GenAI4ELab/papercli-papers huggingface dataset:
Information-Driven Design of Imaging Systems
Authors: Henry Pinkard; Leyla A Kabuli; Eric Markley; Tiffany Chien; Jiantao Jiao; Laura Waller
Venue: NeurIPS 2025 (NeurIPS 2025 poster)

Abstract: Imaging systems have traditionally been designed to mimic the human eye and produce visually interpretable measurements. Modern imaging systems, however, process raw measurements computationally before or instead of human viewing. As a result, the information content of raw measurements matters more than their visual interpretability. Despite the importance of measurement information content, current approaches for evaluating imaging system performance do not quantify it: they instead either use alternative metrics that assess specific aspects of measurement quality or assess measurements indirectly with performance on secondary tasks. 

We developed the theoretical foundations and a practical method to directly quantify mutual information between noisy measurements and unknown objects. By fitting probabilistic models to measurements and their noise characteristics, our method estimates information by upper bounding its true value. By applying gradient-based optimization to these estimates, we also developed a technique for designing imaging systems called Information-Driven Encoder Analysis Learning (IDEAL). 

Our information estimates accurately captured system performance differences across four imaging domains (color photography, radio astronomy, lensless imaging, and microscopy). Systems designed with IDEAL matched the performance of those designed with end-to-end optimization, the prevailing approach that jointly optimizes hardware and image processing algorithms. These results establish mutual information as a universal performance metric for imaging systems that enables both computationally efficient design optimization and evaluation in real-world conditions.

A video summary of this work can be found at: https://waller-lab.github.io/EncodingInformationWebsite/
Matchings Under Biased and Correlated Evaluations
Authors: Amit Kumar; Nisheeth K. Vishnoi
Venue: NeurIPS 2025 (NeurIPS 2025 poster)

Abstract: We study a two-institution stable matching model in which candidates from two distinct groups are evaluated using partially correlated signals that are group-biased. This extends prior work (which assumes institutions evaluate candidates in an identical manner) to a more realistic setting in which institutions rely on overlapping, but independently processed, criteria. These evaluations could consist of a variety of informative tools such as standardized tests, shared recommendation systems, or AI-based assessments with local noise.  Two key parameters govern evaluations: the bias parameter $\beta \in (0,1]$, which models systematic disadvantage faced by one group, and the correlation parameter $\gamma \in [0,1]$, which captures the alignment between institutional rankings. We study the representation ratio $\mathcal{R}(\beta, \gamma)$, i.e., the ratio of disadvantaged to advantaged candidates selected by the matching process in this setting. Focusing on a regime in which all candidates prefer the same institution, we characterize the large-market equilibrium and derive a closed-form expression for the resulting representation ratio. Prior work shows that when $\gamma = 1$, this ratio scales linearly with $\beta$.  In contrast, we show that $\mathcal{R}(\beta, \gamma)$ increases nonlinearly with $\gamma$ and even modest losses in correlation can cause sharp drops in the representation ratio. Our analysis identifies critical $\gamma$-thresholds where institutional selection behavior undergoes discrete transitions, and reveals structural conditions under which evaluator alignment or bias mitigation are most effective. Finally, we show how this framework and results enable interventions for fairness-aware design in decentralized selection systems.
Steering Generative Models with Experimental Data for Protein Fitness Optimization
Authors: Jason Yang; Wenda Chu; Daniel Khalil; Raul Astudillo; Bruce James Wittmann; Frances H. Arnold; Yisong Yue
Venue: NeurIPS 2025 (NeurIPS 2025 poster)

Abstract: Protein fitness optimization involves finding a protein sequence that maximizes desired quantitative properties in a combinatorially large design space of possible sequences. Recent advances in steering protein generative models (e.g., diffusion models and language models) with labeled data offer a promising approach. However, most previous studies have optimized surrogate rewards and/or utilized large amounts of labeled data for steering, making it unclear how well existing methods perform and compare to each other in real-world optimization campaigns where fitness is measured through low-throughput wet-lab assays. In this study, we explore fitness optimization using small amounts (hundreds) of labeled sequence-fitness pairs and comprehensively evaluate strategies such as classifier guidance and posterior sampling for guiding generation from different discrete diffusion models of protein sequences. We also demonstrate how guidance can be integrated into adaptive sequence selection akin to Thompson sampling in Bayesian optimization, showing that plug-and-play guidance strategies offer advantages over alternatives such as reinforcement learning with protein language models. Overall, we provide practical insights into how to effectively steer modern generative models for next-generation protein fitness optimization.
Regression-adjusted Monte Carlo Estimators for Shapley Values and Probabilistic Values
Authors: R. Teal Witter; Yurong Liu; Christopher Musco
Venue: NeurIPS 2025 (NeurIPS 2025 poster)

