39 accepted papers
We present CrystalDiT, a diffusion transformer for crystal structure generation that achieves state-of-the-art performance by challenging the trend of architectural complexity. Instead of intricate, multi-stream designs, CrystalDiT employs a unified transformer that imposes a powerful inductive bias
Masked graph modeling (MGM) is a promising approach for molecular representation learning (MRL). However, extending the success of re-mask decoding from 2D to 3D MGM is non-trivial, primarily due to two conflicting challenges: avoiding 2D structure leakage to the decoder, while still providing suffi…
Machine learning models must continuously self-adjust themselves for novel data distribution in the open world. As the predominant principle, entropy minimization (EM) has been proven to be a simple yet effective cornerstone in existing test-time adaption (TTA) methods. While unfortunately its fatal…
Advancements in the text-to-image diffusion model have raised security concerns due to their potential to generate images with inappropriate themes such as societal biases and copyright infringements. Current studies have made notable progress in preventing the model from generating images containin…
Recently, there has been a surge of interest in extending the success of large language models (LLMs) from texts to molecules. Most existing approaches adopt a graph neural network to represent a molecule as a series of node tokens for molecule-language alignment, which, however, have overlooked the…
Exploring chemical space to find novel molecules that simultaneously satisfy multiple properties is crucial in drug discovery. However, existing methods often struggle with trading off multiple properties due to the conflicting or correlated nature of chemical properties. To tackle this issue, we i…
Meta-learning enables learning systems to adapt quickly to new tasks, similar to humans. Different meta-learning approaches all work under/with the mini-batch episodic training framework. Such framework naturally gives the information about task identity, which can serve as additional supervision f…
Large language models (LLMs) are widely adopted to generate synthetic datasets for various natural language processing (NLP) tasks, such as text classification and summarization. However, accurately measuring the diversity of these synthetic datasets—an aspect crucial for robust model performance—re…
The conceptual knowledge in Large Language Models (LLMs) can become outdated over time, and concept editing is often an option. Current evaluations on conceptual knowledge editing primarily focus on whether the definitions of concepts are successfully edited, neglecting the impact on the model’s rel…
Existing methods to enhance the reasoning capability of large language models predominantly rely on supervised fine-tuning (SFT) followed by reinforcement learning (RL) on reasoning-specific data. These approaches critically depend on external supervisions--such as labeled reasoning traces, verified…
The remarkable success of Large Language Models (LLMs) across diverse tasks has driven the research community to extend their capabilities to molecular applications. However, most molecular LLMs employ adapter-based architectures that fail to equally integrate molecule and text modalities and lack e
Protein complex formation, a pivotal challenge in contemporary biology, has recently gained interest from the machine learning community, particularly concerning protein-ligand docking tasks. In this paper, we delve into the equally crucial but comparatively under-investigated domain of protein-prot…
Learning neural subset selection tasks, such as compound selection in AI-aided drug discovery, have become increasingly pivotal across diverse applications. The existing methodologies in the field primarily concentrate on constructing models that capture the relationship between utility function val…
Interpretable graph neural networks (XGNNs ) are widely adopted in various scientific applications involving graph-structured data. Existing XGNNs predominantly adopt the attention-based mechanism to learn edge or node importance for extracting and making predictions with the interpretable subgraph.…
Out-of-distribution (OOD) detection is essential for model trustworthiness which aims to sensitively identity semantic OOD samples and robustly generalize for covariate-shifted OOD samples. However, we discover that the superior OOD detection performance of state-of-the-art methods is achieved by se…
Text watermarking has emerged as a pivotal technique for identifying machine-generated text. However, existing methods often rely on arbitrary vocabulary partitioning during decoding to embed watermarks, which compromises the availability of suitable tokens and significantly degrades the quality of…
Neural networks suffer from catastrophic forgetting when sequentially learning tasks phase-by-phase, making them inapplicable in dynamically updated systems. Class-incremental learning (CIL) aims to enable neural networks to learn different categories at multi-stages. Recently, dynamic-structure-bas…
Large language models (LLMs) outperform information retrieval techniques for downstream knowledge-intensive tasks when being prompted to generate world knowledge. However, community concerns abound regarding the factuality and potential implications of using this uncensored knowledge. In light of th…
Invariant graph representation learning aims to learn the invariance among data from different environments for out-of-distribution generalization on graphs. As the graph environment partitions are usually expensive to obtain, augmenting the environment information has become the de facto approach.…
