22 accepted papers
Innovation is a key driving force of human civilization. As the body of knowledge has grown considerably, bridging knowledge across different disciplines, where significant innovation often emerges, has become increasingly challenging. The recent advancements in machine learning models, particularly…
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…
We introduce NeuralOS, a neural framework that simulates graphical user interfaces (GUIs) of operating systems by directly predicting screen frames in response to user inputs such as mouse movements, clicks, and keyboard events. NeuralOS combines a recurrent neural network (RNN), which tracks the co…
Building _Virtual Cells_ that can accurately simulate cellular responses to perturbations is a long-standing goal in systems biology. A fundamental challenge is that high-throughput single-cell sequencing is destructive: the same cell cannot be observed both before and after a perturbation. Thus, pe…
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…
Proteins adopt multiple structural conformations to perform their diverse biological functions, and understanding these conformations is crucial for advancing drug discovery. Traditional physics-based simulation methods often struggle with sampling equilibrium conformations and are computationally e…
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…
Conversational humor is the key to capturing dialogue semantics and dialogue comprehension, which is usually generated in multiple modalities, such as linguistic rhetoric (textual modality), exaggerated facial expressions or movements (visual modality), and quirky intonation (acoustic modality). How…
Recently, significant progress has been made in generating high-quality sentence representations through contrastive learning. SimCSE-like models improve the uniformity of the representation space by pulling in positive examples and pushing out negative examples. However, these models often suffer f…
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…
In protein biophysics, the separation between the functionally important residues (forming the active site or binding surface) and those that create the overall structure (the fold) is a well-established and fundamental concept. Identifying and modifying those functional sites is critical for protei…
We present a simple and yet effective interpolation-based regularization technique, aiming to improve the generalization of Graph Neural Networks (GNNs) on supervised graph classification. We leverage Mixup, an effective regularizer for vision, where random sample pairs and their labels are interp…
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…
Mixup, which creates synthetic training instances by linearly interpolating random sample pairs, is a simple and yet effective regularization technique to boost the performance of deep models trained with SGD. In this work, we report a previously unobserved phenomenon in Mixup raining: on a number o…
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…
Reliably predicting the products of chemical reactions presents a fundamental challenge in synthetic chemistry. Existing machine learning approaches typically produce a reaction product by sequentially forming its subparts or intermediate molecules. Such autoregressive methods, however, not only req…
This paper studies unsupervised/self-supervised whole-graph representation learning, which is critical in many tasks such as molecule properties prediction in drug and material discovery. Existing methods mainly focus on preserving the local similarity structure between different graph instances but…
Leveraging the framework of Optimal Transport, we introduce a new family of generative autoencoders with a learnable prior, called Symmetric Wasserstein Autoencoders (SWAEs). We propose to symmetrically match the joint distributions of the observed data and the latent representation induced by the e…
A fundamental problem in computational chemistry is to find a set of reactants to synthesize a target molecule, a.k.a. retrosynthesis prediction. Existing state-of-the-art methods rely on matching the target molecule with a large set of reaction templates, which are very computationally expensive an…
The chain-structured long short-term memory (LSTM) has showed to be effective in a wide range of problems such as speech recognition and machine translation. In this paper, we propose to extend it to tree structures, in which a memory cell can reflect the history memories of multiple child cells or…