Abstract: With origins in game-theory, probabilistic values like Shapley values, Banzhaf values, and semi-values have emerged as a central tool in explainable AI. They are used for feature attribution, data attribution, data valuation, and more. Since all of these values require exponential time to compute exactly, research has focused on efficient approximation methods using two techniques: Monte Carlo sampling and linear regression formulations. In this work, we present a new way of combining both of these techniques. Our approach is more flexible than prior algorithms, allowing for linear regression to be replaced with any function family whose probabilistic values can be computed efficiently. This allows us to harness the accuracy of tree-based models like XGBoost, while still producing unbiased estimates. From experiments across eight datasets, we find that our methods give state-of-the-art performance for estimating probabilistic values. For Shapley values, the error of our methods is up to $6\times$ lower than Permutation SHAP (the most popular Monte Carlo method), $2.75\times$ lower than Kernel SHAP (the most popular linear regression method), and $1.75\times$ lower than Leverage SHAP (the prior state-of-the-art Shapley value estimator). For more general probabilistic values, we can obtain error up to $60\times$ lower than prior work.
The Matrix: Infinite-Horizon World Generation with Real-Time Moving Control
Authors: Ruili Feng; Han Zhang; Zhilei Shu; Zhantao Yang; Longxiang Tang; Zhicai Wang; Andy Zheng; Jie Xiao; Zhiheng Liu; Ruihang Chu; Yukun Huang; Yu Liu; Hongyang Zhang
Venue: NeurIPS 2025 (NeurIPS 2025 poster)

Abstract: We present The Matrix, a foundational realistic world simulator capable of generating infinitely long 720p high-fidelity real-scene video streams with real-time, responsive control in both first- and third-person perspectives. Trained on limited supervised data from video games like Forza Horizon 5 and Cyberpunk 2077, complemented by large-scale unsupervised footage from real-world settings like Tokyo streets, The Matrix allows users to traverse diverse terrains—deserts, grasslands, water bodies, and urban landscapes—in continuous, uncut hour-long sequences. With speeds of up to 16 FPS, the system supports real-time interactivity and demonstrates zero-shot generalization, translating virtual game environments to real-world contexts where collecting continuous movement data is often infeasible. For example, The Matrix can simulate a BMW X3 driving through an office setting—an environment present in neither gaming data nor real-world sources. This approach showcases the potential of game data to advance robust world models, bridging the gap between simulations and real-world applications in scenarios with limited data.
Tracking and Understanding Object Transformations
Authors: Yihong Sun; Xinyu Yang; Jennifer J. Sun; Bharath Hariharan
Venue: NeurIPS 2025 (NeurIPS 2025 poster)

Abstract: Real-world objects frequently undergo state transformations. From an apple being cut into pieces to a butterfly emerging from its cocoon, tracking through these changes is important for understanding real-world objects and dynamics. However, existing methods often lose track of the target object after transformation, due to significant changes in object appearance. To address this limitation, we introduce the task of Track Any State: tracking objects through transformations while detecting and describing state changes, accompanied by a new benchmark dataset, VOST-TAS. To tackle this problem, we present TubeletGraph, a zero-shot system that recovers missing objects after transformation and maps out how object states are evolving over time. TubeletGraph first identifies potentially overlooked tracks, and determines whether they should be integrated based on semantic and proximity priors. Then, it reasons about the added tracks and generates a state graph describing each observed transformation. TubeletGraph achieves state-of-the-art tracking performance under transformations, while demonstrating deeper understanding of object transformations and promising capabilities in temporal grounding and semantic reasoning for complex object transformations. Code, additional results, and the benchmark dataset are available at https://tubelet-graph.github.io.
Robust Distributed Estimation: Extending Gossip Algorithms to Ranking and Trimmed Means
Authors: Anna van Elst; Igor Colin; Stephan Clémençon
Venue: NeurIPS 2025 (NeurIPS 2025 poster)

