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Probabilistic Methods · Gaussian Processes

Xinxing Shi, Xiaoyu Jiang, Mauricio Álvarez

Gaussian Process (GP) Variational Autoencoders (VAEs) extend standard VAEs by replacing the fully factorised Gaussian prior with a GP prior, thereby capturing richer correlations among latent variables. However, performing exact GP inference in large-scale GPVAEs is computationally prohibitive, often forcing existing approaches to rely on restrictive kernel assumptions or large sets of inducing points. In this work, we propose a neighbour-driven approximation strategy that exploits local adjacencies in the latent space to achieve scalable GPVAE inference. By confining computations to the nearest neighbours of each data point, our method preserves essential latent dependencies, allowing more flexible kernel choices and mitigating the need for numerous inducing points. Through extensive experiments on tasks including representation learning, data imputation, and conditional generation, we demonstrate that our approach outperforms other GPVAE variants in both predictive performance and computational efficiency.

Deep Learning · Self-Supervised Learning

Hongbin Pei, Jingxin Hai, Yu Li, Huiqi Deng, Denghao Ma, Jie Ma, Pinghui Wang, Jing Tao, Xiaohong Guan

Pseudo-labeling is a widely used strategy in semi-supervised learning. Existing methods typically select predicted labels with high confidence scores and high training stationarity, as pseudo-labels to augment training sets. In contrast, this paper explores the pseudo-labeling potential of predicted labels that **do not** exhibit these characteristics. We discover a new type of predicted labels suitable for pseudo-labeling, termed *two-phase labels*, which exhibit a two-phase pattern during training: *they are initially predicted as one category in early training stages and switch to another category in subsequent epochs.* Case studies show the two-phase labels are informative for decision boundaries. To effectively identify the two-phase labels, we design a 2-*phasic* metric that mathematically characterizes their spatial and temporal patterns. Furthermore, we propose a loss function tailored for two-phase pseudo-labeling learning, allowing models not only to learn correct correlations but also to eliminate false ones. Extensive experiments on eight datasets show that **our proposed 2-*phasic* metric acts as a powerful booster** for existing pseudo-labeling methods by additionally incorporating the two-phase labels, achieving an average classification accuracy gain of 1.73% on image datasets and 1.92% on graph datasets.

Deep Learning · Graph Neural Networks

Tianlang Chen, Charilaos Kanatsoulis, Jure Leskovec

Predictive tasks on relational databases are critical in real-world applications spanning e-commerce, healthcare, and social media. To address these tasks effectively, Relational Deep Learning (RDL) encodes relational data as graphs, enabling Graph Neural Networks (GNNs) to exploit relational structures for improved predictions. However, existing RDL methods often overlook the intrinsic structural properties of the graphs built from relational databases, leading to modeling inefficiencies, particularly in handling many-to-many relationships. Here we introduce RelGNN, a novel GNN framework specifically designed to leverage the unique structural characteristics of the graphs built from relational databases. At the core of our approach is the introduction of atomic routes, which are simple paths that enable direct single-hop interactions between the source and destination nodes. Building upon these atomic routes, RelGNN designs new composite message passing and graph attention mechanisms that reduce redundancy, highlight key signals, and enhance predictive accuracy. RelGNN is evaluated on 30 diverse real-world tasks from Relbench (Fey et al., 2024), and achieves state-of-the-art performance on the vast majority of tasks, with improvements of up to 25%.

Deep Learning · Everything Else

Suorong Yang, Peng Ye, Furao Shen, Dongzhan Zhou

Dynamic data selection aims to accelerate training with lossless performances.However, reducing training data inherently limits data diversity, potentially hindering generalization.While data augmentation is widely used to enhance diversity, it is typically not optimized in conjunction with selection.As a result, directly combining these techniques fails to fully exploit their synergies.To tackle the challenge, we propose a novel online data training framework that, for the first time, unifies dynamic data selection and augmentation, achieving both training efficiency and enhanced performance.Our method estimates each sample's joint distribution of local density and multimodal semantic consistency, allowing for the targeted selection of augmentation-suitable samples while suppressing the inclusion of noisy or ambiguous data.This enables a more significant reduction in dataset size without sacrificing model generalization.Experimental results demonstrate that our method outperforms existing state-of-the-art approaches on various benchmark datasets and architectures, e.g., reducing 50% training costs on ImageNet-1k with lossless performance.Furthermore, our approach enhances noise resistance and improves model robustness, reinforcing its practical utility in real-world scenarios.

