GenAI4ELab/papercli-papers huggingface dataset:
Learning Sparse Approximate Inverse Preconditioners for Conjugate Gradient Solvers on GPUs
Authors: Zherui Yang; Zhehao Li; Kangbo Lyu; Yixuan Li; Tao Du; Ligang Liu
Venue: NeurIPS 2025 (NeurIPS 2025 poster)

Abstract: The conjugate gradient solver (CG) is a prevalent method for solving symmetric and positive definite linear systems $\mathbf{Ax} = \mathbf{b}$, where effective preconditioners are crucial for fast convergence. Traditional preconditioners rely on prescribed algorithms to offer rigorous theoretical guarantees, while limiting their ability to exploit optimization from data. Existing learning-based methods often utilize Graph Neural Networks (GNNs) to improve the performance and speed up the construction. However, their reliance on incomplete factorization leads to significant challenges: the associated triangular solve hinders GPU parallelization in practice, and introduces long-range dependencies which are difficult for GNNs to model. To address these issues, we propose a learning-based method to generate GPU-friendly preconditioners, particularly using GNNs to construct Sparse Approximate Inverse (SPAI) preconditioners, which avoids triangular solves and requires only two matrix-vector products at each CG step. The locality of matrix-vector product is compatible with the local propagation mechanism of GNNs. The flexibility of GNNs also allows our approach to be applied in a wide range of scenarios. Furthermore, we introduce a statistics-based scale-invariant loss function. Its design matches CG's property that the convergence rate depends on the condition number, rather than the absolute scale of $\mathbf{A}$, leading to improved performance of the learned preconditioner. Evaluations on three PDE-derived datasets and one synthetic dataset demonstrate that our method outperforms standard preconditioners (Diagonal, IC, and traditional SPAI) and previous learning-based preconditioners on GPUs. We reduce solution time on GPUs by 40%-53% (68%-113% faster), along with better condition numbers and superior generalization performance.
Scaling Language-centric Omnimodal Representation Learning
Authors: Chenghao Xiao; Hou Pong Chan; Hao Zhang; Weiwen Xu; Mahani Aljunied; Yu Rong
Venue: NeurIPS 2025 (NeurIPS 2025 poster)

Abstract: Recent multimodal embedding approaches leveraging multimodal large language models (MLLMs) fine-tuned with contrastive learning (CL) have shown promising results, yet the underlying reasons behind their superiority remain underexplored. This work argues that a crucial advantage of MLLM-based approaches stems from implicit cross-modal alignment achieved during generative pretraining, where the language decoder learns to exploit multimodal signals within a shared representation space for generating unimodal outputs. Through analysis of anisotropy and kernel similarity structure, we empirically confirm that latent alignment emerges within MLLM representations, allowing CL to serve as a lightweight refinement stage. Leveraging this insight, we propose a Language-Centric Omnimodal Embedding framework, termed LCO-Embed. Extensive experiments across diverse backbones and benchmarks demonstrate its effectiveness, achieving state-of-the-art performance across modalities. Furthermore, we identify a Generation-Representation Scaling Law (GRSL), showing that the representational capabilities gained through contrastive refinement scale positively with the MLLM's generative capabilities. This suggests that improving generative abilities evolves as an effective paradigm for enhancing representation quality. We provide a theoretical explanation of GRSL, which formally links the MLLM's generative quality to the upper bound on its representation performance, and validate it on a challenging, low-resource visual-document retrieval task, showing that continual generative pretraining before CL can further enhance the potential of a model's embedding capabilities. Codes, models, and resources are available at https://github.com/LCO-Embedding/LCO-Embedding.
Towards Unsupervised Open-Set Graph Domain Adaptation via Dual Reprogramming
Authors: Zhen Zhang; Bingsheng He
Venue: NeurIPS 2025 (NeurIPS 2025 poster)

