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1. Understanding Synthetic Context Extension via Retrieval Heads

   Zhao, Xinyu; Yin, Fangcong; Durrett, Greg (May 2025, ICML 2025)

   Long-context LLMs are increasingly in demand for applications such as retrieval-augmented generation. To defray the cost of pretraining LLMs over long contexts, recent work takes an approach of synthetic context extension: fine-tuning LLMs with synthetically generated long-context data in a post-training stage. However, it remains unclear how and why this synthetic context extension imparts abilities for downstream long-context tasks. In this paper, we investigate fine-tuning on synthetic data for three long-context tasks that require retrieval and reasoning. We vary the realism of "needle" concepts to be retrieved and diversity of the surrounding "haystack" context, from using LLMs to construct synthetic documents to using templated relations and creating symbolic datasets. We find that models trained on synthetic data fall short of the real data, but surprisingly, the mismatch can be interpreted and even predicted in terms of a special set of attention heads that are responsible for retrieval over long context, retrieval heads (Wu et al., 2024). The retrieval heads learned on synthetic data have high overlap with retrieval heads learned on real data, and there is a strong correlation between the recall of heads learned and the downstream performance of a model. Furthermore, with attention knockout and activation patching, we mechanistically show that retrieval heads are necessary and explain model performance, although they are not totally sufficient. Our results shed light on how to interpret synthetic data fine-tuning performance and how to approach creating better data for learning real-world capabilities over long contexts. 

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2. Edge Prompt Tuning for Graph Neural Networks

   Fu, Xingbo; He, Yinhan; Li, Jundong (April 2025, International Conference on Learning Representations)

   Pre-training powerful Graph Neural Networks (GNNs) with unlabeled graph data in a self-supervised manner has emerged as a prominent technique in recent years. However, inevitable objective gaps often exist between pre-training and downstream tasks. To bridge this gap, graph prompt tuning techniques design and learn graph prompts by manipulating input graphs or reframing downstream tasks as pre-training tasks without fine-tuning the pre-trained GNN models. While recent graph prompt tuning methods have proven effective in adapting pre-trained GNN models for downstream tasks, they overlook the crucial role of edges in graph prompt design, which can significantly affect the quality of graph representations for downstream tasks. In this study, we propose EdgePrompt, a simple yet effective graph prompt tuning method from the perspective of edges. Unlike previous studies that design prompt vectors on node features, EdgePrompt manipulates input graphs by learning additional prompt vectors for edges and incorporates the edge prompts through message passing in the pre-trained GNN models to better embed graph structural information for downstream tasks. Our method is compatible with prevalent GNN architectures pre-trained under various pre-training strategies and is universal for different downstream tasks. We provide comprehensive theoretical analyses of our method regarding its capability of handling node classification and graph classification as downstream tasks. Extensive experiments on ten graph datasets under four pre-training strategies demonstrate the superiority of our proposed method against six baselines. 

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3. Molecule design by latent space energy-based modeling and gradual distribution shifting

   Kong, D.; Pang, B.; Han, T.; Wu, Y. N. (August 2023, Uncertainty in Artificial Intelligence (UAI, 2023))

   Generation of molecules with desired chemical and biological properties such as high drug-likeness, high binding affinity to target proteins, is critical for drug discovery. In this paper, we propose a probabilistic generative model to capture the joint distribution of molecules and their properties. Our model assumes an energy-based model (EBM) in the latent space. Conditional on the latent vector, the molecule and its properties are modeled by a molecule generation model and a property regression model respectively. To search for molecules with desired properties, we propose a sampling with gradual distribution shifting (SGDS) algorithm, so that after learning the model initially on the training data of existing molecules and their properties, the proposed algorithm gradually shifts the model distribution towards the region supported by molecules with desired values of properties. Our experiments show that our method achieves very strong performances on various molecule design tasks. 

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4. Multi-Objective Molecule Generation using Interpretable Substructures

   Jin, Wengong; Barzilay, Regina; Jaakkola, Tommi (January 2020, Proceedings of the 37th International Conference on Machine Learning)

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   Drug discovery aims to find novel compounds with specified chemical property profiles. In terms of generative modeling, the goal is to learn to sample molecules in the intersection of multiple property constraints. This task becomes increasingly challenging when there are many property constraints. We propose to offset this complexity by composing molecules from a vocabulary of substructures that we call molecular rationales. These rationales are identified from molecules as substructures that are likely responsible for each property of interest. We then learn to expand rationales into a full molecule using graph generative models. Our final generative model composes molecules as mixtures of multiple rationale completions, and this mixture is fine-tuned to preserve the properties of interest. We evaluate our model on various drug design tasks and demonstrate significant improvements over state-of-the-art baselines in terms of accuracy, diversity, and novelty of generated compounds. 

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5. Formulating Few-shot Fine-tuning Towards Language Model Pre-training: A Pilot Study on Named Entity Recognition

   Wang, Zihan; Zhao, Kewen; Wang, Zilong; Shang, Jingbo (January 2022, Findings of the Association for Computational Linguistics: EMNLP 2022)

   Fine-tuning pre-trained language models is a common practice in building NLP models for various tasks, including the case with less supervision. We argue that under the few-shot setting, formulating fine-tuning closer to the pre-training objective shall be able to unleash more benefits from the pre-trained language models. In this work, we take few-shot named entity recognition (NER) for a pilot study, where existing fine-tuning strategies are much different from pre-training. We propose a novel few-shot fine-tuning framework for NER, FFF-NER. Specifically, we introduce three new types of tokens, “is-entity”, “which-type” and “bracket”, so we can formulate the NER fine-tuning as (masked) token prediction or generation, depending on the choice of the pre-training objective. In our experiments, we apply to fine-tune both BERT and BART for few-shot NER on several benchmark datasets and observe significant improvements over existing fine-tuning strategies, including sequence labeling, prototype meta-learning, and prompt-based approaches. We further perform a series of ablation studies, showing few-shot NER performance is strongly correlated with the similarity between fine-tuning and pre-training. 

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