GenAI4ELab/papercli-papers huggingface dataset:
FLUX: Efficient Descriptor-Driven Clustered Federated Learning under Arbitrary Distribution Shifts
Authors: Dario Fenoglio; Mohan Li; Pietro Barbiero; Nicholas D. Lane; Marc Langheinrich; Martin Gjoreski
Venue: NeurIPS 2025 (NeurIPS 2025 poster)

Abstract: Federated Learning (FL) enables collaborative model training across multiple clients while preserving data privacy. Traditional FL methods often use a global model to fit all clients, assuming that clients' data are independent and identically distributed (IID). However, when this assumption does not hold, the global model accuracy may drop significantly, limiting FL applicability in real-world scenarios. To address this gap, we propose FLUX, a novel clustering-based FL (CFL) framework that addresses the four most common types of distribution shifts during both training and test time. To this end, FLUX leverages privacy-preserving client-side descriptor extraction and unsupervised clustering to ensure robust performance and scalability across varying levels and types of distribution shifts. Unlike existing CFL methods addressing non-IID client distribution shifts, FLUX i) does not require any prior knowledge of the types of distribution shifts or the number of client clusters, and ii) supports test-time adaptation, enabling unseen and unlabeled clients to benefit from the most suitable cluster-specific models. Extensive experiments across four standard benchmarks, two real-world datasets and ten state-of-the-art baselines show that FLUX improves performance and stability under diverse distribution shifts—achieving an average accuracy gain of up to 23 percentage points over the best-performing baselines—while maintaining computational and communication overhead comparable to FedAvg.
Securing the Language of Life: Inheritable Watermarks from DNA Language Models to Proteins
Authors: ZAIXI ZHANG; Ruofan Jin; Le Cong; Mengdi Wang
Venue: NeurIPS 2025 (NeurIPS 2025 poster)

Abstract: DNA language models have revolutionized our ability to design and manipulate DNA sequences—the fundamental language of life—with unprecedented precision, enabling transformative applications in therapeutics, synthetic biology, and gene editing. However, this capability also poses significant dual-use risks, including the potential creation of harmful biological agents. To address these biosecurity challenges, we introduce two innovative watermarking techniques: DNAMark and CentralMark. DNAMark employs synonymous codon substitutions to embed robust watermarks in DNA sequences while preserving the function of encoded proteins. CentralMark advances this by creating inheritable watermarks that transfer from DNA to translated proteins, leveraging protein embeddings to ensure detection across the central dogma. Both methods utilize state-of-the-art embeddings to generate watermark logits, enhancing resilience against natural mutations, synthesis errors, and adversarial attacks. Evaluated on a therapeutic DNA benchmark, DNAMark and CentralMark achieve F1 detection scores above 0.85 under diverse conditions, while maintaining over 60\% sequence similarity to ground truth and degeneracy scores below 15\%. A case study on a CRISPR-Cas9 system underscores CentralMark’s utility in real-world synthetic biology. This work establishes a vital framework for securing DNA language models, balancing innovation with accountability to mitigate biosecurity risks.
Inference with correlated priors using sisters cells
Authors: Sina Tootoonian; Andreas T. Schaefer
Venue: NeurIPS 2025 (NeurIPS 2025 poster)

