GenAI4ELab/papercli-papers huggingface dataset:
Semantic and Visual Crop-Guided Diffusion Models for Heterogeneous Tissue Synthesis in Histopathology
Authors: Saghir Alfasly; Wataru Uegami; Md. Enamul Hoq; Ghazal Alabtah; Hamid Tizhoosh
Venue: NeurIPS 2025 (NeurIPS 2025 poster)

Abstract: Synthetic data generation in histopathology faces unique challenges: preserving tissue heterogeneity, capturing subtle morphological features, and scaling to unannotated datasets. We present a latent diffusion model that generates realistic heterogeneous histopathology images through a novel dual-conditioning approach combining semantic segmentation maps with tissue-specific visual crops. Unlike existing methods that rely on text prompts or abstract visual embeddings, our approach preserves critical morphological details by directly incorporating raw tissue crops from corresponding semantic regions. For annotated datasets (i.e., Camelyon16, Panda), we extract patches ensuring 20-80% tissue heterogeneity. For unannotated data (i.e., TCGA), we introduce a self-supervised extension that clusters whole-slide images into 100 tissue types using foundation model embeddings, automatically generating pseudo-semantic maps for training. Our method synthesizes high-fidelity images with precise region-wise annotations, achieving superior performance on downstream segmentation tasks. When evaluated on annotated datasets, models trained on our synthetic data show competitive performance to those trained on real data, demonstrating the utility of controlled heterogeneous tissue generation. In quantitative evaluation, prompt‐guided synthesis reduces Fréchet Distance by up to 6× on Camelyon16 (from 430.1 to 72.0) and yields 2–3× lower FD across Panda and TCGA. Downstream DeepLabv3+ models trained solely on synthetic data attain test IoU of 0.71 and 0.95 on Camelyon16 and Panda, within 1–2% of real‐data baselines (0.72 and 0.96). By scaling to 11,765 TCGA whole‐slide images without manual annotations, our framework offers a practical solution for an urgent need for generating diverse, annotated histopathology data, addressing a critical bottleneck in computational pathology.
Let Brain Rhythm Shape Machine Intelligence for Connecting Dots on Graphs
Authors: Jiaqi Ding; Tingting Dan; Zhixuan Zhou; Guorong Wu
Venue: NeurIPS 2025 (NeurIPS 2025 poster)

Abstract: In both neuroscience and artificial intelligence (AI), it is well-established that neural “coupling” gives rise to dynamically distributed systems. These systems exhibit self-organized spatiotemporal patterns of synchronized neural oscillations, enabling the representation of abstract concepts. By capitalizing on the unprecedented amount of human neuroimaging data, we propose that advancing the theoretical understanding of rhythmic coordination in neural circuits can offer powerful design principles for the next generation of machine learning models with improved efficiency and robustness. To this end, we introduce a physics-informed deep learning framework for \underline{B}rain \underline{R}hythm \underline{I}dentification by \underline{K}uramoto and \underline{C}ontrol (coined \textit{BRICK}) to characterize the synchronization of neural oscillations that shapes the dynamics of evolving cognitive states.  Recognizing that brain networks are structurally connected yet behaviorally dynamic, we further conceptualize rhythmic neural activity as an artificial dynamical system of coupled oscillators, offering a shared mechanistic bridge to brain-inspired machine intelligence. By treating each node as an oscillator interacting with its neighbors, this approach moves beyond the conventional paradigm of graph heat diffusion and establishes a new regime of representation compression through oscillatory synchronization. Empirical evaluations demonstrate that this synchronization-driven mechanism not only mitigates over-smoothing in deep GNNs but also enhances the model’s capacity for reasoning and solving complex graph-based problems.
Hybrid Autoencoders for Tabular Data: Leveraging Model-Based Augmentation in Low-Label Settings
Authors: Erel Naor; Ofir Lindenbaum
Venue: NeurIPS 2025 (NeurIPS 2025 poster)