Abstract: This paper addresses the problem of robust estimation in gossip algorithms over arbitrary communication graphs. Gossip algorithms are fully decentralized, relying only on local neighbor-to-neighbor communication, making them well-suited for situations where communication is constrained. A fundamental challenge in existing mean-based gossip algorithms is their vulnerability to malicious or corrupted nodes. In this paper, we show that an outlier-robust mean can be computed by globally estimating a robust statistic. More specifically, we propose a novel gossip algorithm for rank estimation, referred to as \textsc{GoRank}, and leverage it to design a gossip procedure dedicated to trimmed mean estimation, coined \textsc{GoTrim}. In addition to a detailed description of the proposed methods, a key contribution of our work is a precise convergence analysis: we establish an $\mathcal{O}(1/t)$ rate for rank estimation and an $\mathcal{O}(1 / {t})$ rate for trimmed mean estimation, where by $t$ is meant the number of iterations. Moreover, we provide a breakdown point analysis of \textsc{GoTrim}. We empirically validate our theoretical results through experiments on diverse network topologies, data distributions and contamination schemes.
seq-JEPA: Autoregressive Predictive Learning of Invariant-Equivariant World Models
Authors: Hafez Ghaemi; Eilif Benjamin Muller; Shahab Bakhtiari
Venue: NeurIPS 2025 (NeurIPS 2025 poster)

Abstract: Joint-embedding self-supervised learning (SSL) commonly relies on transformations such as data augmentation and masking to learn visual representations, a task achieved by enforcing invariance or equivariance with respect to these transformations applied to two views of an image. This dominant two-view paradigm in SSL often limits the flexibility of learned representations for downstream adaptation by creating performance trade-offs between high-level invariance-demanding tasks such as image classification and more fine-grained equivariance-related tasks. In this work, we propose \emph{seq-JEPA}, a world modeling framework that introduces architectural inductive biases into joint-embedding predictive architectures to resolve this trade-off. Without relying on dual equivariance predictors or loss terms, seq-JEPA simultaneously learns two architecturally separate representations for equivariance- and invariance-demanding tasks. To do so, our model processes short sequences of different views (observations) of inputs. Each encoded view is concatenated with an embedding of the relative transformation (action) that produces the next observation in the sequence. These view-action pairs are passed through a transformer encoder that outputs an aggregate representation. A predictor head then conditions this aggregate representation on the upcoming action to predict the representation of the next observation. Empirically, seq-JEPA demonstrates strong performance on both equivariance- and invariance-demanding downstream tasks without sacrificing one for the other. Furthermore, it excels at tasks that inherently require aggregating a sequence of observations, such as path integration across actions and predictive learning across eye movements.
Adaptive Frontier Exploration on Graphs with Applications to Network-Based Disease Testing
Authors: Davin Choo; Yuqi Pan; Tonghan Wang; Milind Tambe; Alastair van Heerden; Cheryl Johnson
Venue: NeurIPS 2025 (NeurIPS 2025 poster)

Abstract: We study a sequential decision-making problem on a $n$-node graph $\mathcal{G}$ where each node has an unknown label from a finite set $\mathbf{\Omega}$, drawn from a joint distribution $\mathcal{P}$ that is Markov with respect to $\mathcal{G}$. At each step, selecting a node reveals its label and yields a label-dependent reward. The goal is to adaptively choose nodes to maximize expected accumulated discounted rewards. We impose a frontier exploration constraint, where actions are limited to neighbors of previously selected nodes, reflecting practical constraints in settings such as contact tracing and robotic exploration. We design a Gittins index-based policy that applies to general graphs and is provably optimal when $\mathcal{G}$ is a forest. Our implementation runs in $\mathcal{O}(n^2 \cdot |\mathbf{\Omega}|^2)$ time while using $\mathcal{O}(n \cdot |\mathbf{\Omega}|^2)$ oracle calls to $\mathcal{P}$ and $\mathcal{O}(n^2 \cdot |\mathbf{\Omega}|)$ space. Experiments on synthetic and real-world graphs show that our method consistently outperforms natural baselines, including in non-tree, budget-limited, and undiscounted settings. For example, in HIV testing simulations on real-world sexual interaction networks, our policy detects nearly all positive cases with only half the population tested, substantially outperforming other baselines.
Wavelet Canonical Coherence for Nonstationary Signals
Authors: Haibo Wu; Marina I. Knight; Keiland W. Cooper; Norbert J. Fortin; Hernando Ombao
Venue: NeurIPS 2025 (NeurIPS 2025 spotlight)

