Towards A Universal Graph Structural Encoder

Recent advancements in large-scale pre-training have shown the potential to learn generalizable representations for downstream tasks. In the graph domain, however, capturing and transferring structural information across different graph domains remains challenging, primarily due to the inherent differences in topological patterns across various contexts. Additionally, most existing models struggle to capture the complexity of rich graph structures, leading to inadequate exploration of the embedding space. To address these challenges, we propose GFSE, a universal graph structural encoder designed to capture transferable structural patterns across diverse domains such as molecular graphs, social networks, and citation networks. GFSE is the first cross-domain graph structural encoder pre-trained with multiple self-supervised learning objectives. Built on a Graph Transformer, GFSE incorporates attention mechanisms informed by graph inductive bias, enabling it to encode intricate multi-level and fine-grained topological features. The pre-trained GFSE produces generic and theoretically expressive positional and structural encoding for graphs, which can be seamlessly integrated with various downstream graph feature encoders, including graph neural networks for vectorized features and Large Language Models for text-attributed graphs. Comprehensive experiments on synthetic and real-world datasets demonstrate GFSE's capability to significantly enhance the model's performance while requiring substantially less task-specific fine-tuning. Notably, GFSE achieves state-of-the-art performance in 81.6% evaluated cases, spanning diverse graph models and datasets, highlighting its potential as a powerful and versatile encoder for graph-structured data.

MatterTune: An Integrated, User-Friendly Platform for Fine-Tuning Atomistic Foundation Models to Accelerate Materials Simulation and Discovery

Geometric machine learning models such as graph neural networks have achieved remarkable success in recent years in chemical and materials science research for applications such as high-throughput virtual screening and atomistic simulations. The success of these models can be attributed to their ability to effectively learn latent representations of atomic structures directly from the training data. Conversely, this also results in high data requirements for these models, hindering their application to problems which are data sparse which are common in this domain. To address this limitation, there is a growing development in the area of pre-trained machine learning models which have learned general, fundamental, geometric relationships in atomistic data, and which can then be fine-tuned to much smaller application-specific datasets. In particular, models which are pre-trained on diverse, large-scale atomistic datasets have shown impressive generalizability and flexibility to downstream applications, and are increasingly referred to as atomistic foundation models. To leverage the untapped potential of these foundation models, we introduce MatterTune, a modular and extensible framework that provides advanced fine-tuning capabilities and seamless integration of atomistic foundation models into downstream materials informatics and simulation workflows, thereby lowering the barriers to adoption and facilitating diverse applications in materials science. In its current state, MatterTune supports a number of state-of-the-art foundation models such as ORB, MatterSim, JMP, and EquformerV2, and hosts a wide range of features including a modular and flexible design, distributed and customizable fine-tuning, broad support for downstream informatics tasks, and more.

Automating Personalization: Prompt Optimization for Recommendation Reranking

Modern recommender systems increasingly leverage large language models (LLMs) for reranking to improve personalization. However, existing approaches face two key limitations: (1) heavy reliance on manually crafted prompts that are difficult to scale, and (2) inadequate handling of unstructured item metadata that complicates preference inference. We present AGP (Auto-Guided Prompt Refinement), a novel framework that automatically optimizes user profile generation prompts for personalized reranking. AGP introduces two key innovations: (1) position-aware feedback mechanisms for precise ranking correction, and (2) batched training with aggregated feedback to enhance generalization.

Structural Alignment Improves Graph Test-Time Adaptation

Graph-based learning has achieved remarkable success in domains ranging from recommendation to fraud detection and particle physics by effectively capturing underlying interaction patterns. However, it often struggles to generalize when distribution shifts occur, particularly those involving changes in network connectivity or interaction patterns. Existing approaches designed to mitigate such shifts typically require retraining with full access to source data, rendering them infeasible under strict computational or privacy constraints. To address this limitation, we propose a test-time structural alignment (TSA) algorithm for Graph Test-Time Adaptation (GTTA), a novel method that aligns graph structures during inference without revisiting the source domain. Built upon a theoretically grounded treatment of graph data distribution shifts, TSA integrates three key strategies: an uncertainty-aware neighborhood weighting that accommodates structure shifts, an adaptive balancing of self-node and neighborhood-aggregated representations driven by node representations' signal-to-noise ratio, and a decision boundary refinement that corrects remaining label and feature shifts. Extensive experiments on synthetic and real-world datasets demonstrate that TSA can consistently outperform both non-graph TTA methods and state-of-the-art GTTA baselines.