General Machine Learning · Everything Else

Jingyang Qiao, zhizhong zhang, Xin Tan, Yanyun Qu, Shouhong Ding, Yuan Xie

Continual Instruction Tuning (CIT) is adopted to continually instruct Large Models to follow human intent data by data. It is observed that existing gradient update would heavily destroy the performance on previous datasets during CIT process. Instead, Exponential Moving Average (EMA), owns the ability to trace previous parameters, which can aid in decreasing forgetting. Nonetheless, its stable balance weight fails to deal with the ever-changing datasets, leading to the out-of-balance between plasticity and stability. In this paper, we propose a general continual instruction tuning framework to address the challenge. Starting from the trade-off prerequisite and EMA update, we propose the plasticity and stability ideal condition. Based on Taylor expansion in the loss function, we find the optimal balance weight can be automatically determined by the gradients and learned parameters. Therefore, we propose a stable-plasticity balanced coefficient to avoid knowledge interference. Based on the semantic similarity of the instructions, we can determine whether to retrain or expand the training parameters and allocate the most suitable parameters for the testing instances. Extensive experiments across multiple continual instruction tuning benchmarks demonstrate that our approach not only enhances anti-forgetting capabilities but also significantly improves overall continual tuning performance. Our code is available at https://github.com/JingyangQiao/CoIN.

General Machine Learning · Kernel methods

Hideaki Kim, Tomoharu Iwata, Akinori Fujino

Kernel method-based intensity estimators, formulated within reproducing kernel Hilbert spaces (RKHSs), and classical kernel intensity estimators (KIEs) have been among the most easy-to-implement and feasible methods for estimating the intensity functions of inhomogeneous Poisson processes. While both approaches share the term "kernel", they are founded on distinct theoretical principles, each with its own strengths and limitations. In this paper, we propose a novel regularized kernel method for Poisson processes based on the least squares loss and show that the resulting intensity estimator involves a specialized variant of the representer theorem: it has the dual coefficient of unity and coincides with classical KIEs. This result provides new theoretical insights into the connection between classical KIEs and kernel method-based intensity estimators, while enabling us to develop an efficient KIE by leveraging advanced techniques from RKHS theory. We refer to the proposed model as the *kernel method-based kernel intensity estimator* (K$^2$IE). Through experiments on synthetic datasets, we show that K$^2$IE achieves comparable predictive performance while significantly surpassing the state-of-the-art kernel method-based estimator in computational efficiency.

Deep Learning · Large Language Models

Zihang Liu, Tianyu Pang, Oleg Balabanov, Chaoqun Yang, Tianjin Huang, Lu Yin, Yaoqing Yang, Shiwei Liu

Recent studies have shown that supervised fine-tuning of LLMs on a small number of high-quality datasets can yield strong reasoning capabilities. However, full fine-tuning (Full FT), while powerful, is computationally expensive and susceptible to overfitting and catastrophic forgetting, particularly when data is limited. Sparse fine-tuning, which previously achieved notable success by updating only a small subset of model parameters, offers a promising trade-off between efficiency and effectiveness. Yet, it has lagged behind in the LLM era due to the difficulty of identifying parameters truly critical for reasoning. In this work, we state that weights with the largest magnitude after low-rank approximation are critical weights for fine-tuning, which we call *Principal Weights*. Surprisingly, while magnitude-based sparse fine-tuning performs poorly as a baseline on LLM fine-tuning, it becomes highly effective after rank reduction. These insights motivate our method: **L**ow-rank **I**nformed Sparse **F**ine-**T**uning ($\texttt{LIFT}$). $\texttt{LIFT}$ only updates the top 5% *Principal Weights* throughout training and consistently achieves better performance on reasoning tasks than Full FT, while maintaining memory efficiency on par with popular parameter-efficient fine-tuning methods. In addition to strong performance on target domains such as arithmetic reasoning, $\texttt{LIFT}$ also retains up to 20% more source-domain knowledge, compared to Full FT and LoRA. Our code is available at: https://github.com/zihanghliu/LIFT.