Abstract: Deep neural networks often under-perform on tabular data due to their sensitivity to irrelevant features and a spectral bias toward smooth, low-frequency functions. These limitations hinder their ability to capture the sharp, high-frequency signals that often define tabular structure, especially under limited labeled samples. While self-supervised learning (SSL) offers promise in such settings, it remains challenging in tabular domains due to the lack of effective data augmentations. We propose a hybrid autoencoder that combines a neural encoder with an oblivious soft decision tree (OSDT) encoder, each guided by its own stochastic gating network that performs sample-specific feature selection. Together, these structurally different encoders and model-specific gating networks implement model-based augmentation, producing complementary input views tailored to each architecture. The two encoders, trained with a shared decoder and cross-reconstruction loss, learn distinct yet aligned representations that reflect their respective inductive biases. During training, the OSDT encoder (robust to noise and effective at modeling localized, high-frequency structure) guides the neural encoder toward representations more aligned with tabular data. At inference, only the neural encoder is used, preserving flexibility and SSL compatibility. Spectral analysis highlights the distinct inductive biases of each encoder. Our method achieves consistent gains in low-label classification and regression across diverse tabular datasets, outperforming deep and tree-based supervised baselines.
Purifying Approximate Differential Privacy with Randomized Post-processing
Authors: Yingyu Lin; Erchi Wang; Yian Ma; Yu-Xiang Wang
Venue: NeurIPS 2025 (NeurIPS 2025 spotlight)

Abstract: We propose a framework to convert $(\varepsilon, \delta)$-approximate Differential Privacy (DP) mechanisms into $(\varepsilon', 0)$-pure DP mechanisms under certain conditions, a process we call ``purification.'' This algorithmic technique leverages randomized post-processing with calibrated noise to eliminate the $\delta$ parameter while achieving near-optimal privacy-utility tradeoff for pure DP. It enables a new design strategy for pure DP algorithms: first run an approximate DP algorithm with certain conditions, and then purify. This approach allows one to leverage techniques such as strong composition and propose-test-release that require $\delta>0$ in designing pure-DP methods with $\delta=0$. We apply this framework in various settings, including Differentially Private Empirical Risk Minimization (DP-ERM), stability-based release, and query release tasks. To the best of our knowledge, this is the first work with a statistically and computationally efficient reduction from approximate DP to pure DP. Finally, we illustrate the use of this reduction for proving lower bounds under approximate DP constraints with explicit dependence in $\delta$, avoiding the sophisticated fingerprinting code construction.
Sketched Adaptive Distributed Deep Learning: A Sharp Convergence Analysis
Authors: Zhijie Chen; Qiaobo Li; Arindam Banerjee
Venue: NeurIPS 2025 (NeurIPS 2025 poster)

Abstract: Combining gradient compression with adaptive optimizers is a highly desirable goal in distributed learning, with potential benefits in both fewer communication rounds and less per-round communication. In spite of preliminary empirical promise, certain major challenges in the convergence analysis of such methods have stayed open: handling compression based approximation of both first and second moments (pre-conditioner) which appear as a ratio; avoiding dependence on the number of parameters, which is extremely large in modern deep models; and providing high-probability guarantees instead of in-expectation, which can hide high variance behavior.

In this work, we introduce a family of Sketched Adaptive Distributed Learning (SADL) algorithms which can use suitable unbiased gradient sketching for compression with suitable adaptive optimization algorithms. As our main contribution, we provide theoretical convergence guarantees of SADL algorithms which addresses all of the existing challenges. In particular, our guarantees hold with high probability, picks up only a logarithmic dependence on the number of parameters, and the first and second moment approximation is handled precisely yielding a dependence on the intrinsic dimension of the loss Hessian, which is significantly smaller than the full dimensionality of deep learning models.  Empirically, the SADL algorithms are shown to be competitive with and often outperform baselines on both vision and language tasks, in both supervised fine-tuning and training-from-scratch regimes. Further, the SADL algorithms are also competitive with the state-of-the-art communication-efficient distributed learning algorithms based on error feedback.
Greedy Sampling Is Provably Efficient For RLHF
Authors: Di Wu; Chengshuai Shi; Jing Yang; Cong Shen
Venue: NeurIPS 2025 (NeurIPS 2025 poster)