Abstract: A common view of sensory processing is as probabilistic inference of latent causes from receptor activations. Standard approaches often assume these causes are \textit{a priori} independent, yet real-world generative factors are typically correlated. Representing such structured priors in neural systems poses architectural challenges, particularly when direct interactions between units representing latent causes are biologically implausible or computationally expensive. Inspired by the architecture of the olfactory bulb, we propose a novel circuit motif that enables inference with correlated priors without requiring direct interactions among latent cause units. The key insight lies in using \textit{sister cells}: neurons receiving shared receptor input but connected differently to local interneurons. The required interactions among latent units are implemented indirectly through their connections to the sister cells, such that correlated connectivity implies anti-correlation in the prior and vice versa. We use geometric arguments to construct connectivity that implements a given prior and to bound the number of causes for which such priors can be constructed. Using simulations, we demonstrate the efficacy of such priors for inference in noisy environments and compare the inference dynamics to those experimentally observed. Finally, we show how, under certain assumptions on latent representations, the prior used can be inferred from sister cell activations. While biologically grounded in the olfactory system, our mechanism generalises to other natural and artificial sensory systems and may inform the design of architectures for efficient inference under correlated latent structure.
Stable Gradients for Stable Learning at Scale in Deep Reinforcement Learning
Authors: Roger Creus Castanyer; Johan Obando-Ceron; Lu Li; Pierre-Luc Bacon; Glen Berseth; Aaron Courville; Pablo Samuel Castro
Venue: NeurIPS 2025 (NeurIPS 2025 spotlight)

Abstract: Scaling deep reinforcement learning networks is challenging and often results in degraded performance, yet the root causes of this failure mode remain poorly understood. Several recent works have proposed mechanisms to address this, but they are often complex and fail to highlight the causes underlying this difficulty. In this work, we conduct a series of empirical analyses which suggest that the combination of non-stationarity with gradient pathologies, due to suboptimal architectural choices, underlie the challenges of scale. We propose a series of direct interventions that stabilize gradient flow, enabling robust performance across a range of network depths and widths. Our interventions are simple to implement and compatible with well-established algorithms, and result in an effective mechanism that enables strong performance even at large scales. We validate our findings on a variety of agents and suites of environments.
Differentiable Generalized Sliced Wasserstein Plans
Authors: Laetitia Chapel; Romain Tavenard; Samuel Vaiter
Venue: NeurIPS 2025 (NeurIPS 2025 poster)

Abstract: Optimal Transport (OT) has attracted significant interest in the machine learning community, not only for its ability to define meaningful distances between probability distributions -- such as the Wasserstein distance -- but also for its formulation of OT plans. 
Its computational complexity remains a bottleneck, though, and slicing techniques have been developed to scale OT to large datasets. Recently, a novel slicing scheme, dubbed min-SWGG, lifts a single one-dimensional plan back to the original multidimensional space, finally selecting the slice that yields the lowest Wasserstein distance as an approximation of the full OT plan. Despite its computational and theoretical advantages, min-SWGG inherits typical limitations of slicing methods: (i) the number of required slices grows exponentially with the data dimension, and (ii) it is constrained to linear projections. Here, we reformulate  min-SWGG as a bilevel optimization problem and propose a differentiable approximation scheme to efficiently identify the optimal slice, even in high-dimensional settings. We furthermore define its generalized extension for accommodating data living on manifolds. Finally, we demonstrate the practical value of our approach in various applications, including gradient flows on manifolds and high-dimensional spaces, as well as a novel sliced OT-based conditional flow matching for image generation -- where fast computation of transport plans is essential.
SpecMER: Fast Protein Generation with K-mer Guided Speculative Decoding
Authors: Thomas Walton; Darin Tsui; Aryan Musharaf; Amirali Aghazadeh
Venue: NeurIPS 2025 (NeurIPS 2025 spotlight)

Abstract: Autoregressive models have transformed protein engineering by enabling the generation of novel protein sequences beyond those found in nature. However, their sequential inference introduces significant latency, limiting their utility in high-throughput protein screening. Speculative decoding accelerates generation by employing a lightweight draft model to sample tokens, which a larger target model then verifies and refines. Yet in protein sequence generation, draft models are typically agnostic to the structural and functional constraints of the target protein, leading to biologically implausible outputs and a shift in the likelihood distribution of generated sequences. We introduce SpecMER (Speculative Decoding via k-mer Guidance), a novel framework that incorporates biological, structural, and functional priors using k-mer motifs extracted from multiple sequence alignments. By scoring candidate sequences in parallel and selecting those most consistent with known biological patterns, SpecMER significantly improves sequence plausibility while retaining the efficiency of speculative decoding. SpecMER achieves 24–32% speedup over standard autoregressive decoding, along with higher acceptance rates and improved sequence likelihoods.
SpecEdge: Scalable Edge-Assisted Serving Framework for Interactive LLMs
Authors: Jinwoo Park; Seunggeun Cho; Dongsu Han
Venue: NeurIPS 2025 (NeurIPS 2025 spotlight)