Abstract: Unsupervised Graph Domain Adaptation has become a promising paradigm for transferring knowledge from a fully labeled source graph to an unlabeled target graph. Existing graph domain adaptation models primarily focus on the closed-set setting, where the source and target domains share the same label spaces. However, this assumption might not be practical in the real-world scenarios, as the target domain might include classes that are not present in the source domain. In this paper, we investigate the problem of unsupervised open-set graph domain adaptation, where the goal is to not only correctly classify target nodes into the known classes, but also recognize previously unseen node types into the unknown class. Towards this end, we propose a novel framework called GraphRTA, which conducts reprogramming on both the graph and model sides. Specifically, we reprogram the graph by modifying target graph structure and node features, which facilitates better separation of known and unknown classes. Meanwhile, we also perform model reprogramming by pruning domain-specific parameters to reduce bias towards the source graph while preserving parameters that capture transferable patterns across graphs. Additionally, we extend the classifier with an extra dimension for the unknown class, thus eliminating the need of manually specified threshold in open-set recognition. Comprehensive experiments on several public datasets demonstrate that our proposed model can achieve satisfied performance compared with recent state-of-the-art baselines. Our source codes and datasets are publicly available at https://github.com/cszhangzhen/GraphRTA.
BrainFlow: A Holistic Pathway of Dynamic Neural System on Manifold
Authors: Zhixuan Zhou; Tingting Dan; Guorong Wu
Venue: NeurIPS 2025 (NeurIPS 2025 poster)

Abstract: A fundamental challenge in cognitive neuroscience is understanding how cognition emerges from the interplay between structural connectivity (SC) and dynamic functional connectivity (FC) in the brain. 
Network neuroscience has emerged as a powerful framework to understand brain function through a holistic perspective on structure-function relationships. In this context, current machine learning approaches typically seek to establish direct mappings between structural connectivity (SC) and functional connectivity (FC) associated with specific cognitive states.
However, these state-independent methods often yield inconsistent results due to overlapping brain networks across cognitive states. 
To address this limitation, we conceptualize to uncover the dendritic coupling mechanism between one static SC and multiple FCs by solving a flow problem that bridges the distribution of SC to a mixed distribution of FCs, conditioned on various cognitive states, along a Riemannian manifold of symmetric positive-definite (SPD) manifold.
We further prove the equivalence between flow matching on the SPD manifold and on the computationally efficient Cholesky manifold. 
Since a spare of functional connections is shared across cognitive states, we introduce the notion of consensus control to promote the shared kinetic structures between multiple FC-to-SC pathways via synchronized coordination, yielding a biologically meaningful underpinning on SC-FC coupling mechanism.
Together, we present BrainFlow, a reversible generative model that achieves state-of-the-art performance on not only synthetic data but also large-scale neuroimaging datasets from UK Biobank and Human Connectome Project.
Federated Dialogue-Semantic Diffusion for Emotion Recognition under Incomplete Modalities
Authors: Xihang Qiu; Jiarong Cheng; Yuhao Fang; Wanpeng Zhang; Yao Lu; Ye Zhang; Chun Li
Venue: NeurIPS 2025 (NeurIPS 2025 poster)

Abstract: Multimodal Emotion Recognition in Conversations (MERC) enhances emotional understanding through the fusion of multimodal signals. However, unpredictable modality absence in real-world scenarios significantly degrades the performance of existing methods. Conventional missing-modality recovery approaches, which depend on training with complete multimodal data, often suffer from semantic distortion under extreme data distributions, such as fixed-modality absence. To address this, we propose the Federated Dialogue-guided and Semantic-Consistent Diffusion (FedDISC) framework, pioneering the integration of federated learning into missing-modality recovery. By federated aggregation of modality-specific diffusion models trained on clients and broadcasting them to clients missing corresponding modalities, FedDISC overcomes single-client reliance on modality completeness. Additionally, the DISC-Diffusion module ensures consistency in context, speaker identity, and semantics between recovered and available modalities, using a Dialogue Graph Network to capture conversational dependencies and a Semantic Conditioning Network to enforce semantic alignment. We further introduce a novel Alternating Frozen Aggregation strategy, which cyclically freezes recovery and classifier modules to facilitate collaborative optimization. Extensive experiments on the IEMOCAP, CMUMOSI, and CMUMOSEI datasets demonstrate that FedDISC achieves superior emotion classification performance across diverse missing modality patterns, outperforming existing approaches.
Continuous Thought Machines
Authors: Luke Nicholas Darlow; Ciaran Regan; Sebastian Risi; Jeffrey Seely; Llion Jones
Venue: NeurIPS 2025 (NeurIPS 2025 spotlight)

