GenAI4ELab/papercli-papers huggingface dataset:
Adaptive Cannistraci-Hebb Network Automata Modelling of Complex Networks for Path-based Link Prediction
Authors: Jialin Zhao; Alessandro Muscoloni; Umberto Michieli; Yingtao Zhang; Carlo Vittorio Cannistraci
Venue: NeurIPS 2025 (NeurIPS 2025 poster)

Abstract: Many complex networks have partially observed or evolving connectivity, making link prediction a fundamental task. 
Topological link prediction infers missing links using only network topology, with applications in social, biological, and technological systems. 
The Cannistraci-Hebb (CH) theory provides a topological formulation of Hebbian learning, grounded on two pillars: 
(1) the **minimization of external links** within local communities, and 
(2) the **path-based definition of local communities** that capture homophilic (similarity-driven) interactions via paths of length 2 and synergetic (diversity-driven) interactions via paths of length 3. 
Building on this, we introduce the Cannistraci-Hebb Adaptive (CHA) network automata, an adaptive learning machine that automatically selects the optimal CH rule and path length to model each network. 
CHA unifies theoretical interpretability and data-driven adaptivity, bridging physics-inspired network science and machine intelligence. 
Across 1,269 networks from 14 domains, CHA consistently surpasses state-of-the-art methods—including SPM, SBM, graph embedding methods, and message-passing graph neural networks—while revealing the mechanistic principles governing link formation. Our code is available at https://github.com/biomedical-cybernetics/Cannistraci_Hebb_network_automata.
SceneForge: Enhancing 3D-text alignment with Structured Scene Compositions
Authors: Cristian Sbrolli; Matteo Matteucci
Venue: NeurIPS 2025 (NeurIPS 2025 poster)

Abstract: The whole is greater than the sum of its parts, even in 3D-text contrastive learning. We introduce SceneForge, a novel framework that enhances contrastive alignment between 3D point clouds and text through structured multi-object scene compositions. SceneForge leverages individual 3D shapes to construct multi-object scenes with explicit spatial relations, pairing them with coherent multi-object descriptions refined by a large language model. By augmenting contrastive training with these structured, compositional samples, SceneForge effectively addresses the scarcity of large-scale 3D-text datasets, significantly enriching data complexity and diversity. We systematically investigate critical design elements, such as the optimal number of objects per scene, the proportion of compositional samples in training batches, and scene construction strategies. Extensive experiments demonstrate that SceneForge delivers substantial performance gains across multiple tasks, including zero-shot classification on ModelNet, ScanObjNN, Objaverse-LVIS, and ScanNet, as well as few-shot part segmentation on ShapeNetPart. SceneForge’s compositional augmentations are model-agnostic, consistently improving performance across multiple encoder architectures. Moreover, SceneForge improves 3D visual question answering on ScanQA, generalizes robustly to retrieval scenarios with increasing scene complexity, and showcases spatial reasoning capabilities by adapting spatial configurations to align precisely with textual instructions.
Knowledge Insulating Vision-Language-Action Models: Train Fast, Run Fast, Generalize Better
Authors: Danny Driess; Jost Tobias Springenberg; brian ichter; LILI YU; Adrian Li-Bell; Karl Pertsch; Allen Z. Ren; Homer Walke; Quan Vuong; Lucy Xiaoyang Shi; Sergey Levine
Venue: NeurIPS 2025 (NeurIPS 2025 spotlight)

