on 22 of them, including a 27% improvement on the LD50 task. These results validate its robustness to 3D conformer noise and the effectiveness of multimodal fusion in molecular representation. The code is available at: github.com/selmiss/MuMo.
Sound Logical Explanations for Mean Aggregation Graph Neural Networks
Venue: Conference NeurIPS 2025
Year: 2025

Graph neural networks (GNNs) are frequently used for knowledge graph completion. Their black-box nature has motivated work that uses sound logical rules to explain predictions and characterise their expressivity. However, despite the prevalence of GNNs that use mean as an aggregation function, explainability and expressivity results are lacking for them. We consider GNNs with mean aggregation and non-negative weights (MAGNNs), proving the precise class of monotonic rules that can be sound for them, as well as providing a restricted fragment of first-order logic to explain any MAGNN prediction. Our experiments show that restricting mean-aggregation GNNs to have non-negative weights yields comparable or improved performance on standard inductive benchmarks, that sound rules are obtained in practice, that insightful explanations can be generated in practice, and that the sound rules can expose issues in the trained models.
Better Tokens for Better 3D: Advancing Vision-Language Modeling in 3D Medical Imaging
Venue: Conference NeurIPS 2025
Year: 2025

Recent progress in vision-language modeling for 3D medical imaging has been fueled by large-scale computed tomography (CT) corpora with paired free-text reports, stronger architectures, and powerful pretrained models. This has enabled applications such as automated report generation and text-conditioned 3D image synthesis. Yet, current approaches struggle with high-resolution, long-sequence volumes: contrastive pretraining often yields vision encoders that are misaligned with clinical language, and slice-wise tokenization blurs fine anatomy, reducing diagnostic performance on downstream tasks. We introduce BTB3D (Better Tokens for Better 3D), a causal convolutional encoder-decoder that unifies 2D and 3D training and inference while producing compact, frequency-aware volumetric tokens. A three-stage training curriculum enables (i) local reconstruction, (ii) overlapping-window tiling, and (iii) long-context decoder refinement, during which the model learns from short slice excerpts yet generalizes to scans exceeding 300 slices without additional memory overhead. BTB3D sets a new state-of-the-art on two key tasks: it improves BLEU scores and increases clinical F1 by 40% over CT2Rep, CT-CHAT, and Merlin for report generation; and it reduces FID by 75% and halves FVD compared to GenerateCT and MedSyn for text-to-CT synthesis, producing anatomically consistent 512*512*241 volumes. These results confirm that precise three-dimensional tokenization, rather than larger language backbones alone, is essential for scalable vision-language modeling in 3D medical imaging. The codebase is available at: https://github.com/ibrahimethemhamamci/BTB3D
QSVD: Efficient Low-rank Approximation for Unified Query-Key-Value Weight Compression in Low-Precision Vision-Language Models
Venue: Conference NeurIPS 2025
Year: 2025

Vision-Language Models (VLMs) are integral to tasks such as image captioning and visual question answering, but their high computational cost, driven by large memory footprints and processing time, limits their scalability and real-time applicability. In this work, we propose leveraging Singular-Value Decomposition (SVD) over the joint query (Q), key (K), and value (V) weight matrices to reduce KV cache size and computational overhead. We in addition introduce an efficient rank allocation strategy that dynamically adjusts the SVD rank based on its impact on VLM accuracy, achieving a significant reduction in both memory usage and computational cost. Finally, we extend this approach by applying quantization to both VLM weights and activations, resulting in a highly efficient VLM. Our method outperforms previous approaches that rely solely on quantization or SVD by achieving more than $10\%$ accuracy improvement while consuming less hardware cost, making it better for real-time deployment on resource-constrained devices. We open source our code at \href{https://github.com/SAI-Lab-NYU/QSVD}{\texttt{https://github.com/SAI-Lab-NYU/QSVD}}.
Caption This, Reason That: VLMs Caught in the Middle
Venue: Conference NeurIPS 2025
Year: 2025

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. category identification), a significant gap persists, particularly in tasks requiring spatial understanding or selective attention. Investigating the source of these failures and potential methods for improvement, we employ a vision-text decoupling analysis, finding that models struggling with direct visual reasoning show marked improvement when reasoning over their own generated text captions. These experiments reveal a strong need for improved VLM Chain-of-Thought (CoT) abilities, even in models that consistently exceed human performance. Furthermore, we demonstrate the potential of targeted fine-tuning on composite visual reasoning tasks and show that fine-tuning smaller VLMs substantially improves core cognitive abilities. While this improvement does not translate to large enhancements on challenging, out-of-distribution benchmarks, we show broadly that VLM performance on our datasets strongly correlates with performance on these other benchmarks. Our work provides a detailed analysis of VLM cognitive strengths and weaknesses and identifies key bottlenecks in simultaneous perception and reasoning while also providing an effective and simple solution.
3D Gaussian Flats: Hybrid 2D/3D Photometric Scene Reconstruction
Venue: Conference NeurIPS 2025
Year: 2025

Recent advances in radiance fields and novel view synthesis enable creation of realistic digital twins from photographs. However, current methods struggle with flat, texture-less surfaces, creating uneven and semi-transparent reconstructions, due to an ill-conditioned photometric reconstruction objective. Surface reconstruction methods solve this issue but sacrifice visual quality. We propose a novel hybrid 2D/3D representation that jointly optimizes constrained planar (2D) Gaussians for modeling flat surfaces and freeform (3D) Gaussians for the rest of the scene. Our end-to-end approach dynamically detects and refines planar regions, improving both visual fidelity and geometric accuracy. It achieves state-of-the-art depth estimation on ScanNet++ and ScanNetv2, and excels at mesh extraction without overfitting to a specific camera model, showing its effectiveness in producing high-quality reconstruction of indoor scenes.
INC: An Indirect Neural Corrector for Auto-Regressive Hybrid PDE Solvers
Venue: Conference NeurIPS 2025
Year: 2025