AI-aided drug discovery (AIDD) is gaining popularity due to its potential to make the search for new pharmaceuticals faster, less expensive, and more effective. Despite its extensive use in numerous fields (e.g., ADMET prediction, virtual screening), little research has been conducted on the out-of-…
Large language models have demonstrated surprising ability to perform in-context learning, i.e., these models can be directly applied to solve numerous downstream tasks by conditioning on a prompt constructed by a few input-output examples. However, prior research has shown that in-context learning…
Molecular representation learning lays the foundation for drug discovery. However, existing methods suffer from poor out-of-distribution (OOD) generalization, particularly when data for training and testing originate from different environments. To address this issue, we propose a new framework for…
Recently, there has been a growing surge of interest in enabling machine learning systems to generalize well to Out-of-Distribution (OOD) data. Most efforts are devoted to advancing optimization objectives that regularize models to capture the underlying invariance; however, there often are compromi…
Tabular-format data is widely adopted in various real-world applications. Various machine learning models have achieved remarkable success in both industrial applications and data-science competitions. Despite these successes, most current machine learning methods for tabular data lack accurate conf…
Learning representations on large-sized graphs is a long-standing challenge due to the inter-dependence nature involved in massive data points. Transformers, as an emerging class of foundation encoders for graph-structured data, have shown promising performance on small graphs due to its global atte…
A common explanation for the failure of out-of-distribution (OOD) generalization is that the model trained with empirical risk minimization (ERM) learns spurious features instead of invariant features. However, several recent studies challenged this explanation and found that deep networks may have…
Graph neural networks (GNNs) have demonstrated superior performance for semi-supervised node classification on graphs, as a result of their ability to exploit node features and topological information simultaneously. However, most GNNs implicitly assume that the labels of nodes and their neighbors i…
Valuation problems, such as feature interpretation, data valuation and model valuation for ensembles, become increasingly more important in many machine learning applications. Such problems are commonly solved by well-known game-theoretic criteria, such as Shapley value or Banzhaf value. In this wor…
Recently, the pretrain-finetuning paradigm has attracted tons of attention in graph learning community due to its power of alleviating the lack of labels problem in many real-world applications. Current studies use existing techniques, such as weight constraint, representation constraint, which are…
Protein complex formation is a central problem in biology, being involved in most of the cell's processes, and essential for applications, e.g. drug design or protein engineering. We tackle rigid body protein-protein docking, i.e., computationally predicting the 3D structure of a protein-protein com…
Despite recent success in using the invariance principle for out-of-distribution (OOD) generalization on Euclidean data (e.g., images), studies on graph data are still limited. Different from images, the complex nature of graphs poses unique challenges to adopting the invariance principle. In partic…
Learning set functions becomes increasingly important in many applications like product recommendation and compound selection in AI-aided drug discovery. The majority of existing works study methodologies of set function learning under the function value oracle, which, however, requires expensive su…
Subpopulation shift widely exists in many real-world machine learning applications, referring to the training and test distributions containing the same subpopulation groups but varying in subpopulation frequencies. Importance reweighting is a normal way to handle the subpopulation shift issue by im…
Given the input graph and its label/property, several key problems of graph learning, such as finding interpretable subgraphs, graph denoising and graph compression, can be attributed to the fundamental problem of recognizing a subgraph of the original one. This subgraph shall be as informative…
Graph Convolutional Networks (GCNs) are promising deep learning approaches in learning representations for graph-structured data. Despite the proliferation of such methods, it is well known that they are vulnerable to carefully crafted adversarial attacks on the graph structure. In this paper, we fi…
Recently, the teacher-student knowledge distillation framework has demonstrated its potential in training Graph Neural Networks (GNNs). However, due to the difficulty of training over-parameterized GNN models, one may not easily obtain a satisfactory teacher model for distillation. Furthermore, the…
Submodular functions have been studied extensively in machine learning and data mining. In particular, the optimization of submodular functions over the integer lattice (integer submodular functions) has recently attracted much interest, because this domain relates naturally to many practical proble…
How to obtain informative representations of molecules is a crucial prerequisite in AI-driven drug design and discovery. Recent researches abstract molecules as graphs and employ Graph Neural Networks (GNNs) for molecular representation learning. Nevertheless, two issues impede the usage of GNNs in…
Mean field inference for discrete graphical models is generally a highly nonconvex problem, which also holds for the class of probabilistic log-submodular models. Existing optimization methods, e.g., coordinate ascent algorithms, typically only find local optima. In this work we propose provable mea…