33 accepted papers
Generative self-supervised learning on graphs has emerged as a popular learning paradigm and demonstrated its efficacy in handling non-Euclidean data. However, several remaining issues limit the capability of existing methods: 1) the disregard of uneven node significance in masking, 2) the underutil
In-context learning lets large models adapt to new tasks from a few demonstrations, but it has shown limited success in molecular design, where labeled data are scarce and properties span millions of biological assays and material measurements. We introduce demonstration-conditioned diffusion models…
Generative foundation models (GenFMs), such as large language models and text-to-image systems, have demonstrated remarkable capabilities in various downstream applications. As they are increasingly deployed in high-stakes applications, assessing their trustworthiness has become both a critical nece…
Molecular editing—modifying a given molecule to improve desired properties—is a fundamental task in drug discovery. While LLMs hold the potential to solve this task using natural language to drive the editing, straightforward prompting achieves limited accuracy. In this work, we propose AgentDrug, a
The rapid advent of machine learning (ML) and artificial intelligence (AI) has catalyzed major transformations in chemistry, yet the application of these methods to spectroscopic and spectrometric data—termed Spectroscopy Machine Learning (SpectraML)—remains relatively underexplored. Modern spectros
Large language models (LLMs) are powerful tools capable of handling diverse tasks. Comparing and selecting appropriate LLMs for specific tasks requires systematic evaluation methods, as models exhibit varying capabilities across different domains. However, finding suitable benchmarks is difficult gi…
Graph learning tasks often hinge on identifying key substructure patterns---such as triadic closures in social networks or benzene rings in molecular graphs---that underpin downstream performance. However, most existing graph neural networks (GNNs) rely on message passing, which aggregates local nei…
Empowering large language models (LLMs) with chemical intelligence remains a challenge due to the scarcity of high-quality, domain-specific instruction-response datasets and the misalignment of existing synthetic data generation pipelines with the inherently hierarchical and rule-governed structure…
The challenge of delivering efficient explanations is a critical barrier that prevents the adoption of model explanations in real-world applications. Existing approaches often depend on extensive model queries for sample-level explanations or rely on expert's knowledge of specific model structures t
LLM-as-a-Judge has been widely utilized as an evaluation method in various benchmarks and served as supervised rewards in model training. However, despite their excellence in many domains, potential issues are under-explored, undermining their reliability and the scope of their utility. Therefore,…
In low-and middle-income countries (LMICs) pediatric cancer patients and their caregivers often suffer from effects of underfunded, fragmented and outdated healthcare systems. One of these effects is a breakdown of communication between hospital staff and caregivers, which is felt stronger among vul
Diet plays a critical role in human health, yet tailoring dietary reasoning to individual health conditions remains a major challenge. Nutrition Question Answering (QA) has emerged as a popular method for addressing this problem. However, current research faces two critical limitations. On one hand,…
Foundation models are pretrained on large-scale corpora to learn generalizable patterns across domains and tasks---such as contours, textures, and edges in images, or tokens and sentences in text. In contrast, discovering such generalities in graph-structured data, especially across heterogeneous gr…
Bias towards people experiencing homelessness (PEH) is prevalent in online spaces. This project will leverage natural language processing (NLP) and large language models (LLMs) to identify, classify, and measure bias using geolocalized data collected from X (formerly Twitter), Reddit, meeting minute
Inverse molecular generation is an essential task for drug discovery, and generative models offer a very promising avenue, especially when diffusion models are used. Despite their great success, existing methods are inherently limited by the lack of a semantic latent space that can not be navigated…
Large Language Models (LLMs) have shown significant problem-solving capabilities across predictive and generative tasks in chemistry. However, their proficiency in multi-step chemical reasoning remains underexplored. We introduce a new challenge: molecular structure elucidation, which involves de…
Given a graph with textual attributes, we enable users to `chat with their graph': that is, to ask questions about the graph using a conversational interface. In response to a user's questions, our method provides textual replies and highlights the relevant parts of the graph. While existing works i…
Inspired by the success of foundation models in applications such as ChatGPT, as graph data has been ubiquitous, one can envision the far-reaching impacts that can be brought by Graph Foundation Models (GFMs) with broader applications in the areas such as scientific research, social network analysis…
Large language models (LLMs) have shown remarkable generalization capability with exceptional performance in various language modeling tasks. However, they still exhibit inherent limitations in precisely capturing and returning grounded knowledge. While existing work has explored utilizing knowledge…
The human race is facing one of the most meaningful public health emergencies in the modern era caused by the COVID-19 pandemic. This pandemic introduced various challenges, from lock-downs with significant economic costs to fundamentally altering the way of life for many people around the world. Th…
Large Language Models (LLMs) have achieved remarkable success across a wide array of tasks. Due to their notable capabilities in planning and reasoning, LLMs have been utilized as autonomous agents for the automatic execution of various tasks. Recently, LLM-based agent systems have rapidly evolved f…
Protein-protein bindings play a key role in a variety of fundamental biological processes, and thus predicting the effects of amino acid mutations on protein-protein binding is crucial. To tackle the scarcity of annotated mutation data, pre-training with massive unlabeled data has emerged as a promi…
Protein-Protein Interactions (PPIs) are fundamental in various biological processes and play a key role in life activities. The growing demand and cost of experimental PPI assays require computational methods for efficient PPI prediction. While existing methods rely heavily on protein sequence for P…
Message Passing Neural Networks (MPNNs) have emerged as the {\em de facto} standard in graph representation learning. However, when it comes to link prediction, they are not always superior to simple heuristics such as Common Neighbor (CN). This discrepancy stems from a fundamental limitation: while…
Graph Contrastive Learning (GCL) has emerged as a highly effective self-supervised approach in graph representation learning. However, prevailing GCL methods confront two primary challenges: 1) They predominantly operate under homophily assumptions, focusing on low-frequency signals in node features…
Graph neural networks (GNNs) have shown remarkable performance on diverse graph mining tasks. While sharing the same message passing framework, our study shows that different GNNs learn distinct knowledge from the same graph. This implies potential performance improvement by distilling the complemen…
Cross-domain graph few-shot learning attempts to address the prevalent data scarcity issue in graph mining problems. However, the utilization of cross-domain data induces another intractable domain shift issue which severely degrades the generalization ability of cross-domain graph few-shot learning…
Molecular representation learning (MRL) is a key step to build the connection between machine learning and chemical science. In particular, it encodes molecules as numerical vectors preserving the molecular structures and features, on top of which the downstream tasks (e.g., property prediction) can…
Generative self-supervised learning (SSL), especially masked autoencoders, has become one of the most exciting learning paradigms and has shown great potential in handling graph data. However, real-world graphs are always heterogeneous, which poses three critical challenges that existing methods ign…
Large Language Models (LLMs) with strong abilities in natural language processing tasks have emerged and have been applied in various kinds of areas such as science, finance and software engineering. However, the capability of LLMs to advance the field of chemistry remains unclear. In this paper, ra…
Graph representation learning has attracted tremendous attention due to its remarkable performance in many real-world applications. However, prevailing supervised graph representation learning models for specific tasks often suffer from label sparsity issue as data labeling is always time and resour…
Learning effective recipe representations is essential in food studies. Unlike what has been developed for image-based recipe retrieval or learning structural text embeddings, the combined effect of multi-modal information (i.e., recipe images, text, and relation data) receives less attention. In th…
Recipe recommendation systems play an essential role in helping people decide what to eat. Existing recipe recommendation systems typically focused on content-based or collaborative filtering approaches, ignoring the higher-order collaborative signal such as relational structure information among us…