24 accepted papers
Chromosomes are the carriers of genetic information. Further understanding their 3D structure can help reveal gene-regulatory mechanisms and cellular functions. A standard pipeline for reconstructing the chromosome 3D structure first applies the single-cell Hi-C high-throughput screening method to m…
In this work, we propose K-Flow, a novel generative learning paradigm that flows along the $K$-amplitude domain, where $K$ is a scaling parameter that organizes projected coefficients (frequency bands), and amplitude refers to the norm of such coefficients. We instantiate K-Flow with three concrete…
Transformer-based autoregressive models have emerged as a unifying paradigm across modalities such as text and images, but their extension to 3D molecule generation remains underexplored. The gap stems from two fundamental challenges: (1) how to tokenize molecules into a canonical 1D sequence of tok…
Large Language Models have shown growing ability to generate fluent and coherent texts that are highly similar to the writing style of humans. Current detectors for Machine-Generated Text (MGT) perform well when they are trained and tested in the same domain but generalize poorly to unseen domains,
Protein design stands as one of biology’s most important frontiers, with the potential to transform medicine, advance human health, and drive sustainability. Protein generation, a central task in protein design, has been greatly accelerated by AI-driven models—such as FoldFlow, MultiFlow, and AlphaF…
Molecular assembly, where a cluster of rigid molecules aggregated into strongly correlated forms, is fundamental to determining the properties of materials. However, traditional numerical methods for simulating this process are computationally expensive, and existing generative models on material ge…
Enzymes are important proteins that catalyze chemical reactions. In recent years, machine learning methods have emerged to predict enzyme function from sequence; however, there are no standardized benchmarks to evaluate these methods. We introduce CARE, a benchmark and dataset suite for the Classif…
Recent advancements in conversational large language models (LLMs), such as ChatGPT, have demonstrated remarkable promise in various domains, including drug discovery. However, existing works mainly focus on investigating the capabilities of conversational LLMs on chemical reactions and retrosynthes…
The burgeoning generative capabilities of large language models (LLMs) have raised growing concerns about abuse, demanding automatic machine-generated text detectors. DetectGPT, a zero-shot metric-based detector, first introduces perturbation and shows great performance improvement. However, in Dete…
Distribution shift presents a significant challenge in machine learning, where models often underperform during the test stage when faced with a different distribution than the one they were trained on. In this paper, we focus on domain shifts, which occur when the model is applied to new domains th…
Molecule pretraining has quickly become the go-to schema to boost the performance of AI-based drug discovery. Naturally, molecules can be represented as 2D topological graphs or 3D geometric point clouds. Although most existing pertaining methods focus on merely the single modality, recent research…
Graph Self-Supervised Learning (GSSL) provides a robust pathway for acquiring embeddings without expert labelling, a capability that carries profound implications for molecular graphs due to the staggering number of potential molecules and the high cost of obtaining labels. However, GSSL methods are…
We explore the downstream task performances for graph neural network (GNN) self-supervised learning (SSL) methods trained on subgraphs extracted from relational databases (RDBs). Intuitively, this joint use of SSL and GNNs should allow to leverage more of the available data, which could translate to…
Molecule property prediction has gained significant attention in recent years. The main bottleneck is the label insufficiency caused by expensive lab experiments. In order to alleviate this issue and to better leverage textual knowledge for tasks, this study investigates the feasibility of employing…
Molecular representation pretraining is critical in various applications for drug and material discovery due to the limited number of labeled molecules, and most existing work focuses on pretraining on 2D molecular graphs. However, the power of pretraining on 3D geometric structures has been less ex…
Recently, artificial intelligence for drug discovery has raised increasing interest in both machine learning and chemistry domains. The fundamental building block for drug discovery is molecule geometry and thus, the molecule's geometrical representation is the main bottleneck to better utilize mach…
Artificial intelligence for scientific discovery has recently generated significant interest within the machine learning and scientific communities, particularly in the domains of chemistry, biology, and material discovery. For these scientific problems, molecules serve as the fundamental building b…
Molecular graph representation learning is a fundamental problem in modern drug and material discovery. Molecular graphs are typically modeled by their 2D topological structures, but it has been recently discovered that 3D geometric information plays a more vital role in predicting molecular functio…
Multi-task learning for molecular property prediction is becoming increasingly important in drug discovery. However, in contrast to other domains, the performance of multi-task learning in drug discovery is still not satisfying as the number of labeled data for each task is too limited, which calls…
Sentence ordering aims at arranging a list of sentences in the correct order. Based on the observation that sentence order at different distances may rely on different types of information, we devise a new approach based on multi-granular orders between sentences. These orders form multiple constrai…
Several works have aimed to explain why overparameterized neural networks generalize well when trained by Stochastic Gradient Descent (SGD). The consensus explanation that has emerged credits the randomized nature of SGD for the bias of the training process towards low-complexity models and, thus,…
Over the last decade, there has been significant progress in the field of machine learning for de novo drug design, particularly in generative modeling of novel chemical structures. However, current generative approaches exhibit a significant challenge: they do not ensure that the proposed molecular…
Machine learning techniques have recently been adopted in various applications in medicine, biology, chemistry, and material engineering. An important task is to predict the properties of molecules, which serves as the main subroutine in many downstream applications such as virtual screening and dru…
Distributed model training suffers from communication overheads due to frequent gradient updates transmitted between compute nodes. To mitigate these overheads, several studies propose the use of sparsified stochastic gradients. We argue that these are facets of a general sparsification method that…