Harper Hua, Zhen Han, Zhengyuan Shen, Meng-Chieh Lee, Sheng Guan, Qi Zhu, Sullam Jeoung, Yueyan Chen, Yunfei Bai, Shuai Wang, Vassilis N. Ioannidis, Huzefa Rangwala. Proceedings of the 64th Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers). 2026.

Yuqing Yang, Qi Zhu, Zhen Han, Boran Han, Zhengyuan Shen, Shuai Wang, Vassilis N. Ioannidis, Huzefa Rangwala. Proceedings of the 64th Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers). 2026.

Kiran Ramnath, Kang Zhou, Sheng Guan, Soumya Smruti Mishra, Xuan Qi, Zhengyuan Shen, Shuai Wang, Sangmin Woo, Sullam Jeoung, Yawei Wang, Haozhu Wang, Han Ding, Yuzhe Lu, Zhichao Xu, Yun Zhou, Balasubramaniam Srinivasan, Qiaojing Yan, Yueyan Chen, Haibo Ding, Panpan Xu, Lin Lee Cheong. Proceedings of the 2025 Conference on Empirical Methods in Natural Language Processing. 2025.

The ability to construct transferable descriptors for molecular and biological systems has broad applications in drug discovery, molecular dynamics, and protein analysis. Geometric graph neural networks (Geom-GNNs) utilizing all-atom information have revolutionized atomistic simulations by enabling the prediction of interatomic potentials and molecular properties. Despite these advances, the application of all-atom Geom-GNNs in protein modeling remains limited due to computational constraints. In this work, we first demonstrate the potential of pre-trained Geom-GNNs as zero-shot transfer learners, effectively modeling protein systems with all-atom granularity. Through extensive experimentation to evaluate their expressive power, we characterize the scaling behaviors of Geom-GNNs across self-supervised, supervised, and unsupervised setups. Interestingly, we find that Geom-GNNs deviate from conventional power-law scaling observed in other domains, with no predictable scaling principles for molecular representation learning. Furthermore, we show how pre-trained graph embeddings can be directly used for analysis and synergize with other architectures to enhance expressive power for protein modeling.

Costas Mavromatis, Balasubramaniam Srinivasan, Zhengyuan Shen, Jiani Zhang, Huzefa Rangwala, Christos Faloutsos, George Karypis. Proceedings of the 2024 Conference on Empirical Methods in Natural Language Processing. 2024.

Large Language Models (LLMs) trained on large volumes of data excel at various natural language tasks, but they cannot handle tasks requiring knowledge that has not been trained on previously. One solution is to use a retriever that fetches relevant information to expand LLM's knowledge scope. However, existing textual-oriented retrieval-based LLMs are not ideal on structured table data due to diversified data modalities and large table sizes. In this work, we propose OpenTab, an open-domain table reasoning framework powered by LLMs. Overall, OpenTab leverages table retriever to fetch relevant tables and then generates SQL programs to parse the retrieved tables efficiently. Utilizing the intermediate data derived from the SQL executions, it conducts grounded inference to produce accurate response. Extensive experimental evaluation shows that OpenTab significantly outperforms baselines in both open- and closed-domain settings, achieving up to 21.5% higher accuracy. We further run ablation studies to validate the efficacy of our proposed designs of the system.

Recent advances in tabular data generation have greatly enhanced synthetic data quality. However, extending diffusion models to tabular data is challenging due to the intricately varied distributions and a blend of data types of tabular data. This paper introduces TabSyn, a methodology that synthesizes tabular data by leveraging a diffusion model within a variational autoencoder (VAE) crafted latent space. The key advantages of the proposed Tabsyn include (1) Generality: the ability to handle a broad spectrum of data types by converting them into a single unified space and explicitly capturing inter-column relations; (2) Quality: optimizing the distribution of latent embeddings to enhance the subsequent training of diffusion models, which helps generate high-quality synthetic data; (3) Speed: much fewer number of reverse steps and faster synthesis speed than existing diffusion-based methods. Extensive experiments on six datasets with five metrics demonstrate that Tabsyn outperforms existing methods. Specifically, it reduces the error rates by 86% and 67% for column-wise distribution and pair-wise column correlation estimations compared with the most competitive baselines. The code has been made available at https://github.com/amazon-science/tabsyn.

Recent advances in large language models have revolutionized many sectors, including the database industry.One common challenge when dealing with large volumes of tabular data is the pervasive use of abbreviated column names, which can negatively impact performance on various data search, access, and understanding tasks.To address this issue, we introduce a new task, called NAMEGUESS, to expand column names (used in database schema) as a natural language generation problem.We create a training dataset of 384K abbreviatedexpanded column pairs using a new data fabrication method and a human-annotated evaluation benchmark that includes 9.2K examples from real-world tables.To tackle the complexities associated with polysemy and ambiguity in NAMEGUESS, we enhance autoregressive language models by conditioning on table content and column header namesyielding a fine-tuned model (with 2.7B parameters) that matches human performance.Furthermore, we conduct a comprehensive analysis (on multiple LLMs) to validate the effectiveness of table content in NAMEGUESS and identify promising future opportunities.Code has been made available at https://github. com/amazon-science/nameguess.