arXiv subjects

Howard Dai

Publications and source records attributed to Howard Dai.

4 recordsLinked to original sources

arXiv2025

A Graph Laplacian Eigenvector-based Pre-training Method for Graph Neural Networks

The development of self-supervised graph pre-training methods is a crucial ingredient in recent efforts to design robust graph foundation models (GFMs). Structure-based pre-training methods are under-explored yet crucial for downstream applications which rely on underlying graph structure. In addition, pre-training traditional message passing GNNs to capture global and regional structure is often challenging due to the risk of oversmoothing as network depth increases. We address these gaps by proposing the Laplacian Eigenvector Learning Module (LELM), a novel pre-training module for graph neural networks (GNNs) based on predicting the low-frequency eigenvectors of the graph Laplacian. Moreover, LELM introduces a novel architecture that overcomes oversmoothing, allowing the GNN model to learn long-range interdependencies. Empirically, we show that models pre-trained via our framework outperform baseline models on downstream molecular property prediction tasks.

cs.LG↗

arXiv2025

Polynomial Expectation Property for Max-Polymatrix Games

We address an open problem on the computability of correlated equilibria in a variant of polymatrix where each player's utility is the maximum of their edge payoffs. We demonstrate that this max-variant game has the polynomial expectation property, and the results of Papadimitriou and Roughgarden can thus be applied. We propose ideas for extending these findings to other variants of polymatrix games, as well as briefly address the broader question of necessity for the polynomial expectation property when computing correlated equilibria.

cs.GT↗

arXiv2025

Creativity or Brute Force? Using Brainteasers as a Window into the Problem-Solving Abilities of Large Language Models

Accuracy remains a standard metric for evaluating AI systems, but it offers limited insight into how models arrive at their solutions. In this work, we introduce a benchmark based on brainteasers written in long narrative form to probe more deeply into the types of reasoning strategies that models use. Brainteasers are well-suited for this goal because they can be solved with multiple approaches, such as a few-step solution that uses a creative insight or a longer solution that uses more brute force. We investigate large language models (LLMs) across multiple layers of reasoning, focusing not only on correctness but also on the quality and creativity of their solutions. We investigate many aspects of the reasoning process: (1) semantic parsing of the brainteasers into precise mathematical competition style formats; (2) generating solutions from these mathematical forms; (3) self-correcting solutions based on gold solutions; (4) producing step-by-step sketches of solutions; and (5) making use of hints. We find that LLMs are in many cases able to find creative, insightful solutions to brainteasers, suggesting that they capture some of the capacities needed to solve novel problems in creative ways. Nonetheless, there also remain situations where they rely on brute force despite the availability of more efficient, creative solutions, highlighting a potential direction for improvement in the reasoning abilities of LLMs.

cs.AI↗

arXiv2024

A Survey of Generative AI for de novo Drug Design: New Frontiers in Molecule and Protein Generation

Artificial intelligence (AI)-driven methods can vastly improve the historically costly drug design process, with various generative models already in widespread use. Generative models for de novo drug design, in particular, focus on the creation of novel biological compounds entirely from scratch, representing a promising future direction. Rapid development in the field, combined with the inherent complexity of the drug design process, creates a difficult landscape for new researchers to enter. In this survey, we organize de novo drug design into two overarching themes: small molecule and protein generation. Within each theme, we identify a variety of subtasks and applications, highlighting important datasets, benchmarks, and model architectures and comparing the performance of top models. We take a broad approach to AI-driven drug design, allowing for both micro-level comparisons of various methods within each subtask and macro-level observations across different fields. We discuss parallel challenges and approaches between the two applications and highlight future directions for AI-driven de novo drug design as a whole. An organized repository of all covered sources is available at https://github.com/gersteinlab/GenAI4Drug.

q-bio.BM↗