Abstract: Reinforcement Learning from Human Feedback (RLHF) has emerged as a key technique for post‑training large language models. Despite its empirical success, the theoretical understanding of RLHF is still limited, as learning the KL-regularized target with only preference feedback poses additional challenges compared with canonical RL.  Existing works mostly study the reward-based Bradley-Terry (BT) preference model, and extend classical designs utilizing optimism or pessimism. This work, instead, considers the general preference model (whose practical relevance has been observed recently) and obtains performance guarantees with major, order-wise improvements over existing ones. Surprisingly, these results are derived from algorithms that directly use empirical estimates (i.e., greedy sampling), as opposed to constructing optimistic or pessimistic estimates in previous works. This insight has a deep root in the unique structural property of the optimal policy class under the KL-regularized target, and we further specialize it to the BT model, highlighting the surprising sufficiency of greedy sampling in RLHF.
Learning Individual Behavior in Agent-Based Models with Graph Diffusion Networks
Authors: Francesco Cozzi; Marco Pangallo; Alan Perotti; André Panisson; Corrado Monti
Venue: NeurIPS 2025 (NeurIPS 2025 poster)

Abstract: Agent-Based Models (ABMs) are powerful tools for studying emergent properties in complex systems. In ABMs, agent behaviors are governed by local interactions and stochastic rules. However, these rules are ad hoc and, in general, non-differentiable, limiting the use of gradient-based methods for optimization, and thus integration with real-world data. We propose a novel framework to learn a differentiable surrogate of any ABM by observing its generated data. Our method combines diffusion models to capture behavioral stochasticity and graph neural networks to model agent interactions. Distinct from prior surrogate approaches, our method introduces a fundamental shift: rather than approximating system-level outputs, it models individual agent behavior directly, preserving the decentralized, bottom-up dynamics that define ABMs. We validate our approach on two ABMs (Schelling's segregation model and a Predator-Prey ecosystem) showing that it replicates individual-level patterns and accurately forecasts emergent dynamics beyond training. Our results demonstrate the potential of combining diffusion models and graph learning for data-driven ABM simulation.
Trust Region Constrained Measure Transport in Path Space for Stochastic Optimal Control and Inference
Authors: Denis Blessing; Julius Berner; Lorenz Richter; Carles Domingo-Enrich; Yuanqi Du; Arash Vahdat; Gerhard Neumann
Venue: NeurIPS 2025 (NeurIPS 2025 spotlight)

Abstract: Solving stochastic optimal control problems with quadratic control costs can be viewed as approximating a target path space measure, e.g. via gradient-based optimization. In practice, however, this optimization is challenging in particular if the target measure differs substantially from the prior. In this work, we therefore approach the problem by iteratively solving constrained problems incorporating trust regions that aim for approaching the target measure gradually in a systematic way. It turns out that this trust region based strategy can be understood as a geometric annealing from the prior to the target measure, where, however, the incorporated trust regions lead to a principled and educated way of choosing the time steps in the annealing path. We demonstrate in multiple optimal control applications that our novel method can improve performance significantly, including tasks in diffusion-based sampling and fine-tuning of diffusion models.
SPRINT: Enabling Interleaved Planning and Parallelized Execution in Reasoning Models
Authors: Emil Biju; Shayan Talaei; Zhemin Huang; Mohammadreza Pourreza; Azalia Mirhoseini; Amin Saberi
Venue: NeurIPS 2025 (NeurIPS 2025 poster)

Abstract: Large reasoning models (LRMs) excel at complex reasoning tasks but typically generate lengthy sequential chains-of-thought, resulting in long inference times before arriving at the final answer. To address this challenge, we introduce SPRINT, a novel post-training and inference-time framework designed to enable LRMs to dynamically identify and exploit opportunities for parallelization during their reasoning process. SPRINT incorporates an innovative data curation pipeline that reorganizes natural language reasoning trajectories into structured rounds of long-horizon planning and parallel execution. By fine-tuning LRMs on a small amount of such curated data, the models learn to dynamically identify independent subtasks within extended reasoning processes and effectively execute them in parallel. Through extensive evaluations, we demonstrate that models fine-tuned with the SPRINT framework match the performance of reasoning models on complex domains such as mathematics while generating up to 39% fewer sequential tokens on problems requiring more than 8,000 output tokens. Finally, we observe consistent results transferred to two out-of-distribution tasks, namely GPQA and Countdown, with up to 45% and 65% reduction in average sequential tokens respectively for longer reasoning trajectories, while matching the performance of the fine-tuned reasoning model.
Prot2Text-V2: Protein Function Prediction with Multimodal Contrastive Alignment
Authors: Xiao Fei; Michail Chatzianastasis; Sarah Almeida Carneiro; Hadi Abdine; Lawrence Paul Petalidis; Michalis Vazirgiannis
Venue: NeurIPS 2025 (NeurIPS 2025 poster)