Abstract: Biological brains demonstrate complex neural activity, where neural dynamics are critical to how brains process information. Most artificial neural networks ignore the complexity of individual neurons. We challenge that paradigm. By incorporating neuron-level processing and synchronization, we reintroduce neural timing as a foundational element. We present the Continuous Thought Machine (CTM), a model designed to leverage neural dynamics as its core representation. The CTM has two innovations: (1) neuron-level temporal processing}, where each neuron uses unique weight parameters to process incoming histories; and (2) neural synchronization as a latent representation. The CTM aims to strike a balance between neuron abstractions and biological realism. It operates at a level of abstraction that effectively captures essential temporal dynamics while remaining computationally tractable. We demonstrate the CTM's performance and versatility across a range of tasks, including solving 2D mazes, ImageNet-1K classification, parity computation, and more. Beyond displaying rich internal representations and offering a natural avenue for interpretation owing to its internal process, the CTM is able to perform tasks that require complex sequential reasoning. The CTM can also leverage adaptive compute, where it can stop earlier for simpler tasks, or keep computing when faced with more challenging instances. The goal of this work is to share the CTM and its associated innovations, rather than pushing for new state-of-the-art results. To that end, we believe the CTM represents a significant step toward developing more biologically plausible and powerful artificial intelligence systems. We provide an accompanying [interactive online demonstration](https://pub.sakana.ai/ctm/) and an [extended technical report](https://pub.sakana.ai/ctm/paper).
UGoDIT: Unsupervised Group Deep Image Prior Via Transferable Weights
Authors: Shijun Liang; Ismail Alkhouri; Siddhant Gautam; Qing Qu; Saiprasad Ravishankar
Venue: NeurIPS 2025 (NeurIPS 2025 poster)

Abstract: Recent advances in data-centric deep generative models have led to significant progress in solving inverse imaging problems. However, these models (e.g., diffusion models (DMs)) typically require large amounts of fully sampled (clean) training data, which is often impractical in medical and scientific settings such as dynamic imaging. On the other hand, training-data-free approaches like the Deep Image Prior (DIP) do not require clean ground-truth images but suffer from noise overfitting and can be computationally expensive as the network parameters need to be optimized for each measurement vector independently. Moreover, DIP-based methods often overlook the potential of learning a prior using a small number of sub-sampled measurements (or degraded images) available during training. In this paper, we propose **UGoDIT**—an **U**nsupervised **G**r**o**up **DI**P with **T**ransferable weights—designed for the low-data regime where only a very small number, $M$, of sub-sampled measurement vectors are available during training. Our method learns a set of transferable weights by optimizing a shared encoder and $M$ disentangled decoders. At test time, we reconstruct the unseen degraded image using a DIP network, where part of the parameters are fixed to the learned weights, while the remaining are optimized to enforce measurement consistency. We evaluate \our on both medical (multi-coil MRI) and natural (super resolution and non-linear deblurring) image recovery tasks under various settings. Compared to recent standalone DIP methods, \our provides accelerated convergence and notable improvement in reconstruction quality. Furthermore, our method achieves performance competitive with SOTA DM-based and supervised approaches, despite not requiring large amounts of clean training data. Our code is available at: https://github.com/sjames40/UGoDIT.
Private Statistical Estimation via Truncation
Authors: Manolis Zampetakis; Felix Zhou
Venue: NeurIPS 2025 (NeurIPS 2025 poster)

Abstract: We introduce a novel framework for differentially private (DP) statistical estimation via data truncation, addressing a key challenge in DP estimation when the data support is unbounded. Traditional approaches rely on problem-specific sensitivity analysis, limiting their applicability. By leveraging techniques from truncated statistics, we develop computationally efficient DP estimators for exponential family distributions, including Gaussian mean and covariance estimation, achieving near-optimal sample complexity. Previous works on exponential families only consider bounded or one-dimensional families. Our approach mitigates sensitivity through truncation while carefully correcting for the introduced bias using maximum likelihood estimation and DP stochastic gradient descent. Along the way, we establish improved uniform convergence guarantees for the log-likelihood function of exponential families, which may be of independent interest. Our results provide a general blueprint for DP algorithm design via truncated statistics.
Rethinking Circuit Completeness in Language Models: AND, OR, and ADDER Gates
Authors: Hang Chen; Jiaying Zhu; Xinyu Yang; Wenya Wang
Venue: NeurIPS 2025 (NeurIPS 2025 poster)

