Attention Bootstrapping for Multi-Modal Test-Time Adaptation

Test-time adaptation aims to adapt a well-trained model to potential distribution shifts at test time using only unlabeled test data, without access to the original training data. While previous efforts mainly focus on a single modality, test-time distribution shift in the multi-modal setting is more complex and calls for new solutions. This paper tackles the problem of multi-modal test-time adaptation by proposing a novel method named Attention Bootstrapping with Principal Entropy Minimization (ABPEM). We observe that test-time distribution shift causes misalignment across modalities, leading to a large gap between intra-modality discrepancies (measured by self-attention) and inter-modality discrepancies (measured by cross-attention). We name this the attention gap. This attention gap widens with more severe distribution shifts, hindering effective modality fusion. To mitigate this attention gap and encourage better modality fusion, we propose attention bootstrapping that promotes cross-attention with the guidance of self-attention. Moreover, to reduce the gradient noise in the commonly-used entropy minimization, we adopt principal entropy minimization, a refinement of entropy minimization that reduces gradient noise by focusing on the principal parts of entropy, excluding less reliable gradient information. Extensive experiments on the benchmarks validate the effectiveness of the proposed ABPEM in comparison with competing baselines.

Protein Large Language Models: A Comprehensive Survey

Protein-specific large language models (Protein LLMs) are revolutionizing protein science by enabling more efficient protein structure prediction, function annotation, and design. While existing surveys focus on specific aspects or applications, this work provides the first comprehensive overview of Protein LLMs, covering their architectures, training datasets, evaluation metrics, and diverse applications. Through a systematic analysis of over 100 articles, we propose a structured taxonomy of state-of-the-art Protein LLMs, analyze how they leverage large-scale protein sequence data for improved accuracy, and explore their potential in advancing protein engineering and biomedical research. Additionally, we discuss key challenges and future directions, positioning Protein LLMs as essential tools for scientific discovery in protein science. Resources are maintained at https://github.com/Yijia-Xiao/Protein-LLM-Survey.

Iterative Feature Space Optimization through Incremental Adaptive Evaluation

Iterative feature space optimization involves systematically evaluating and adjusting the feature space to improve downstream task performance. However, existing works suffer from three key limitations:1) overlooking differences among data samples leads to evaluation bias; 2) tailoring feature spaces to specific machine learning models results in overfitting and poor generalization; 3) requiring the evaluator to be retrained from scratch during each optimization iteration significantly reduces the overall efficiency of the optimization process. To bridge these gaps, we propose a gEneralized Adaptive feature Space Evaluator (EASE) to efficiently produce optimal and generalized feature spaces. This framework consists of two key components: Feature-Sample Subspace Generator and Contextual Attention Evaluator. The first component aims to decouple the information distribution within the feature space to mitigate evaluation bias. To achieve this, we first identify features most relevant to prediction tasks and samples most challenging for evaluation based on feedback from the subsequent evaluator. This decoupling strategy makes the evaluator consistently target the most challenging aspects of the feature space. The second component intends to incrementally capture evolving patterns of the feature space for efficient evaluation. We propose a weighted-sharing multi-head attention mechanism to encode key characteristics of the feature space into an embedding vector for evaluation. Moreover, the evaluator is updated incrementally, retaining prior evaluation knowledge while incorporating new insights, as consecutive feature spaces during the optimization process share partial information. Extensive experiments on fourteen real-world datasets demonstrate the effectiveness of the proposed framework. Our code and data are publicly available.

RobustFT: Robust Supervised Fine-tuning for Large Language Models under Noisy Response

Supervised fine-tuning (SFT) plays a crucial role in adapting large language models (LLMs) to specific domains or tasks. However, as demonstrated by empirical experiments, the collected data inevitably contains noise in practical applications, which poses significant challenges to model performance on downstream tasks. Therefore, there is an urgent need for a noise-robust SFT framework to enhance model capabilities in downstream tasks. To address this challenge, we introduce a robust SFT framework (RobustFT) that performs noise detection and relabeling on downstream task data. For noise identification, our approach employs a multi-expert collaborative system with inference-enhanced models to achieve superior noise detection. In the denoising phase, we utilize a context-enhanced strategy, which incorporates the most relevant and confident knowledge followed by careful assessment to generate reliable annotations. Additionally, we introduce an effective data selection mechanism based on response entropy, ensuring only high-quality samples are retained for fine-tuning. Extensive experiments conducted on multiple LLMs across five datasets demonstrate RobustFT's exceptional performance in noisy scenarios.

Embracing Large Language Models in Traffic Flow Forecasting

Traffic flow forecasting aims to predict future traffic flows based on the historical traffic conditions and the road network. It is an important problem in intelligent transportation systems, with a plethora of methods been proposed. Existing efforts mainly focus on capturing and utilizing spatio-temporal dependencies to predict future traffic flows. Though promising, they fall short in adapting to test-time environmental changes of traffic conditions. To tackle this challenge, we propose to introduce large language models (LLMs) to help traffic flow forecasting and design a novel method named Large Language Model Enhanced Traffic Flow Predictor (LEAF). LEAF adopts two branches, capturing different spatio-temporal relations using graph and hypergraph structures respectively. The two branches are first pre-trained individually, and during test-time, they yield different predictions. Based on these predictions, a large language model is used to select the most likely result. Then, a ranking loss is applied as the learning objective to enhance the prediction ability of the two branches. Extensive experiments on several datasets demonstrate the effectiveness of the proposed LEAF.