Abstract: Vision-language-action (VLA) models provide a powerful approach to training control policies for physical systems, such as robots, by combining end-to-end learning with transfer of semantic knowledge from web-scale vision-language model (VLM) training. However, the constraints of real-time control are often at odds with the design of VLMs: the most powerful VLMs have tens or hundreds of billions of parameters, presenting an obstacle to real-time inference, and operate on discrete tokens rather than the continuous-valued outputs that are required for controlling robots. To address this challenge, recent VLA models have used specialized modules for efficient continuous control, such as action experts or continuous output heads, which typically require adding new untrained parameters to the pretrained VLM backbone. While these modules improve real-time and control capabilities, it remains an open question whether they preserve or degrade the semantic knowledge contained in the pretrained VLM, and what effect they have on the VLA training dynamics. In this paper, we study this question in the context of VLAs that include a continuous diffusion or flow matching action expert, showing that naively including such experts significantly harms both training speed and knowledge transfer. We provide an extensive analysis of various design choices, their impact on performance and knowledge transfer, and propose a technique for insulating the VLM backbone during VLA training that mitigates this issue. Videos are available at https://pi.website/research/knowledge_insulation and open-source model weights are available at https://github.com/Physical-Intelligence/openpi.
Thompson Sampling in Function Spaces via Neural Operators
Authors: Rafael Oliveira; Xuesong Wang; Kian Ming A. Chai; Edwin V. Bonilla
Venue: NeurIPS 2025 (NeurIPS 2025 poster)

Abstract: We propose an extension of Thompson sampling to optimization problems over function spaces where the objective is a known functional of an unknown operator's output. We assume that queries to the operator (such as running a high-fidelity simulator or physical experiment) are costly, while functional evaluations on the operator's output are inexpensive. Our algorithm employs a sample-then-optimize approach using neural operator surrogates. This strategy avoids explicit uncertainty quantification by treating trained neural operators as approximate samples from a Gaussian process (GP) posterior. We derive regret bounds and theoretical results connecting neural operators with GPs in infinite-dimensional settings. Experiments benchmark our method against other Bayesian optimization baselines on functional optimization tasks involving partial differential equations of physical systems, demonstrating better sample efficiency and significant performance gains.
Investigating and Mitigating Catastrophic Forgetting in Medical Knowledge Injection through Internal Knowledge Augmentation Learning
Authors: Yuxuan Zhou; Xien Liu; Xiao Zhang; Chen Ning; Shijin Wang; Guoping Hu; Ji Wu
Venue: NeurIPS 2025 (NeurIPS 2025 poster)

Abstract: Large Language Models (LLMs) are expected to possess comprehensive medical knowledge to support real-world clinical applications. While domain-specific fine-tuning effectively injects medical knowledge into LLMs, it often causes catastrophic forgetting of previously acquired knowledge and instruction-following capabilities. In this paper, we investigate this issue and reveal a pattern of proximity-dependent forgetting: knowledge that is semantically or topically close to the injected content is more likely to be forgotten, while unrelated knowledge shows minimal degradation. Moreover, we observe that existing mitigation techniques fail to address this type of forgetting effectively. Motivated by this observation and inspired by human learning mechanisms, we proposeInternAL (\Internal Knowledge Augmentation Learning), a novel approach that leverages LLMs' own internal knowledge to mitigate forgetting. InternAL first probes internal knowledge closely related to the injection by prompting the model with questions derived from the injected knowledge. This knowledge is then used to augment the original injection dataset, guiding the model to retain related prior knowledge during training. Experimental results on multiple LLMs (LLaMA, Qwen) demonstrate that InternAL significantly mitigates proximity-related forgetting while maintaining strong knowledge injection performance. Our findings provide new insights into the nature of catastrophic forgetting in medical knowledge injection and highlight a promising direction for robust domain adaptation in LLMs. Code and datasets are available at https://github.com/THUMLP/InternAL.
Estimation of Stochastic Optimal Transport Maps
Authors: Sloan Nietert; Ziv Goldfeld
Venue: NeurIPS 2025 (NeurIPS 2025 poster)