Abstract: Understanding the evolving dependence between two sets of multivariate signals is fundamental in neuroscience and other domains where sub-networks in a system interact dynamically over time. Despite the growing interest in multivariate time series analysis, existing methods for between-clusters dependence typically rely on the assumption of stationarity and lack the temporal resolution to capture transient, frequency-specific interactions. To overcome this limitation, we propose scale-specific wavelet canonical coherence (WaveCanCoh), a novel framework that extends canonical coherence analysis to the nonstationary setting by leveraging the multivariate locally stationary wavelet model. The proposed WaveCanCoh enables the estimation of time-varying canonical coherence between clusters, providing interpretable insight into scale-specific time-varying interactions between clusters. Through extensive simulation studies, we demonstrate that WaveCanCoh accurately recovers true coherence structures under both locally stationary and general nonstationary conditions. Application to local field potential (LFP) activity data recorded from the hippocampus reveals distinct dynamic coherence patterns between correct and incorrect memory-guided decisions, illustrating capacity of the method to detect behaviorally relevant neural coordination. These results highlight WaveCanCoh as a flexible and principled tool for modeling complex cross-group dependencies in nonstationary multivariate systems. Code for implementing WaveCanCoh is available at https://github.com/mhaibo/WaveCanCoh.git.
Lessons Learned: A Multi-Agent Framework for Code LLMs to Learn and Improve
Authors: Yuanzhe Liu; Ryan Deng; Tim Kaler; Xuhao Chen; Charles Leiserson; Yao Ma; Jie Chen
Venue: NeurIPS 2025 (NeurIPS 2025 poster)

Abstract: Recent studies show that LLMs possess different skills and specialize in different tasks. In fact, we observe that their varied performance occur in several levels of granularity. For example, in the code optimization task, code LLMs excel at different optimization categories and no one dominates others. This observation prompts the question of how one leverages multiple LLM agents to solve a coding problem without knowing their complementary strengths a priori. We argue that a team of agents can learn from each other's successes and failures so as to improve their own performance. Thus, a lesson is the knowledge produced by an agent and passed on to other agents in the collective solution process. We propose a lesson-based collaboration framework, design the lesson solicitation--banking--selection mechanism, and demonstrate that a team of small LLMs with lessons learned can outperform a much larger LLM and other multi-LLM collaboration methods.
ShorterBetter: Guiding Reasoning Models to Find Optimal Inference Length for Efficient Reasoning
Authors: Jingyang Yi; Justin Wang; Sida Li
Venue: NeurIPS 2025 (NeurIPS 2025 poster)

Abstract: Recent models such as OpenAI o1 and DeepSeek-R1 have demonstrated strong performance on reasoning-intensive tasks by generating extended Chain-of-Thought (CoT) traces. While longer reasoning helps with thorough exploration of solution paths for complex problems, it also often leads to inefficient and redundant outputs—a phenomenon commonly described as $\textit{overthinking}$.  In this paper, we propose $\texttt{ShorterBetter}$, a simple yet effective reinforcement learning method that enables reasoning models to learn their own optimal CoT lengths without manual supervision. We define the $\textit{Sample Optimal Length}$ (SOL) as the length of the shortest correct response among multiple generations, which serves as a dynamic reward signal to guide the model toward efficient reasoning. Applied to DeepSeek-Distill-Qwen-1.5B/7B as base models, $\texttt{ShorterBetter}$ achieves 50\%-80\% reduction in output lengths in both in-domain and out-of-domain reasoning tasks while maintaining accuracy. Our reasoning trace analysis shows that $\texttt{ShorterBetter}$ refines the structure of the reasoning traces by reducing unnecessary repetition, excessive self-verification, and over-exploration of alternatives.
RefLoRA: Refactored Low-Rank Adaptation for Efficient Fine-Tuning of Large Models
Authors: Yilang Zhang; Bingcong Li; Georgios B. Giannakis
Venue: NeurIPS 2025 (NeurIPS 2025 poster)