Abstract: Circuit discovery has gradually become one of the prominent methods for mechanistic interpretability, and research on circuit completeness has also garnered increasing attention. Methods of circuit discovery that do not guarantee completeness not only result in circuits that are not fixed across different runs but also cause key mechanisms to be omitted. The nature of incompleteness arises from the presence of OR gates within the circuit, which are often only partially detected in standard circuit discovery methods. To this end, we systematically introduce three types of logic gates: AND, OR, and ADDER gates, and decompose the circuit into combinations of these logical gates. Through the concept of these gates, we derive the minimum requirements necessary to achieve faithfulness and completeness. Furthermore, we propose a framework that combines noising-based and denoising-based interventions, which can be easily integrated into existing circuit discovery methods without significantly increasing computational complexity. This framework is capable of fully identifying the logic gates and distinguishing them within the circuit. In addition to the extensive experimental validation of the framework's ability to restore the faithfulness, completeness, and sparsity of circuits, using this framework, we uncover fundamental properties of the three logic gates, such as their proportions and contributions to the output, and explore how they behave among the functionalities of language models.
Flexible MOF Generation with Torsion-Aware Flow Matching
Authors: Nayoung Kim; Seongsu Kim; Sungsoo Ahn
Venue: NeurIPS 2025 (NeurIPS 2025 poster)

Abstract: Designing metal-organic frameworks (MOFs) with novel chemistries is a longstanding challenge due to their large combinatorial space and complex 3D arrangements of the building blocks. While recent deep generative models have enabled scalable MOF generation, they assume (1) a fixed set of building blocks and (2) known local 3D coordinates of building blocks. However, this limits their ability to (1) design novel MOFs and (2) generate the structure using novel building blocks. We propose a two-stage MOF generation framework that overcomes these limitations by modeling both chemical and geometric degrees of freedom. First, we train an SMILES-based autoregressive model to generate metal and organic building blocks, paired with a cheminformatics toolkit for 3D structure initialization. Second, we introduce a flow matching model that predicts translations, rotations, and torsional angles to assemble the blocks into valid 3D frameworks. Our experiments demonstrate improved reconstruction accuracy, the generation of valid, novel, and unique MOFs, and the ability to create novel building blocks. Our code is available at https://github.com/nayoung10/MOFFlow-2.
Proper Hölder-Kullback Dirichlet Diffusion: A Framework for High Dimensional Generative Modeling
Authors: Wanpeng Zhang; Yuhao Fang; Xihang Qiu; Jiarong Cheng; Jialong Hong; Bin Zhai; Qing Zhou; Yao Lu; Ye Zhang; Chun Li
Venue: NeurIPS 2025 (NeurIPS 2025 poster)

Abstract: Diffusion-based generative models have long depended on Gaussian priors, with little exploration of alternative distributions. We introduce a Proper Hölder-Kullback Dirichlet framework that uses time-varying multiplicative transformations to define both forward and reverse diffusion processes. Moving beyond conventional reweighted evidence lower bounds (ELBO) or Kullback–Leibler upper bounds (KLUB), we propose two novel divergence measures: the Proper Hölder Divergence (PHD) and the Proper Hölder–Kullback (PHK) divergence, the latter designed to restore symmetry missing in existing formulations. When optimizing our Dirichlet diffusion model with PHK, we achieve a Fréchet Inception Distance (FID) of 2.78 on unconditional CIFAR-10. Comprehensive experiments on natural-image datasets validate the generative strengths of model and confirm PHK’s effectiveness in model training. These contributions expand the diffusion-model family with principled non-Gaussian processes and effective optimization tools, offering new avenues for versatile, high-fidelity generative modeling.
Generative Model Inversion Through the Lens of the Manifold Hypothesis
Authors: Xiong Peng; Bo Han; Fengfei Yu; Tongliang Liu; Feng Liu; Mingyuan Zhou
Venue: NeurIPS 2025 (NeurIPS 2025 poster)