Abstract: The optimal transport (OT) map is a geometry-driven transformation between high-dimensional probability distributions which underpins a wide range of tasks in statistics, applied probability, and machine learning. 
However, existing statistical theory for OT map estimation is quite restricted, hinging on Brenier's theorem (quadratic cost, absolutely continuous source) to guarantee existence and uniqueness of a deterministic OT map, on which various additional regularity assumptions are imposed to obtain quantitative error bounds. In many real‐world problems these conditions fail or cannot be certified, in which case optimal transportation is possible only via stochastic maps that can split mass.
To broaden the scope of map estimation theory to such settings, this work introduces a novel metric for evaluating the transportation quality of stochastic maps. Under this metric, we develop computationally efficient map estimators with near-optimal finite-sample risk bounds, subject to easy-to-verify minimal assumptions. Our analysis further accommodates common forms of adversarial sample contamination, yielding estimators with robust estimation guarantees. Empirical experiments are provided which validate our theory and demonstrate the utility of the proposed 
framework in settings where existing theory fails. These contributions constitute the first general-purpose theory for map estimation, compatible with a wide spectrum of real-world applications where optimal transport may be intrinsically stochastic.
A Latent Multilayer Graphical Model For Complex, Interdependent Systems
Authors: Martin Ondrus; Ivor Cribben; Yang Feng
Venue: NeurIPS 2025 (NeurIPS 2025 poster)

Abstract: Networks have been extensively used and have provided novel insights across a wide variety of research areas. However, many real-world systems are, in fact, a ``network of networks'', or a multilayer network, which interact as components of a larger multimodal system. A major difficulty in this multilayer framework is the estimation of interlayer edges or connections.  In this work, we propose a new estimation method, called multilayer sparse + low-rank inverse covariance estimation (multiSLICE), which estimates the interlayer edges. multiSLICE bridges latent variable Gaussian graphical methods with multilayer networks, offering a flexible framework for modeling processes with irregular sampling and heterogeneous graph structures.  We develop an effective algorithm to compute the estimator. We also establish theoretical conditions for the recoverability of the joint space, analyze how inter-layer interactions influence joint parameter estimation, and provide theoretical bounds on their relationships. Finally, we rigorously evaluate our method on both simulated and multimodal neuroimaging data, demonstrating improvements over state-of-the-art approaches.  Finally, all the relevant R code implementing the method in the article is available on [GitHub](https://github.com/mondrus96/multiSLICE).
Time-Masked Transformers with Lightweight Test-Time Adaptation for Neural Speech Decoding
Authors: Ebrahim Feghhi; Shreyas Kaasyap; Nima Ryan Hadidi; Jonathan Kao
Venue: NeurIPS 2025 (NeurIPS 2025 poster)

Abstract: Speech neuroprostheses aim to restore communication for people with severe paralysis by decoding speech directly from neural activity. To accelerate algorithmic progress, a recent benchmark released intracranial recordings from a paralyzed participant attempting to speak, along with a baseline decoding algorithm. Prior work on the benchmark showed impressive accuracy gains. However, these gains increased computational costs and were not demonstrated in a real-time decoding setting. Here, we make three contributions that pave the way towards accurate, efficient, and real-time neural speech decoding. First, we incorporate large amounts of time-masking during training. On average, over $50\%$ of each trial is masked. Second, we replace the gated recurrent unit (GRU) architecture used in the baseline algorithm with a compact Transformer. The Transformer architecture uses $83\%$ fewer parameters, cuts peak GPU memory usage by $52\%$, and is significantly faster to calibrate relative to the GRU. Third, we design a lightweight variant of an existing test-time adaptation method developed for decoding handwriting from neural activity. Our variant adapts the model using multiple time-masked augmentations of a single trial and requires only one gradient step per trial. Together, these contributions reduce word error rate by over $20\%$ and effectively mitigate performance degradations across held-out days in a real-time decoding setting while substantially lowering computational costs.
Time-Embedded Algorithm Unrolling for Computational MRI
Authors: Junno Yun; Yasar Utku Alcalar; Mehmet Akcakaya
Venue: NeurIPS 2025 (NeurIPS 2025 poster)