The Blessing of Reasoning: LLM-Based Contrastive Explanations in Black-Box Recommender Systems

Modern recommender systems use ML models to predict consumer preferences from consumption history. Although these "black-box" models achieve impressive predictive performance, they often suffer from a lack of transparency and explainability. Contrary to the presumed tradeoff between explainability and accuracy, we show that integrating large language models (LLMs) with deep neural networks (DNNs) can improve both. We propose LR-Recsys, which augments DNN-based systems with LLM reasoning capabilities. LR-Recsys introduces a contrastive-explanation generator that produces human-readable positive explanations and negative explanations. These explanations are embedded via a fine-tuned autoencoder and combined with consumer and product features to improve predictions. Beyond offering explainability, we show that LR-Recsys also improves learning efficiency and predictive accuracy, as supported by high-dimensional, multi-environment statistical learning theory. LR-Recsys outperforms state-of-the-art recommender systems by 3-14% on three real-world datasets. Importantly, our analysis reveals that these gains primarily derive from LLMs' reasoning capabilities rather than their external domain knowledge. LR-RecSys presents an effective approach to combine LLMs with traditional DNNs, two of the most widely used ML models today. The explanations generated by LR-Recsys provide actionable insights for consumers, sellers, and platforms, helping to build trust, optimize product offerings, and inform targeting strategies.

Model Generalization on Text Attribute Graphs: Principles with Large Language Models

Large language models (LLMs) have recently been introduced to graph learning, aiming to extend their zero-shot generalization success to tasks where labeled graph data is scarce. Among these applications, inference over text-attributed graphs (TAGs) presents unique challenges: existing methods struggle with LLMs' limited context length for processing large node neighborhoods and the misalignment between node embeddings and the LLM token space. To address these issues, we establish two key principles for ensuring generalization and derive the framework LLM-BP accordingly: (1) Unifying the attribute space with task-adaptive embeddings, where we leverage LLM-based encoders and task-aware prompting to enhance generalization of the text attribute embeddings; (2) Developing a generalizable graph information aggregation mechanism, for which we adopt belief propagation with LLM-estimated parameters that adapt across graphs. Evaluations on 11 real-world TAG benchmarks demonstrate that LLM-BP significantly outperforms existing approaches, achieving 8.10% improvement with task-conditional embeddings and an additional 1.71% gain from adaptive aggregation.

Rethinking Addressing in Language Models via Contexualized Equivariant Positional Encoding

Transformers rely on both content-based and position-based addressing mechanisms to make predictions, but existing positional encoding techniques often diminish the effectiveness of position-based addressing. Many current methods enforce rigid patterns in attention maps, limiting the ability to model long-range dependencies and adapt to diverse tasks. Additionally, most positional encodings are learned as general biases, lacking the specialization required for different instances within a dataset. To address this, we propose con$\textbf{T}$extualized equivari$\textbf{A}$nt $\textbf{P}$osition $\textbf{E}$mbedding ($\textbf{TAPE}$), a novel framework that enhances positional embeddings by incorporating sequence content across layers. TAPE introduces dynamic, context-aware positional encodings, overcoming the constraints of traditional fixed patterns. By enforcing permutation and orthogonal equivariance, TAPE ensures the stability of positional encodings during updates, improving robustness and adaptability. Our method can be easily integrated into pre-trained transformers, offering parameter-efficient fine-tuning with minimal overhead. Extensive experiments shows that TAPE achieves superior performance in language modeling, arithmetic reasoning, and long-context retrieval tasks compared to existing positional embedding techniques.