Abstract: Model inversion attacks (MIAs) aim to reconstruct class-representative samples from trained models. Recent generative MIAs utilize generative adversarial networks to learn image priors that guide the inversion process, yielding reconstructions with high visual quality and strong fidelity to the private data. To explore the reason behind their effectiveness, we begin by examining the gradients of inversion loss w.r.t. synthetic inputs, and find that these gradients are surprisingly noisy. Further analysis shows that generative model inversion approaches implicitly denoise the gradients by projecting them onto the tangent space of the generator manifold—filtering out directions that deviate from the manifold structure while preserving informative components aligned with it. Our empirical measurements show that, in models trained with standard supervision, loss gradients exhibit large angular deviations from the data manifold, indicating poor alignment with class-relevant directions. This observation motivates our central hypothesis: models become more vulnerable to MIAs when their loss gradients align more closely with the generator manifold. We validate this hypothesis by designing a novel training objective that explicitly promotes such alignment. Building on this insight, we further introduce a training-free approach to enhance gradient–manifold alignment during inversion, leading to consistent improvements over state-of-the-art generative MIAs.
Dual-Comb Ghost Imaging with Transformer-Based Reconstruction for Optical Fiber Endomicroscopy
Authors: David Dang; Myoung-Gyun Suh; Maodong Gao; ByoungJun Park; Beyonce Hu; Yucheng Jin; Wilton J. M. Kort-Kamp; Ho Wai Howard Lee
Venue: NeurIPS 2025 (NeurIPS 2025 poster)

Abstract: Endoscopic imaging is indispensable for visualizing internal organs, yet conventional systems remain bulky and costly because they rely on large, multi-element optics, which limits their ability to access and image certain areas of the body. Achieving high-quality endomicroscopy with hundred micron-scale and inexpensive hardware remains a grand challenge. Optical fibers offer a sub-millimeter-scale imaging conduit that could meet this need, but existing fiber-based approaches typically require either raster scanning or multicore bundles, which limit resolution and speed of imaging. In this work, we overcome these limitations by combining dual-comb interferometry with optical ghost imaging and advanced algorithm. Optical frequency combs enable precise and parallel speckle illumination via wavelength-division multiplexing through a single-core fiber, while our dual-comb compressive ghost imaging approach enables snapshot detection of bucket-sum signals using a single-pixel detector, eliminating the need for both spatial and spectral scanning. To reconstruct images from these highly compressed measurements, we introduce Optical Ghost-GPT, a transformer-based image reconstruction model that enables fast, high-fidelity recovery at low sampling rates. Our dual-comb ghost imaging approach, combined with the novel algorithm, outperforms classical ghost imaging techniques in both speed and accuracy, enabling real-time, high-resolution endoscopic imaging with a significantly reduced device footprint. This advancement paves the way for non-invasive, high-resolution, low-cost endomicroscopy and other sensing applications constrained by hardware size and complexity.
CodeGEMM: A Codebook-Centric Approach to Efficient GEMM in Quantized LLMs
Authors: Gunho Park; Jeongin Bae; Byeongwook Kim; Baeseong park; Jiwon Ryu; Hoseung Kim; Se Jung Kwon; Dongsoo Lee
Venue: NeurIPS 2025 (NeurIPS 2025 poster)

Abstract: Weight-only quantization is widely used to mitigate the memory-bound nature of LLM inference. Codebook-based methods extend this trend by achieving strong accuracy in the extremely low-bit regime (e.g., 2-bit). However, current kernels rely on dequantization, which repeatedly fetches centroids and reconstructs weights, incurring substantial latency and cache pressure. We present CodeGEMM, a codebook-centric GEMM kernel that replaces dequantization with precomputed inner products between centroids and activations stored in a lightweight Psumbook. At inference, code indices directly gather these partial sums, eliminating per-element lookups and reducing the on-chip footprint. The kernel supports the systematic exploration of latency–memory–accuracy trade-offs under a unified implementation.
On Llama-3 models, CodeGEMM delivers 1.83x (8B) and 8.93x (70B) speedups in the 2-bit configuration compared to state-of-the-art codebook-based quantization at comparable accuracy and further improves computing efficiency and memory subsystem utilization.