Abstract: Large language models (LLMs) power many modern applications, but serving them at scale remains costly and resource-intensive. Current server-centric systems overlook consumer-grade GPUs at the edge. We introduce SpecEdge, an edge-assisted inference framework that splits LLM workloads between edge and server GPUs using a speculative decoding scheme, exchanging only token outputs over the network. SpecEdge employs proactive edge drafting to overlap edge token creation with server verification and pipeline-aware scheduling that interleaves multiple user requests to increase server-side throughput. Experiments show SpecEdge enhances overall cost efficiency by **1.91×** through achieving **2.22×** server throughput, and reduces inter token latency by **11.24\%** compared to a server-only baseline, introducing a scalable, cost-effective paradigm for LLM serving. The code is available at https://github.com/kaist-ina/specedge
Mitigating Intra- and Inter-modal Forgetting in Continual Learning of Unified Multimodal Models
Authors: Xiwen Wei; Mustafa Munir; Radu Marculescu
Venue: NeurIPS 2025 (NeurIPS 2025 poster)

Abstract: Unified Multimodal Generative Models (UMGMs) unify visual understanding and image generation within a single autoregressive framework. However, their ability to continually learn new tasks is severely hindered by catastrophic forgetting, both within a modality (intra-modal) and across modalities (inter-modal). While intra-modal forgetting has been studied in prior continual learning (CL) work, inter-modal forgetting remains largely unexplored. In this paper, we identify and empirically validate this phenomenon in UMGMs and provide a theoretical explanation rooted in gradient conflict between modalities. To address both intra- and inter-modal forgetting, we propose Modality-Decoupled Experts (MoDE), a lightweight and scalable architecture that isolates modality-specific updates to mitigate the gradient conflict and leverages knowledge distillation to prevent catastrophic forgetting and preserve pre-trained capabilities. Unlike previous CL methods that remain modality-coupled and suffer from modality gradient conflict, MoDE explicitly decouples modalities to prevent interference. Experiments across diverse benchmarks demonstrate that MoDE significantly mitigates both inter- and intra-modal forgetting, outperforming prior CL baselines in unified multimodal generation settings.
SSTAG: Structure-Aware Self-Supervised Learning Method for Text-Attributed Graphs
Authors: LiuRuyue; Rong Yin; Xiangzhen Bo; Xiaoshuai Hao; Yong Liu; Jinwen Zhong; Can Ma; Weiping Wang
Venue: NeurIPS 2025 (NeurIPS 2025 poster)

Abstract: Large-scale pre-trained models have revolutionized Natural Language Processing (NLP) and Computer Vision (CV), showcasing remarkable cross-domain generalization abilities. However, in graph learning, models are typically trained on individual graph datasets, limiting their capacity to transfer knowledge across different graphs and tasks. This approach also heavily relies on large volumes of annotated data, which presents a significant challenge in resource-constrained settings. Unlike NLP and CV, graph-structured data presents unique challenges due to its inherent heterogeneity, including domain-specific feature spaces and structural diversity across various applications. To address these challenges, we propose a novel structure-aware self-supervised learning method for Text-Attributed Graphs (SSTAG). By leveraging text as a unified representation medium for graph learning, SSTAG bridges the gap between the semantic reasoning of Large Language Models (LLMs) and the structural modeling capabilities of Graph Neural Networks (GNNs). Our approach introduces a dual knowledge distillation framework that co-distills both LLMs and GNNs into structure-aware multilayer perceptrons (MLPs), enhancing the scalability of large-scale TAGs. Additionally, we introduce an in-memory mechanism that stores typical graph representations, aligning them with memory anchors in an in-memory repository to integrate invariant knowledge, thereby improving the model’s generalization ability. Extensive experiments demonstrate that SSTAG outperforms state-of-the-art models on cross-domain transfer learning tasks, achieves exceptional scalability, and reduces inference costs while maintaining competitive performance.
Universal Visuo-Tactile Video Understanding for Embodied Interaction
Authors: Yifan Xie; Mingyang Li; Shoujie Li; Xingting Li; Guangyu Chen; Fei Ma; Fei Yu; Wenbo Ding
Venue: NeurIPS 2025 (NeurIPS 2025 poster)