Abstract: Predicting protein function from sequence is a central challenge in computational biology. While existing methods rely heavily on structured ontologies or similarity-based techniques, they often lack the flexibility to express structure-free functional descriptions and novel biological functions. In this work, we introduce Prot2Text-V2, a novel multimodal sequence-to-text model that generates free-form natural language descriptions of protein function directly from amino acid sequences. Our method combines a protein language model as a sequence encoder (ESM-3B) and a decoder-only language model (LLaMA-3.1-8B-Instruct) through a lightweight nonlinear modality projector.
A key innovation is our Hybrid Sequence-level Contrastive Alignment Learning (H-SCALE), which improves cross-modal learning by matching mean- and std-pooled protein embeddings with text representations via contrastive loss. After the alignment phase, we apply instruction-based fine-tuning using LoRA on the decoder to teach the model how to generate accurate protein function descriptions conditioned on the protein sequence. We train Prot2Text-V2 on about 250K curated entries from SwissProt and evaluate it under low-homology conditions, where test sequences have low similarity with training samples. Prot2Text-V2 consistently outperforms traditional and LLM-based baselines across various metrics.
How Well Can Differential Privacy Be Audited in One Run?
Authors: Amit Keinan; Moshe Shenfeld; Katrina Ligett
Venue: NeurIPS 2025 (NeurIPS 2025 spotlight)

Abstract: Recent methods for auditing the privacy of machine learning algorithms have improved computational efficiency by simultaneously intervening on multiple training examples in a single training run. Steinke et al. prove that one-run auditing indeed lower bounds the true privacy parameter of the audited algorithm, and give impressive empirical results. Their work leaves open the question of how precisely one-run auditing can uncover the true privacy parameter of an algorithm, and how that precision depends on the audited algorithm. In this work, we characterize the maximum achievable efficacy of one-run auditing and show that the key barrier to its efficacy is interference between the observable effects of different data elements. We present new conceptual approaches to minimize this barrier, towards improving the performance of one-run auditing of real machine learning algorithms.
Scalable In-context Ranking with Generative Models
Authors: Nilesh Gupta; Chong You; Srinadh Bhojanapalli; Sanjiv Kumar; Inderjit S Dhillon; Felix X. Yu
Venue: NeurIPS 2025 (NeurIPS 2025 poster)

Abstract: In-context Ranking (ICR) is an emerging paradigm for Information Retrieval (IR), which leverages contextual understanding of LLMs by directly incorporating the task description, candidate documents, and the query into the model's input prompt and tasking the LLM to identify relevant document(s). While it is effective, efficiency is a significant challenge in this paradigm, especially as the candidate list grows due to quadratic/super-linear scaling of attention operation with context length. To this end, this paper first identifies inherent and exploitable structures in the attention of LLMs finetuned for ICR: (1) inter-document block sparsity: attention is dense within each document block but sparse across different documents in the context; and (2) query-document block relevance: the attention scores from certain query tokens to a document block in middle layers strongly correlate with that document's actual relevance. Motivated by these observations, we introduce BlockRank (Blockwise In-context Ranking), a novel method that adapts the attention operation in an LLM by (a) architecturally enforcing the observed inter-document block sparsity, reducing attention complexity from quadratic to linear without loss in performance, and (b) optimizing query-document block relevance for true relevant documents during fine-tuning using an auxiliary contrastive training objective, improving retrieval in attention. Experiments on BEIR, MSMarco and NQ with Mistral-7B demonstrate that BlockRank Mistral matches or outperforms existing SOTA listwise rankers and controlled fine-tuned baseline while being significantly more efficient at inference (4.7x for 100 MSMarco documents in context) and scaling gracefully to long-context shortlists, around 500 documents in-context (approximately 100K context length) within a second, presenting a scalable and effective solution for ICR.
One Token per Highly Selective Frame: Towards Extreme Compression for Long Video Understanding
Authors: Zheyu Aqa Zhang; Ziqi Pang; Shixing Chen; Xiang Hao; Vimal Bhat; Yu-Xiong Wang
Venue: NeurIPS 2025 (NeurIPS 2025 poster)