Assessing Personalized AI Mentoring with Large Language Models in the Computing Field

This paper provides an in-depth evaluation of three state-of-the-art Large Language Models (LLMs) for personalized career mentoring in the computing field, using three distinct student profiles that consider gender, race, and professional levels. We evaluated the performance of GPT-4, LLaMA 3, and Palm 2 using a zero-shot learning approach without human intervention. A quantitative evaluation was conducted through a custom natural language processing analytics pipeline to highlight the uniqueness of the responses and to identify words reflecting each student's profile, including race, gender, or professional level. The analysis of frequently used words in the responses indicates that GPT-4 offers more personalized mentoring compared to the other two LLMs. Additionally, a qualitative evaluation was performed to see if human experts reached similar conclusions. The analysis of survey responses shows that GPT-4 outperformed the other two LLMs in delivering more accurate and useful mentoring while addressing specific challenges with encouragement languages. Our work establishes a foundation for developing personalized mentoring tools based on LLMs, incorporating human mentors in the process to deliver a more impactful and tailored mentoring experience.

Graph Fourier Neural ODEs: Bridging Spatial and Temporal Multiscales in Molecular Dynamics

Molecular dynamics simulations are crucial for understanding complex physical, chemical, and biological processes at the atomic level. However, accurately capturing interactions across multiple spatial and temporal scales remains a significant challenge. We present a novel framework that jointly models spatial and temporal multiscale interactions in molecular dynamics. Our approach leverages Graph Fourier Transforms to decompose molecular structures into different spatial scales and employs Neural Ordinary Differential Equations to model the temporal dynamics in a curated manner influenced by the spatial modes. This unified framework links spatial structures with temporal evolution in a flexible manner, enabling more accurate and comprehensive simulations of molecular systems. We evaluate our model on the MD17 dataset, demonstrating consistent performance improvements over state-of-the-art baselines across multiple molecules, particularly under challenging conditions such as irregular timestep sampling and long-term prediction horizons. Ablation studies confirm the significant contributions of both spatial and temporal multiscale modeling components. Our method advances the simulation of complex molecular systems, potentially accelerating research in computational chemistry, drug discovery, and materials science.

GALA: Graph Diffusion-based Alignment with Jigsaw for Source-free Domain Adaptation

Source-free domain adaptation is a crucial machine learning topic, as it contains numerous applications in the real world, particularly with respect to data privacy. Existing approaches predominantly focus on Euclidean data, such as images and videos, while the exploration of non-Euclidean graph data remains scarce. Recent graph neural network (GNN) approaches can suffer from serious performance decline due to domain shift and label scarcity in source-free adaptation scenarios. In this study, we propose a novel method named Graph Diffusion-based Alignment with Jigsaw (GALA), tailored for source-free graph domain adaptation. To achieve domain alignment, GALA employs a graph diffusion model to reconstruct source-style graphs from target data. Specifically, a score-based graph diffusion model is trained using source graphs to learn the generative source styles. Then, we introduce perturbations to target graphs via a stochastic differential equation instead of sampling from a prior, followed by the reverse process to reconstruct source-style graphs. We feed the source-style graphs into an off-the-shelf GNN and introduce class-specific thresholds with curriculum learning, which can generate accurate and unbiased pseudo-labels for target graphs. Moreover, we develop a simple yet effective graph-mixing strategy named graph jigsaw to combine confident graphs and unconfident graphs, which can enhance generalization capabilities and robustness via consistency learning. Extensive experiments on benchmark datasets validate the effectiveness of GALA.

SemiEvol: Semi-supervised Fine-tuning for LLM Adaptation

Supervised fine-tuning (SFT) is crucial in adapting large language models (LLMs) to a specific domain or task. However, only a limited amount of labeled data is available in practical applications, which poses a severe challenge for SFT in yielding satisfactory results. Therefore, a data-efficient framework that can fully exploit labeled and unlabeled data for LLM fine-tuning is highly anticipated. Towards this end, we introduce a semi-supervised fine-tuning framework named SemiEvol for LLM adaptation from a propagate-and-select manner. For knowledge propagation, SemiEvol adopts a bi-level approach, propagating knowledge from labeled data to unlabeled data through both in-weight and in-context methods. For knowledge selection, SemiEvol incorporates a collaborative learning mechanism, selecting higher-quality pseudo-response samples. We conducted experiments using GPT-4o-mini and Llama-3.1 on seven general or domain-specific datasets, demonstrating significant improvements in model performance on target data. Furthermore, we compared SemiEvol with SFT and self-evolution methods, highlighting its practicality in hybrid data scenarios.

Physics-Informed Regularization for Domain-Agnostic Dynamical System Modeling

Learning complex physical dynamics purely from data is challenging due to the intrinsic properties of systems to be satisfied. Incorporating physics-informed priors, such as in Hamiltonian Neural Networks (HNNs), achieves high-precision modeling for energy-conservative systems. However, real-world systems often deviate from strict energy conservation and follow different physical priors. To address this, we present a framework that achieves high-precision modeling for a wide range of dynamical systems from the numerical aspect, by enforcing Time-Reversal Symmetry (TRS) via a novel regularization term. It helps preserve energies for conservative systems while serving as a strong inductive bias for non-conservative, reversible systems. While TRS is a domain-specific physical prior, we present the first theoretical proof that TRS loss can universally improve modeling accuracy by minimizing higher-order Taylor terms in ODE integration, which is numerically beneficial to various systems regardless of their properties, even for irreversible systems. By integrating the TRS loss within neural ordinary differential equation models, the proposed model TREAT demonstrates superior performance on diverse physical systems. It achieves a significant 11.5% MSE improvement in a challenging chaotic triple-pendulum scenario, underscoring TREAT's broad applicability and effectiveness.