When simulating partial differential equations, hybrid solvers combine coarse numerical solvers with learned correctors. They promise accelerated simulations while adhering to physical constraints. However, as shown in our theoretical framework, directly applying learned corrections to solver outputs leads to significant autoregressive errors, which originate from amplified perturbations that accumulate during long-term rollouts, especially in chaotic regimes. To overcome this, we propose the Indirect Neural Corrector ($\mathrm{INC}$), which integrates learned corrections into the governing equations rather than applying direct state updates. Our key insight is that $\mathrm{INC}$ reduces the error amplification on the order of $Δt^{-1} + L$, where $Δt$ is the timestep and $L$ the Lipschitz constant. At the same time, our framework poses no architectural requirements and integrates seamlessly with arbitrary neural networks and solvers. We test $\mathrm{INC}$ in extensive benchmarks, covering numerous differentiable solvers, neural backbones, and test cases ranging from a 1D chaotic system to 3D turbulence. $\mathrm{INC}$ improves the long-term trajectory performance ($R^2$) by up to 158.7%, stabilizes blowups under aggressive coarsening, and for complex 3D turbulence cases yields speed-ups of several orders of magnitude. $\mathrm{INC}$ thus enables stable, efficient PDE emulation with formal error reduction, paving the way for faster scientific and engineering simulations with reliable physics guarantees. Our source code is available at https://github.com/tum-pbs/INC
Efficient Multimodal Dataset Distillation via Generative Models
Venue: Conference NeurIPS 2025
Year: 2025

Dataset distillation aims to synthesize a small dataset from a large dataset, enabling the model trained on it to perform well on the original dataset. With the blooming of large language models and multimodal large language models, the importance of multimodal datasets, particularly image-text datasets, has grown significantly. However, existing multimodal dataset distillation methods are constrained by the Matching Training Trajectories algorithm, which significantly increases the computing resource requirement, and takes days to process the distillation. In this work, we introduce EDGE, a generative distillation method for efficient multimodal dataset distillation. Specifically, we identify two key challenges of distilling multimodal datasets with generative models: 1) The lack of correlation between generated images and captions. 2) The lack of diversity among generated samples. To address the aforementioned issues, we propose a novel generative model training workflow with a bi-directional contrastive loss and a diversity loss. Furthermore, we propose a caption synthesis strategy to further improve text-to-image retrieval performance by introducing more text information. Our method is evaluated on Flickr30K, COCO, and CC3M datasets, demonstrating superior performance and efficiency compared to existing approaches. Notably, our method achieves results 18x faster than the state-of-the-art method.
Random Search Neural Networks for Efficient and Expressive Graph Learning
Venue: Conference NeurIPS 2025
Year: 2025

Random walk neural networks (RWNNs) have emerged as a promising approach for graph representation learning, leveraging recent advances in sequence models to process random walks. However, under realistic sampling constraints, RWNNs often fail to capture global structure even in small graphs due to incomplete node and edge coverage, limiting their expressivity. To address this, we propose \textit{random search neural networks} (RSNNs), which operate on random searches, each of which guarantees full node coverage. Theoretically, we demonstrate that in sparse graphs, only $O(\log |V|)$ searches are needed to achieve full edge coverage, substantially reducing sampling complexity compared to the $O(|V|)$ walks required by RWNNs (assuming walk lengths scale with graph size). Furthermore, when paired with universal sequence models, RSNNs are universal approximators. We lastly show RSNNs are probabilistically invariant to graph isomorphisms, ensuring their expectation is an isomorphism-invariant graph function. Empirically, RSNNs consistently outperform RWNNs on molecular and protein benchmarks, achieving comparable or superior performance with up to 16$\times$ fewer sampled sequences. Our work bridges theoretical and practical advances in random walk based approaches, offering an efficient and expressive framework for learning on sparse graphs.
AutoVLA: A Vision-Language-Action Model for End-to-End Autonomous Driving with Adaptive Reasoning and Reinforcement Fine-Tuning
Venue: Conference NeurIPS 2025
Year: 2025

Recent advancements in Vision-Language-Action (VLA) models have shown promise for end-to-end autonomous driving by leveraging world knowledge and reasoning capabilities. However, current VLA models often struggle with physically infeasible action outputs, complex model structures, or unnecessarily long reasoning. In this paper, we propose AutoVLA, a novel VLA model that unifies reasoning and action generation within a single autoregressive generation model for end-to-end autonomous driving. AutoVLA performs semantic reasoning and trajectory planning directly from raw visual inputs and language instructions. We tokenize continuous trajectories into discrete, feasible actions, enabling direct integration into the language model. For training, we employ supervised fine-tuning to equip the model with dual thinking modes: fast thinking (trajectory-only) and slow thinking (enhanced with chain-of-thought reasoning). To further enhance planning performance and efficiency, we introduce a reinforcement fine-tuning method based on Group Relative Policy Optimization (GRPO), reducing unnecessary reasoning in straightforward scenarios. Extensive experiments across real-world and simulated datasets and benchmarks, including nuPlan, nuScenes, Waymo, and CARLA, demonstrate the competitive performance of AutoVLA in both open-loop and closed-loop settings. Qualitative results showcase the adaptive reasoning and accurate planning capabilities of AutoVLA in diverse scenarios.