Social Aspects · Accountability, Transparency, and Interpretability

Junwei Su, Chuan Wu

This paper investigates the convergence behavior of score-based graph generative models (SGGMs). Unlike common score-based generative models (SGMs) that are governed by a single stochastic differential equation (SDE), SGGMs utilize a system of dependent SDEs, where the graph structure and node features are modeled separately, while accounting for their inherent dependencies. This distinction makes existing convergence analyses from SGMs inapplicable for SGGMs. In this work, we present the first convergence analysis for SGGMs, focusing on the convergence bound (the risk of generative error) across three key graph generation paradigms: (1) feature generation with a fixed graph structure, (2) graph structure generation with fixed node features, and (3) joint generation of both graph structure and node features. Our analysis reveals several unique factors specific to SGGMs (e.g., the topological properties of the graph structure) which significantly affect the convergence bound. Additionally, we offer theoretical insights into the selection of hyperparameters (e.g., sampling steps and diffusion length) and advocate for techniques like normalization to improve convergence. To validate our theoretical findings, we conduct a controlled empirical study using a synthetic graph model. The results in this paper contribute to a deeper theoretical understanding of SGGMs and offer practical guidance for designing more efficient and effective SGGMs.

Deep Learning · Large Language Models

Wenbin Wang, Yongcheng Jing, Liang Ding, Yingjie Wang, Li Shen, Yong Luo, Bo Du, Dacheng Tao

High-resolution (HR) image perception remains a key challenge in multimodal large language models (MLLMs). To drive progress beyond the limits of heuristic methods, this paper advances HR perception capabilities of MLLMs by harnessing cutting-edge long-context techniques such as retrieval-augmented generation (RAG). Towards this end, this paper presents the first study exploring the use of RAG to address HR perception challenges. Specifically, we propose Retrieval-Augmented Perception (RAP), a training-free framework that retrieves and fuses relevant image crops while preserving spatial context using the proposed Spatial-Awareness Layout. To accommodate different tasks, the proposed Retrieved-Exploration Search (RE-Search) dynamically selects the optimal number of crops based on model confidence and retrieval scores. Experimental results on HR benchmarks demonstrate the significant effectiveness of RAP, with LLaVA-v1.5-13B achieving a 43\% improvement on $V^*$ Bench and 19\% on HR-Bench. Code is available at https://github.com/DreamMr/RAP.

Applications · Robotics

Alexandre Capone, Ryan Cosner, Aaron Ames, Sandra Hirche

Control tasks with safety requirements under high levels of model uncertainty are increasingly common. Machine learning techniques are frequently used to address such tasks, typically by leveraging model error bounds to specify robust constraint-based safety filters. However, if the learned model uncertainty is very high, the corresponding filters are potentially invalid, meaning no control input satisfies the constraints imposed by the safety filter. While most works address this issue by assuming some form of safe backup controller, ours tackles it by collecting additional data on the fly using a Gaussian process bandit-type algorithm. We combine a control barrier function with a learned model to specify a robust certificate that ensures safety if feasible. Whenever infeasibility occurs, we leverage the control barrier function to guide exploration, ensuring the collected data contributes toward the closed-loop system safety. By combining a safety filter with exploration in this manner, our method provably achieves safety in a general setting that does not require any prior model or backup controller, provided that the true system lies in a reproducing kernel Hilbert space. To the best of our knowledge, it is the first safe learning-based control method that achieves this.

Theory · Learning Theory

Jongha (Jon) Ryu, Abhin Shah, Gregory Wornell

This paper studies a family of estimators based on noise-contrastive estimation (NCE) for learning unnormalized distributions. The main contribution of this work is to provide a unified perspective on various methods for learning unnormalized distributions, which have been independently proposed and studied in separate research communities, through the lens of NCE. This unified view offers new insights into existing estimators. Specifically, for exponential families, we establish the finite-sample convergence rates of the proposed estimators under a set of regularity assumptions, most of which are new.

General Machine Learning · Supervised Learning

Guanglong Sun, Hongwei Yan, Liyuan Wang, Qian Li, Bo Lei, Yi Zhong

Knowledge distillation (KD) is a powerful strategy for training deep neural networks (DNNs). While it was originally proposed to train a more compact “student” model from a large “teacher” model, many recent efforts have focused on adapting it as an effective way to promote generalization of the model itself, such as online KD and self KD. Here, we propose an easy-to-use and compatible strategy named Spaced KD to improve the effectiveness of both online KD and self KD, in which the student model distills knowledge from a teacher model trained with a space interval ahead. This strategy is inspired by a prominent theory named spacing effect in the field of biological learning and memory, positing that appropriate intervals between learning trials can significantly enhance learning performance. We provide an in-depth theoretical and empirical analysis showing that the benefits of the proposed spacing effect in KD stem from seeking a flat minima during stochastic gradient descent (SGD). We perform extensive experiments to demonstrate the effectiveness of our Spaced KD in improving the learning performance of DNNs (e.g., the additional performance gain is up to 2.31% and 3.34% on Tiny-ImageNet over online KD and self KD, respectively). Our codes have been released on github~\url{https://github.com/SunGL001/Spaced-KD}.