Abstract: Tactile perception is essential for embodied agents to understand the physical attributes of objects that cannot be determined through visual inspection alone. While existing methods have made progress in visual and language modalities for physical understanding, they fail to effectively incorporate tactile information that provides crucial haptic feedback for real-world interaction. In this paper, we present VTV-LLM, the first multi-modal large language model that enables universal Visuo-Tactile Video (VTV) understanding, bridging the gap between tactile perception and natural language. To address the challenges of cross-sensor and cross-modal integration, we contribute VTV150K, a comprehensive dataset comprising 150,000 video frames from 100 diverse objects captured across three different tactile sensors (GelSight Mini, DIGIT, and Tac3D), annotated with four fundamental tactile attributes (hardness, protrusion, elasticity, and friction). We develop a novel three-stage training paradigm that includes VTV enhancement for robust visuo-tactile representation, VTV-text alignment for cross-modal correspondence, and text prompt finetuning for natural language generation. Our framework enables sophisticated tactile reasoning capabilities including feature assessment, comparative analysis, and scenario-based decision-making. Extensive experimental evaluations demonstrate that VTV-LLM achieves superior performance in tactile reasoning tasks, establishing a foundation for more intuitive human-machine interaction in tactile domains.
Spatial-Aware Decision-Making with Ring Attractors in Reinforcement Learning Systems
Authors: Marcos Negre Saura; Richard Allmendinger; Wei Pan; Theodore Papamarkou
Venue: NeurIPS 2025 (NeurIPS 2025 poster)

Abstract: Ring attractors, mathematical models inspired by neural circuit dynamics, provide a biologically plausible mechanism to improve learning speed and accuracy in Reinforcement Learning (RL). Serving as specialized brain-inspired structures that encode spatial information and uncertainty, ring attractors explicitly encode the action space, facilitate the organization of neural activity, and enable the distribution of spatial representations across the neural network in the context of Deep Reinforcement Learning (DRL). These structures also provide temporal filtering that stabilizes action selection during exploration, for example, by preserving the continuity between rotation angles in robotic control or adjacency between tactical moves in game-like environments. The application of ring attractors in the action selection process involves mapping actions to specific locations on the ring and decoding the selected action based on neural activity. We investigate the application of ring attractors by both building an exogenous model and integrating them as part of DRL agents. Our approach significantly improves state-of-the-art performance on the Atari 100k benchmark, achieving a 53\% increase in performance over selected baselines.
Model–Behavior Alignment under Flexible Evaluation: When the Best-Fitting Model Isn’t the Right One
Authors: Itamar Avitan; Tal Golan
Venue: NeurIPS 2025 (NeurIPS 2025 poster)

Abstract: Linearly transforming stimulus representations of deep neural networks yields
high-performing models of behavioral and neural responses to complex stimuli.
But does the test accuracy of such predictions identify genuine representational
alignment? We addressed this question through a large-scale model-recovery study.
Twenty diverse vision models were linearly aligned to 4.5 million behavioral judg-
ments from the THINGS odd-one-out dataset and calibrated to reproduce human
response variability. For each model in turn, we sampled synthetic responses
from its probabilistic predictions, fitted all candidate models to the synthetic data,
and tested whether the data-generating model would re-emerge as the best predictor of the simulated data. Model recovery accuracy improved with training-set
size but plateaued below 80%, even at millions of simulated trials. Regression
analyses linked misidentification primarily to shifts in representational geometry
induced by the linear transformation, as well as to the effective dimensionality
of the transformed features. These findings demonstrate that, even with massive
behavioral data, overly flexible alignment metrics may fail to guide us toward artificial representations that are genuinely more human-aligned. Model comparison
experiments must be designed to balance the trade-off between predictive accuracy
and identifiability—ensuring that the best-fitting model is also the right one.
Improving Decision Trees through the Lens of Parameterized Local Search
Authors: Juha Harviainen; Frank Sommer; Manuel Sorge
Venue: NeurIPS 2025 (NeurIPS 2025 poster)