Abstract: Algorithm unrolling methods have proven powerful for solving the regularized least squares problem in computational magnetic resonance imaging (MRI). These approaches unfold an iterative algorithm with a fixed number of iterations, typically alternating between a neural network-based proximal operator for regularization, a data fidelity operation and auxiliary updates with learnable parameters. While the connection to optimization methods dictate that the proximal operator network should be shared across unrolls, this can introduce artifacts or blurring. Heuristically, practitioners have shown that using distinct networks may be beneficial, but this significantly increases the number of learnable parameters, making it challenging to prevent overfitting. To address these shortcomings, by taking inspirations from proximal operators with varying thresholds in approximate message passing (AMP) and the success of time-embedding in diffusion models, we propose a time-embedded algorithm unrolling scheme for inverse problems. Specifically, we introduce a novel perspective on the iteration-dependent proximal operation in vector AMP (VAMP) and the subsequent Onsager correction in the context of algorithm unrolling, framing them as a time-embedded neural network. Similarly, the scalar weights in the data fidelity operation and its associated Onsager correction are cast as time-dependent learnable parameters. Our extensive experiments on the fastMRI dataset, spanning various acceleration rates and datasets, demonstrate that our method effectively reduces aliasing artifacts and mitigates noise amplification, achieving state-of-the-art performance. Furthermore, we show that our time-embedding strategy extends to existing algorithm unrolling approaches, enhancing reconstruction quality without increasing the computational complexity significantly. Code available at https://github.com/JN-Yun/TE-Unrolling-MRI.
Flow Matching-Based Autonomous Driving Planning with Advanced Interactive Behavior Modeling
Authors: Tianyi Tan; Yinan Zheng; Ruiming Liang; Zexu Wang; Kexin ZHENG; Jinliang Zheng; Jianxiong Li; Xianyuan Zhan; Jingjing Liu
Venue: NeurIPS 2025 (NeurIPS 2025 poster)

Abstract: Modeling interactive driving behaviors in complex scenarios remains a fundamental challenge for autonomous driving planning. Learning-based approaches attempt to address this challenge with advanced generative models, removing the dependency on over-engineered architectures for representation fusion. However, brute-force implementation by simply stacking transformer blocks lacks a dedicated mechanism for modeling interactive behaviors that is common in real driving scenarios. The scarcity of interactive driving data further exacerbates this problem, leaving conventional imitation learning methods ill-equipped to capture high-value interactive behaviors. We propose Flow Planner, which tackles these problems through coordinated innovations in data modeling, model architecture, and learning scheme. Specifically, we first introduce fine-grained trajectory tokenization, which decomposes the trajectory into overlapping segments to decrease the complexity of whole trajectory modeling. With a sophisticatedly designed architecture, we achieve efficient temporal and spatial fusion of planning and scene information, to better capture interactive behaviors. In addition, the framework incorporates flow matching with classifier-free guidance for multi-modal behavior generation, which dynamically reweights agent interactions during inference to maintain coherent response strategies, providing a critical boost for interactive scenario understanding. Experimental results on the large-scale nuPlan dataset demonstrate that Flow Planner achieves state-of-the-art performance among learning-based approaches while effectively modeling interactive behaviors in complex driving scenarios.
Model-Based Policy Adaptation for Closed-Loop End-to-end Autonomous Driving
Authors: Haohong Lin; Yunzhi Zhang; Wenhao Ding; Jiajun Wu; Ding Zhao
Venue: NeurIPS 2025 (NeurIPS 2025 poster)

Abstract: End-to-end (E2E) autonomous driving models have demonstrated strong performance in open-loop evaluations but often suffer from cascading errors and poor generalization in closed-loop settings. To address this gap, we propose Model-based Policy Adaptation (MPA), a general framework that enhances the robustness and safety of pretrained E2E driving agents during deployment. MPA first generates diverse counterfactual trajectories using a geometry-consistent simulation engine, exposing the agent to scenarios beyond the original dataset. Based on this generated data, MPA trains a diffusion-based policy adapter to refine the base policy’s predictions and a multi-step Q value model to evaluate long-term outcomes. At inference time, the adapter proposes multiple trajectory candidates, and the Q value model selects the one with the highest expected utility. Experiments on the nuScenes benchmark using a photorealistic closed-loop simulator demonstrate that MPA significantly improves performance across in-domain, out-of-domain, and safety-critical scenarios. We further investigate how the scale of counterfactual data and inference-time guidance strategies affect overall effectiveness.
Procurement Auctions with Predictions: Improved Frugality for Facility Location
Authors: Eric Balkanski; Nicholas DeFilippis; Vasilis Gkatzelis; Xizhi Tan
Venue: NeurIPS 2025 (NeurIPS 2025 poster)