Abstract: Low-Rank Adaptation (LoRA) lowers the computational and memory overhead of fine-tuning large models by updating a low-dimensional subspace of the pre-trained weight matrix. Albeit efficient, LoRA exhibits suboptimal convergence and noticeable performance degradation, due to inconsistent and imbalanced weight updates induced by its nonunique low-rank factorizations. To overcome these limitations, this article identifies the optimal low-rank factorization per step that minimizes an upper bound on the loss. The resultant refactored low-rank adaptation (RefLoRA) method promotes a flatter loss landscape, along with consistent and balanced weight updates, thus speeding up stable convergence. Extensive experiments evaluate RefLoRA on natural language understanding, and commonsense reasoning tasks with popular large language models including DeBERTaV3, LLaMA-7B, LLaMA2-7B and LLaMA3-8B. The numerical tests corroborate that RefLoRA converges faster, outperforms various benchmarks, and enjoys negligible computational overhead compared to state-of-the-art LoRA variants.
Neural Collapse under Gradient Flow on Shallow ReLU Networks for Orthogonally Separable Data
Authors: Hancheng Min; Zhihui Zhu; Rene Vidal
Venue: NeurIPS 2025 (NeurIPS 2025 poster)

Abstract: Among many mysteries behind the success of deep networks lies the exceptional discriminative power of their learned representations as manifested by the intriguing Neural Collapse (NC) phenomenon, where simple feature structures emerge at the last layer of a trained neural network. Prior works on the theoretical understandings of NC have focused on analyzing the optimization landscape of matrix-factorization-like problems by considering the last-layer features as unconstrained free optimization variables and showing that their global minima exhibit NC. In this paper, we show that gradient flow on a two-layer ReLU network for classifying orthogonally separable data provably exhibits NC, thereby advancing prior results in two ways: First, we relax the assumption of unconstrained features, showing the effect of data structure and nonlinear activations on NC characterizations. Second, we reveal the role of the implicit bias of the training dynamics in facilitating the emergence of NC.
Efficient Spectral Control of Partially Observed Linear Dynamical Systems
Authors: Anand Paresh Brahmbhatt; Gon Buzaglo; Sofiia Druchyna; Elad Hazan
Venue: NeurIPS 2025 (NeurIPS 2025 poster)

Abstract: We propose a new method for the problem of controlling linear dynamical systems under partial observation and adversarial disturbances. Our new algorithm, Double Spectral Control (DSC),  matches the best known regret guarantees while exponentially improving runtime complexity over previous approaches in its dependence on the system's stability margin. Our key innovation is a two-level spectral approximation strategy, leveraging double convolution with a universal basis of spectral filters, enabling efficient and accurate learning of the best linear dynamical controllers.
Same Task, Different Circuits: Disentangling Modality-Specific Mechanisms in VLMs
Authors: Yaniv Nikankin; Dana Arad; Yossi Gandelsman; Yonatan Belinkov
Venue: NeurIPS 2025 (NeurIPS 2025 poster)

Abstract: Vision-Language models (VLMs) show impressive abilities to answer questions on visual inputs (e.g., counting objects in an image), yet demonstrate higher accuracies when performing an analogous task on text (e.g., counting words in a text).
We investigate this accuracy gap by identifying and comparing the circuits---the task-specific computational sub-graphs---in different modalities.
We show that while circuits are largely disjoint between modalities, they implement relatively similar functionalities: the differences lie primarily in processing modality-specific data positions (an image or a text sequence).
Zooming in on the image data representations, we observe they become aligned with the higher-performing analogous textual representations only towards later layers, too late in processing to effectively influence subsequent positions. 
To overcome this, we patch the representations of visual data tokens from later layers back into earlier layers. 
In experiments with multiple tasks and models, this simple intervention closes a third of the performance gap between the modalities, on average.
Our analysis sheds light on the multi-modal performance gap in VLMs and suggests a training-free approach for reducing it.