35 accepted papers
Reinforcement Learning (RL) has emerged as a central paradigm for advancing Large Language Models (LLMs), where both pre-training and RL post-training stages are grounded in the same log-likelihood formulation. In contrast, recent RL approaches for diffusion models, most notably Denoising Diffusion …
Efficiently scaling Large Language Models (LLMs) necessitates exploring alternatives to dominant autoregressive (AR) methods, with Masked Diffusion Models (MDMs) emerging as candidates. However, comparing AR (typically decoder-only) and MDM (often encoder-only) paradigms is confounded by differing a…
Recent advances in few-step diffusion models have demonstrated their efficiency and effectiveness by shortcutting the probabilistic paths of diffusion models, especially in training one-step diffusion models from scratch (a.k.a. shortcut models). However, their theoretical derivation and practical i…
Predicting the evolution of complex physical systems remains a central problem in science and engineering. Despite rapid progress in scientific Machine Learning (ML) models, a critical bottleneck is the lack of expensive real-world data, resulting in most current models being trained and validated o…
The application of deep learning for partial differential equation (PDE)-constrained control is gaining increasing attention. However, existing methods rarely consider safety requirements crucial in real-world applications. To address this limitation, we propose Safe Diffusion Models for PDE Control…
Diffusion Probabilistic Models (DPMs) have achieved significant success in generative tasks. However, their training and sampling processes suffer from the issue of distribution mismatch. During the denoising process, the input data distributions differ between the training and inference stages, pot…
Diffusion-based models have shown great promise in molecular generation but often require a large number of sampling steps to generate valid samples. In this paper, we introduce a novel Straight-Line Diffusion Model (SLDM) to tackle this problem, by formulating the diffusion process to follow a line…
Molecular generation and molecular property prediction are both crucial for drug discovery, but they are often developed independently. Inspired by recent studies, which demonstrate that diffusion model, a prominent generative approach, can learn meaningful data representations that enhance predicti…
Simulating and controlling physical systems described by partial differential equations (PDEs) are crucial tasks across science and engineering. Recently, diffusion generative models have emerged as a competitive class of methods for these tasks due to their ability to capture long-term dependencies…
Recently, neural networks have been extensively employed to solve partial differential equations (PDEs) in physical system modeling. While major studies focus on learning system evolution on predefined static mesh discretizations, some methods utilize reinforcement learning or supervised learning te…
Controlling the evolution of complex physical systems is a fundamental task across science and engineering. Classical techniques suffer from limited applicability or huge computational costs. On the other hand, recent deep learning and reinforcement learning-based approaches often struggle to optim…
We present a novel perspective on temporal point processes (TPPs) by reformulating their intensity processes as solutions to stochastic differential equations (SDEs). In particular, we first prove the equivalent SDE formulations of several classical TPPs, including Poisson processes, Hawkes processe…
In the field of Structure-based Drug Design (SBDD), deep learning-based generative models have achieved outstanding performance in terms of docking score. However, further study shows that the existing molecular generative methods and docking scores both have lacked consideration in terms of specifi…
Pocket representations play a vital role in various biomedical applications, such as druggability estimation, ligand affinity prediction, and de novo drug design. While existing geometric features and pretrained representations have demonstrated promising results, they usually treat pockets independ…
While molecular pre-training has shown great potential in enhancing drug discovery, the lack of a solid physical interpretation in current methods raises concerns about whether the learned representation truly captures the underlying explanatory factors in observed data, ultimately resulting in limi…
With the incorporation of the UNet architecture, diffusion probabilistic models have become a dominant force in image generation tasks. One key design in UNet is the skip connections between the encoder and decoder blocks. Although skip connections have been shown to improve training stability and m…
Recently, a noticeable trend has emerged in developing pre-trained foundation models in the domains of CV and NLP. However, for molecular pre-training, there lacks a universal model capable of effectively applying to various categories of molecular tasks, since existing prevalent pre-training method…
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…
Geometric deep learning enables the encoding of physical symmetries in modeling 3D objects. Despite rapid progress in encoding 3D symmetries into Graph Neural Networks (GNNs), a comprehensive evaluation of the expressiveness of these network architectures through a local-to-global analysis lacks tod…
Recently, generalization on out-of-distribution (OOD) data with correlation shift has attracted great attentions. The correlation shift is caused by the spurious attributes that correlate to the class label, as the correlation between them may vary in training and test data. For such a problem, we s…
The proliferation of pretrained models, as a result of advancements in pretraining techniques, has led to the emergence of a vast zoo of publicly available models. Effectively utilizing these resources to obtain models with robust out-of-distribution generalization capabilities for downstream tasks…
Coordinate denoising is a promising 3D molecular pre-training method, which has achieved remarkable performance in various downstream drug discovery tasks. Theoretically, the objective is equivalent to learning the force field, which is revealed helpful for downstream tasks. Nevertheless, there are…
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…
Diffusion Probabilistic Models (DPMs) have achieved considerable success in generation tasks. As sampling from DPMs is equivalent to solving diffusion SDE or ODE which is time-consuming, numerous fast sampling methods built upon improved differential equation solvers are proposed. The majority of su…
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…
We establish upper bounds for the expected excess risk of models trained by proper iterative algorithms which approximate the local minima. Unlike the results built upon the strong globally strongly convexity or global growth conditions e.g., PL-inequality, we only require the population risk to be…
The momentum acceleration technique is widely adopted in many optimization algorithms. However, there is no theoretical answer on how the momentum affects the generalization performance of the optimization algorithms. This paper studies this problem by analyzing the implicit regularization of moment…
Model-based reinforcement learning provides an efficient mechanism to find the optimal policy by interacting with the learned environment. In addition to treating the learned environment like a black-box simulator, a more effective way to use the model is to exploit its differentiability. Such metho…
By inferring latent groups in the training data, recent works introduce invariant learning to the case where environment annotations are unavailable. Typically, learning group invariance under a majority/minority split is empirically shown to be effective in improving out-of-distribution generalizat…
Data augmentation is an effective technique to improve the generalization of deep neural networks. However, previous data augmentation methods usually treat the augmented samples equally without considering their individual impacts on the model. To address this, for the augmented samples from the sa…
Ensemble-based debiasing methods have been shown effective in mitigating the reliance of classifiers on specific dataset bias, by exploiting the output of a bias-only model to adjust the learning target. In this paper, we focus on the bias-only model in these ensemble-based methods, which plays an i…
It is well known that neural networks with rectified linear units (ReLU) activation functions are positively scale-invariant. Conventional algorithms like stochastic gradient descent optimize the neural networks in the vector space of weights, which is, however, not positively scale-invariant. This…
With the fast development of deep learning, it has become common to learn big neural networks using massive training data. Asynchronous Stochastic Gradient Descent (ASGD) is widely adopted to fulfill this task for its efficiency, which is, however, known to suffer from the problem of delayed gradien…
In reinforcement learning (RL), one of the key components is policy evaluation, which aims to estimate the value function (i.e., expected long-term accumulated reward) of a policy. With a good policy evaluation method, the RL algorithms will estimate the value function more accurately and find a bet…
Decision tree (and its extensions such as Gradient Boosting Decision Trees and Random Forest) is a widely used machine learning algorithm, due to its practical effectiveness and model interpretability. With the emergence of big data, there is an increasing need to parallelize the training process of…