Abstract: We study the problem of designing procurement auctions for the strategic uncapacitated facility location problem: a company needs to procure a set of facility locations in order to serve its customers and each facility location is owned by a strategic agent. Each owner has a private cost for providing access to their facility (e.g., renting it or selling it to the company) and needs to be compensated accordingly. The goal is to design truthful auctions that decide which facilities the company should procure and how much to pay the corresponding owners, aiming to minimize the total cost, i.e., the monetary cost paid to the owners and the connection cost suffered by the customers (their distance to the nearest facility). We evaluate the performance of these auctions using the \emph{frugality ratio}.


We first analyze the performance of the classic VCG auction in this context and prove that its frugality ratio is exactly $3$. We then leverage the learning-augmented framework and design auctions that are augmented with predictions regarding the owners' private costs. Specifically, we propose a family of learning-augmented auctions that achieve significant payment reductions when the predictions are accurate, leading to much better frugality ratios. At the same time, we demonstrate that these auctions remain robust even if the predictions are arbitrarily inaccurate, and maintain reasonable frugality ratios even under adversarially chosen predictions. We finally provide a family of ``error-tolerant'' auctions that maintain improved frugality ratios even if the predictions are only approximately accurate, and we provide upper bounds on their frugality ratio as a function of the prediction error.
Interactive and Hybrid Imitation Learning: Provably Beating Behavior Cloning
Authors: Yichen Li; Chicheng Zhang
Venue: NeurIPS 2025 (NeurIPS 2025 poster)

Abstract: Imitation learning (IL) is a paradigm for learning sequential decision-making policies from experts, leveraging offline demonstrations, interactive annotations, or both. Recent advances show that when annotation cost is tallied per trajectory, Behavior Cloning (BC)—which relies solely on offline demonstrations—cannot be improved in general, leaving limited conditions for interactive methods such as DAgger to help. We revisit this conclusion and prove that when the annotation cost is measured per state, algorithms using interactive annotations can provably outperform BC. Specifically: (1) we show that Stagger, a one‑sample‑per‑round variant of DAgger, provably beats BC under low-recovery-cost settings; (2) we initiate the study of hybrid IL where the agent learns from offline demonstrations and interactive annotations. We propose Warm-Stagger whose learning guarantee is not much worse than using either data source alone. Furthermore, motivated by compounding error and cold‑start problem in imitation learning practice, we give an MDP example in which Warm-Stagger has significant better annotation cost; (3) experiments on MuJoCo continuous‑control tasks confirm that, with modest cost ratio between interactive and offline annotations, interactive and hybrid approaches consistently outperform BC. To the best of our knowledge, our work is the first to highlight the benefit of state‑wise interactive annotation and hybrid feedback in imitation learning.
InvFusion: Bridging Supervised and Zero-shot Diffusion for Inverse Problems
Authors: Noam Elata; Hyungjin Chung; Jong Chul Ye; Tomer Michaeli; Michael Elad
Venue: NeurIPS 2025 (NeurIPS 2025 poster)

Abstract: Diffusion Models have demonstrated remarkable capabilities in handling inverse problems, offering high-quality posterior-sampling-based solutions. Despite significant advances, a fundamental trade-off persists regarding the way the conditioned synthesis is employed: Zero-shot approaches can accommodate any linear degradation but rely on approximations that reduce accuracy. In contrast, training-based methods model the posterior correctly, but cannot adapt to the degradation at test-time. Here we introduce InvFusion, the first training-based degradation-aware posterior sampler. InvFusion combines the best of both worlds - the strong performance of supervised approaches and the flexibility of zero-shot methods. This is achieved through a novel architectural design that seamlessly integrates the degradation operator directly into the diffusion denoiser. We compare InvFusion against existing general-purpose posterior samplers, both degradation-aware zero-shot techniques and blind training-based methods. Experiments on the FFHQ and ImageNet datasets demonstrate state-of-the-art performance. Beyond posterior sampling, we further demonstrate the applicability of our architecture, operating as a general Minimum Mean Square Error predictor, and as a Neural Posterior Principal Component estimator.