Abstract: Long video understanding is inherently challenging for vision-language models (VLMs) because of the extensive number of frames. With each video frame typically expanding into tens or hundreds of tokens, the limited context length of large language models (LLMs) forces the VLMs to perceive the frames sparsely and lose temporal information. To address this, we explore extreme video token compression towards *one token per frame* at the final LLM layer. Our key insight is that heuristic-based compression, widely adopted by previous methods, is prone to information loss, and this necessitates supervising LLM layers into *learnable* and *progressive* modules for *token-level compression* (LP-Comp). Such compression enables our VLM to digest 2x-4x more frames with improved performance. To further increase the token efficiency, we investigate *frame-level compression*, which selects the frames most relevant to the queries via the internal attention scores of the LLM layers, named *question-conditioned compression* (QC-Comp). As a notable distinction from previous studies, we mitigate the position bias of LLM attention in long contexts, *i.e.*, the over-concentration on the beginning and end of a sequence, by splitting long videos into short segments and employing local attention. Collectively, our combined *token-level* and *frame-level* leads to an e**x**treme compression model for long video understanding, named **XComp**, achieving a significantly larger compression ratio and enabling denser frame sampling. Our XComp is finetuned from VideoChat-Flash with a data-efficient *supervised compression tuning* stage that only requires 2.5\% of the supervised fine-tuning data, yet boosts the accuracy from 42.9\% to 46.2\% on LVBench and enhances multiple other long video benchmarks.
Training a Scientific Reasoning Model for Chemistry
Authors: Siddharth Narayanan; James D. Braza; Ryan-Rhys Griffiths; Albert Bou; Geemi Wellawatte; Mayk Caldas Ramos; Ludovico Mitchener; Michael Martin Pieler; Samuel G Rodriques; Andrew White
Venue: NeurIPS 2025 (NeurIPS 2025 poster)

Abstract: Reasoning models are large language models that use extra "thought tokens" before answering, providing both higher accuracy and explicit reasoning for their response. A major question has been whether language model reasoning generalizes beyond mathematics, programming, and logic, where most previous work has focused. We demonstrate that reasoning models can be post-trained in scientific domains without additional domain pretraining, and require substantially less data compared to contemporary domain-specific models.
We report ether0, a 24B parameter LLM (based on Mistral-Small-24B) that can reason in natural language and respond with chemical structures. This reasoning model was trained with reinforcement learning on 577,790 experimentally-grounded chemistry tasks involving synthesized organic molecules. Our model outperforms all previous general-purpose chemistry models, frontier models, and humans, and is more data efficient relative to specialized models. We anticipate that this method can be applied to train highly data-efficient language models specialized for predictive and generative tasks across a wide variety of scientific domains.
Active Seriation: Efficient Ordering Recovery with Statistical Guarantees
Authors: James Cheshire; Yann Issartel
Venue: NeurIPS 2025 (NeurIPS 2025 poster)

Abstract: Active seriation aims at recovering an unknown ordering of $n$ items by adaptively querying pairwise similarities. 
The observations are noisy measurements of entries of an underlying $n \times n$ permuted Robinson matrix, whose permutation encodes the latent ordering. The framework allows the algorithm to start with partial information on the latent ordering, including seriation from scratch as a special case. We propose an active seriation algorithm that provably recovers the latent ordering with high probability. Under a uniform separation condition on the similarity matrix, optimal performance guarantees are established, both in terms of the probability of error and the number of observations required for successful recovery.