Understanding and Mitigating Bottlenecks of State Space Models through the Lens of Recency and Over-smoothing

Structured State Space Models (SSMs) have emerged as alternatives to transformers. While SSMs are often regarded as effective in capturing long-sequence dependencies, we rigorously demonstrate that they are inherently limited by strong recency bias. Our empirical studies also reveal that this bias impairs the models' ability to recall distant information and introduces robustness issues. Our scaling experiments then discovered that deeper structures in SSMs can facilitate the learning of long contexts. However, subsequent theoretical analysis reveals that as SSMs increase in depth, they exhibit another inevitable tendency toward over-smoothing, e.g., token representations becoming increasingly indistinguishable. This fundamental dilemma between recency and over-smoothing hinders the scalability of existing SSMs. Inspired by our theoretical findings, we propose to polarize two channels of the state transition matrices in SSMs, setting them to zero and one, respectively, simultaneously addressing recency bias and over-smoothing. Experiments demonstrate that our polarization technique consistently enhances the associative recall accuracy of long-range tokens and unlocks SSMs to benefit further from deeper architectures. All source codes are released at https://github.com/VITA-Group/SSM-Bottleneck.

Underestimated Privacy Risks for Minority Populations in Large Language Model Unlearning

Large Language Models are trained on extensive datasets that often contain sensitive, human-generated information, raising significant concerns about privacy breaches. While certified unlearning approaches offer strong privacy guarantees, they rely on restrictive model assumptions that are not applicable to LLMs. As a result, various unlearning heuristics have been proposed, with the associated privacy risks assessed only empirically. The standard evaluation pipelines typically randomly select data for removal from the training set, apply unlearning techniques, and use membership inference attacks to compare the unlearned models against models retrained without the to-be-unlearned data. However, since every data point is subject to the right to be forgotten, unlearning should be considered in the worst-case scenario from the privacy perspective. Prior work shows that data outliers may exhibit higher memorization effects. Intuitively, they are harder to be unlearn and thus the privacy risk of unlearning them is underestimated in the current evaluation. In this paper, we leverage minority data to identify such a critical flaw in previously widely adopted evaluations. We substantiate this claim through carefully designed experiments, including unlearning canaries related to minority groups, inspired by privacy auditing literature. Using personally identifiable information as a representative minority identifier, we demonstrate that minority groups experience at least 20% more privacy leakage in most cases across six unlearning approaches, three MIAs, three benchmark datasets, and two LLMs of different scales. Given that the right to be forgotten should be upheld for every individual, we advocate for a more rigorous evaluation of LLM unlearning methods. Our minority-aware evaluation framework represents an initial step toward ensuring more equitable assessments of LLM unlearning efficacy.

Dynamic Self-Distillation via Previous Mini-batches for Fine-tuning Small Language Models

Knowledge distillation (KD) has become a widely adopted approach for compressing large language models (LLMs) to reduce computational costs and memory footprints. However, the availability of complex teacher models is a prerequisite for running most KD pipelines. Thus, the traditional KD procedure can be unachievable or budget-unfriendly, particularly when relying on commercial LLMs like GPT4. In this regard, Self-distillation (SelfD) emerges as an advisable alternative, enabling student models to learn without teachers' guidance. Nonetheless, existing SelfD approaches for LMs often involve architectural modifications, assuming the models are open-source, which may not always be practical. In this work, we introduce a model-agnostic and task-agnostic method named dynamic SelfD from the previous minibatch (DynSDPB), which realizes current iterations' distillation from the last ones' generated logits. Additionally, to address prediction inaccuracies during the early iterations, we dynamically adjust the distillation influence and temperature values to enhance the adaptability of fine-tuning. Furthermore, DynSDPB is a novel fine-tuning policy that facilitates the seamless integration of existing self-correction and self-training techniques for small language models (SLMs) because they all require updating SLMs' parameters. We demonstrate the superior performance of DynSDPB on both encoder-only LMs (e.g., BERT model families) and decoder-only LMs (e.g., LLaMA model families), validating its effectiveness across natural language understanding (NLU) and natural language generation (NLG) benchmarks.