Abstract: Algorithms for learning decision trees often include heuristic local-search operations such as (1) adjusting the threshold of a cut or (2) also exchanging the feature of that cut. We study minimizing the number of classification errors by performing a fixed number of a single type of these operations. Although we discover that the corresponding problems are NP-complete in general, we provide a comprehensive parameterized-complexity analysis with the aim of determining those properties of the problems that explain the hardness and those that make the problems tractable. For instance, we show that the problems remain hard for a small number $d$ of features or small domain size $D$ but the combination of both yields fixed-parameter tractability. That is, the problems are solvable in $(D + 1)^{2d} \cdot |\mathcal{I}|^{O(1)}$ time, where $|\mathcal{I}|$ is the size of the input. We also provide a proof-of-concept implementation of this algorithm and report on empirical results.
CG-SSL: Concept-Guided Self-Supervised Learning
Authors: Sara Atito; Josef Kittler; Imran Razzak; Muhammad Awais
Venue: NeurIPS 2025 (NeurIPS 2025 poster)

Abstract: Humans understand visual scenes by first capturing a global impression and then refining this understanding into distinct, object-like components. Inspired by this process, we introduce \textbf{C}oncept-\textbf{G}uided \textbf{S}elf-\textbf{S}upervised \textbf{L}earning (CG-SSL), a novel framework that brings structure and interpretability to representation learning through a curriculum of three training phases: (1) global scene encoding, (2) discovery of visual concepts via tokenised cross-attention, and (3) alignment of these concepts across views.
Unlike traditional SSL methods, which simply enforce similarity between multiple augmented views of the same image, CG-SSL accounts for the fact that these views may highlight different parts of an object or scene. To address this, our method establishes explicit correspondences between views and aligns the representations of meaningful image regions. At its core, CG-SSL augments standard SSL with a lightweight decoder that learns and refines concept tokens via cross-attention with patch features. The concept tokens are trained using masked concept distillation and a feature-space reconstruction objective. A final alignment stage enforces view consistency by geometrically matching concept regions under heavy augmentation, enabling more compact, robust, and disentangled representations of scene regions. 
Across multiple backbone sizes, CG-SSL achieves state-of-the-art results on image segmentation benchmarks using $k$-NN and linear probes, substantially outperforming prior methods and approaching, or even surpassing, the performance of leading SSL models trained on over $100\times$ more data. Code and pretrained models will be released.
Monitoring Risks in Test-Time Adaptation
Authors: Mona Schirmer; Metod Jazbec; Christian A. Naesseth; Eric Nalisnick
Venue: NeurIPS 2025 (NeurIPS 2025 poster)

Abstract: Encountering shifted data at test time is a ubiquitous challenge when deploying predictive machine learning models. Test-time adaptation (TTA) methods aim to address this issue by continuously adapting a deployed model using only unlabeled test data. While TTA can help extend the model's deployment lifespan, there are scenarios where, despite adaptation, the drop in the model's performance remains significant enough to warrant taking the model offline and retraining. To detect such failure cases, we propose pairing TTA with risk monitoring frameworks that track predictive performance and raise alerts when predefined performance criteria are violated. Specifically, we extend existing monitoring tools based on sequential testing with confidence sequences to accommodate scenarios where the model is updated at test time and no test labels are available to estimate the performance metrics of interest. Our extensions unlock the application of rigorous statistical risk monitoring in TTA and we demonstrate applicability of our proposed TTA monitoring framework across a representative set of TTA methods, datasets and distribution shift types.