Deep Learning · Generative Models and Autoencoders

Rajat Rasal, Avinash Kori, Fabio De Sousa Ribeiro, Tian Xia, Ben Glocker

Counterfactual image generation presents significant challenges, including preserving identity, maintaining perceptual quality, and ensuring faithfulness to an underlying causal model. While existing auto-encoding frameworks admit semantic latent spaces which can be manipulated for causal control, they struggle with scalability and fidelity. Advancements in diffusion models present opportunities for improving counterfactual image editing, having demonstrated state-of-the-art visual quality, human-aligned perception and representation learning capabilities. Here, we present a suite of diffusion-based causal mechanisms, introducing the notions of spatial, semantic and dynamic abduction. We propose a general framework that integrates semantic representations into diffusion models through the lens of Pearlian causality to edit images via a counterfactual reasoning process. To the best of our knowledge, ours is the first work to consider high-level semantic identity preservation for diffusion counterfactuals and to demonstrate how semantic control enables principled trade-offs between faithful causal control and identity preservation.

Reinforcement Learning · Deep RL

Jeongmo Kim, Yisak Park, Minung Kim, Seungyul Han

Meta reinforcement learning aims to develop policies that generalize to unseen tasks sampled from a task distribution. While context-based meta-RL methods improve task representation using task latents, they often struggle with out-of-distribution (OOD) tasks. To address this, we propose Task-Aware Virtual Training (TAVT), a novel algorithm that accurately captures task characteristics for both training and OOD scenarios using metric-based representation learning. Our method successfully preserves task characteristics in virtual tasks and employs a state regularization technique to mitigate overestimation errors in state-varying environments. Numerical results demonstrate that TAVT significantly enhances generalization to OOD tasks across various MuJoCo and MetaWorld environments. Our code is available at https://github.com/JM-Kim-94/tavt.git.

Applications · Language, Speech and Dialog

Hongshen Xu, Zichen Zhu, Lei Pan, Zihan Wang, Su Zhu, Da Ma, Ruisheng Cao, Lu Chen, Kai Yu

Large Language Models (LLMs) have expanded their capabilities beyond language generation to interact with external tools, enabling automation and real-world applications. However, tool hallucinations—where models either select inappropriate tools or misuse them—pose significant challenges, leading to erroneous task execution, increased computational costs, and reduced system reliability. To systematically address this issue, we define and categorize tool hallucinations into two main types: tool selection hallucination and tool usage hallucination. To evaluate and mitigate these issues, we introduce RelyToolBench, which integrates specialized test cases and novel metrics to assess hallucination-aware task success and efficiency. Finally, we propose Relign, a reliability alignment framework that expands the tool-use action space to include indecisive actions, allowing LLMs to defer tool use, seek clarification, or adjust tool selection dynamically. Through extensive experiments, we demonstrate that Relign significantly reduces tool hallucinations, improves task reliability, and enhances the efficiency of LLM tool interactions. The code and data will be publicly available.

Applications · Chemistry, Physics, and Earth Sciences

Shuqi Lu, Xiaohong Ji, Bohang Zhang, Lin Yao, Siyuan Liu, Zhifeng Gao, Linfeng Zhang, Guolin Ke

Molecular pretrained representations (MPR) has emerged as a powerful approach for addressing the challenge of limited supervised data in applications such as drug discovery and material design. While early MPR methods relied on 1D sequences and 2D graphs, recent advancements have incorporated 3D conformational information to capture rich atomic interactions. However, these prior models treat molecules merely as discrete atom sets, overlooking the space surrounding them. We argue from a physical perspective that only modeling these discrete points is insufficient. We first present a simple yet insightful observation: naively adding randomly sampled virtual points beyond atoms can surprisingly enhance MPR performance. In light of this, we propose a principled framework that incorporates the entire 3D space spanned by molecules. We implement the framework via a novel Transformer-based architecture, dubbed SpaceFormer, with three key components:(1)grid-based space discretization; (2)grid sampling/merging; and (3)efficient 3D positional encoding.Extensive experiments show that SpaceFormer significantly outperforms previous 3D MPR models across various downstream tasks with limited data, validating the benefit of leveraging the additional 3D space beyond atoms in MPR models.

