Abstract: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.
Abstract: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.
Abstract: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.
Abstract: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.
Abstract: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.
Abstract: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.
Abstract: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.
Abstract:We explore optimally training protein language models, an area of significant interest in biological research where guidance on best practices is limited. Most models are trained with extensive compute resources until performance gains plateau, focusing primarily on increasing model sizes rather than optimizing the efficient compute frontier that balances performance and compute budgets. Our investigation is grounded in a massive dataset consisting of 939 million protein sequences. We trained over 300 models ranging from 3.5 million to 10.7 billion parameters on 5 to 200 billion unique tokens, to investigate the relations between model sizes, training token numbers, and objectives. First, we observed the effect of diminishing returns for the Causal Language Model (CLM) and that of overfitting for the Masked Language Model~(MLM) when repeating the commonly used Uniref database. To address this, we included metagenomic protein sequences in the training set to increase the diversity and avoid the plateau or overfitting effects. Second, we obtained the scaling laws of CLM and MLM on Transformer, tailored to the specific characteristics of protein sequence data. Third, we observe a transfer scaling phenomenon from CLM to MLM, further demonstrating the effectiveness of transfer through scaling behaviors based on estimated Effectively Transferred Tokens. Finally, to validate our scaling laws, we compare the large-scale versions of ESM-2 and PROGEN2 on downstream tasks, encompassing evaluations of protein generation as well as structure- and function-related tasks, all within less or equivalent pre-training compute budgets.
Abstract:Directed acyclic graphs (DAGs) serve as crucial data representations in domains such as hardware synthesis and compiler/program optimization for computing systems. DAG generative models facilitate the creation of synthetic DAGs, which can be used for benchmarking computing systems while preserving intellectual property. However, generating realistic DAGs is challenging due to their inherent directional and logical dependencies. This paper introduces LayerDAG, an autoregressive diffusion model, to address these challenges. LayerDAG decouples the strong node dependencies into manageable units that can be processed sequentially. By interpreting the partial order of nodes as a sequence of bipartite graphs, LayerDAG leverages autoregressive generation to model directional dependencies and employs diffusion models to capture logical dependencies within each bipartite graph. Comparative analyses demonstrate that LayerDAG outperforms existing DAG generative models in both expressiveness and generalization, particularly for generating large-scale DAGs with up to 400 nodes-a critical scenario for system benchmarking. Extensive experiments on both synthetic and real-world flow graphs from various computing platforms show that LayerDAG generates valid DAGs with superior statistical properties and benchmarking performance. The synthetic DAGs generated by LayerDAG enhance the training of ML-based surrogate models, resulting in improved accuracy in predicting performance metrics of real-world DAGs across diverse computing platforms.
Abstract:Large Language Models (LLMs) demonstrate strong reasoning abilities but face limitations such as hallucinations and outdated knowledge. Knowledge Graph (KG)-based Retrieval-Augmented Generation (RAG) addresses these issues by grounding LLM outputs in structured external knowledge from KGs. However, current KG-based RAG frameworks still struggle to optimize the trade-off between retrieval effectiveness and efficiency in identifying a suitable amount of relevant graph information for the LLM to digest. We introduce SubgraphRAG, extending the KG-based RAG framework that retrieves subgraphs and leverages LLMs for reasoning and answer prediction. Our approach innovatively integrates a lightweight multilayer perceptron with a parallel triple-scoring mechanism for efficient and flexible subgraph retrieval while encoding directional structural distances to enhance retrieval effectiveness. The size of retrieved subgraphs can be flexibly adjusted to match the query's need and the downstream LLM's capabilities. This design strikes a balance between model complexity and reasoning power, enabling scalable and generalizable retrieval processes. Notably, based on our retrieved subgraphs, smaller LLMs like Llama3.1-8B-Instruct deliver competitive results with explainable reasoning, while larger models like GPT-4o achieve state-of-the-art accuracy compared with previous baselines -- all without fine-tuning. Extensive evaluations on the WebQSP and CWQ benchmarks highlight SubgraphRAG's strengths in efficiency, accuracy, and reliability by reducing hallucinations and improving response grounding.