Applications · Neuroscience, Cognitive Science

Zachary Brown, David Carlson

The field of hypothesis generation promises to reduce costs in neuroscience by narrowing the range of interventional studies needed to study various phenomena. Existing machine learning methods can generate scientific hypotheses from complex datasets, but many approaches assume causal relationships are static over time, limiting their applicability to systems with dynamic, state-dependent behavior, such as the brain. While some techniques attempt dynamic causal discovery through factor models, they often restrict relationships to linear patterns or impose other simplifying assumptions. We propose a novel method that models dynamic graphs as a conditionally weighted superposition of static graphs, where each static graph can capture nonlinear relationships. This approach enables the detection of complex, time-varying interactions between variables beyond linear limitations. Our method improves f1-scores of predicted dynamic causal patterns by roughly 22-28% on average over baselines in some of our experiments, with some improvements reaching well over 60%. A case study on real brain data demonstrates our method's ability to uncover relationships linked to specific behavioral states, offering valuable insights into neural dynamics.

Deep Learning · Large Language Models

Itay Yona, Ilia Shumailov, Jamie Hayes, Yossi Gandelsman

Large Language Models (LLMs), despite their impressive capabilities, often fail to accurately repeat a single word when prompted to, and instead output unrelated text. This unexplained failure mode represents a *vulnerability*, allowing even end users to diverge models away from their intended behavior. We aim to explain the causes for this phenomenon and link it to the concept of "attention sinks", an emergent LLM behavior crucial for fluency, in which the initial token receives disproportionately high attention scores. Our investigation identifies the neural circuit responsible for attention sinks and shows how long repetitions disrupt this circuit. We extend this finding to other nonrepeating sequences that exhibit similar circuit disruptions. To address this, we propose a targeted patch that effectively resolves the issue without negatively impacting the overall performance of the model. This study provides a mechanistic explanation for an LLM vulnerability, demonstrating how interpretability can diagnose and address issues, and offering insights that pave the way for more secure and reliable models.

General Machine Learning · Scalable Algorithms

Gabriele Visentin, Patrick Cheridito

We present a novel method for efficiently computing optimal transport maps and Wasserstein barycenters in high-dimensional spaces. Our approach uses conditional normalizing flows to approximate the input distributions as invertible pushforward transformations from a common latent space. This makes it possible to directly solve the primal problem using gradient-based minimization of the transport cost, unlike previous methods that rely on dual formulations and complex adversarial optimization. We show how this approach can be extended to compute Wasserstein barycenters by solving a conditional variance minimization problem. A key advantage of our conditional architecture is that it enables the computation of barycenters for hundreds of input distributions, which was computationally infeasible with previous methods. Our numerical experiments illustrate that our approach yields accurate results across various high-dimensional tasks and compares favorably with previous state-of-the-art methods.

Applications · Chemistry, Physics, and Earth Sciences

Chen Hao Xia, Manasa Kaniselvan, Alexandros Nikolaos Ziogas, Marko Mladenovic, Rayen Mahjoub, Alexander Maeder, Mathieu Luisier

Graph neural networks (GNNs) have shown promise in learning the ground-state electronic properties of materials, subverting *ab initio* density functional theory (DFT) calculations when the underlying lattices can be represented as small and/or repeatable unit cells (i.e., molecules and periodic crystals). Realistic systems are, however, non-ideal and generally characterized by higher structural complexity. As such, they require large (10+ Å) unit cells and thousands of atoms to be accurately described. At these scales, DFT becomes computationally prohibitive, making GNNs especially attractive. In this work, we present a strictly local equivariant GNN capable of learning the electronic Hamiltonian (**H**) of realistically extended materials. It incorporates an *augmented partitioning* approach that enables training on arbitrarily large structures while preserving local atomic environments beyond boundaries. We demonstrate its capabilities by predicting the electronic Hamiltonian of various systems with up to 3,000 nodes (atoms), 500,000+ edges, ~ 28 million orbital interactions (nonzero entries of **H**), and $\leq$0.53\% error in the eigenvalue spectra. Our work expands the applicability of current electronic property prediction methods to some of the most challenging cases encountered in computational materials science, namely systems with disorder, interfaces, and defects.