15 accepted papers
Multi-objective discrete optimization problems, such as molecular design, pose significant challenges due to their vast and unstructured combinatorial spaces. Traditional evolutionary algorithms often get trapped in local optima, while expert knowledge can provide crucial guidance for accelerating c…
Flexible docking, which predicts the binding conformations of both proteins and small molecules by modeling their structural flexibility, plays a vital role in structure-based drug design. Although recent generative approaches, particularly diffusion-based models, have shown promising results, they…
ControlNet has significantly advanced controllable image generation by integrating dense conditions (such as depth and canny edges) with text-to-image diffusion models. However, ControlNet's integration requires an additional amount nearly equal to half of the base diffusion model's parameters, maki…
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…
Self-supervised learning has recently gained growing interest in molecular modeling for scientific tasks such as AI-assisted drug discovery. Current studies consider leveraging both 2D and 3D molecular structures for representation learning. However, relying on straightforward alignment strategies t…
We introduced StyleEntity a zero-shot image manipulation model that utilizes named entities as proxies during its training phase. This strategy enables our model to manipulate images using unseen textual descriptions during inference all within a single training phase. Additionally we proposed an in…
The binding between proteins and ligands plays a crucial role in the realm of drug discovery. Previous deep learning approaches have shown promising results over traditional computationally intensive methods, but resulting in poor generalization due to limited supervised data. In this paper, we prop…
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…
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…
Recent progress in diffusion models has revolutionized the popular technology of text-to-image generation. While existing approaches could produce photorealistic high-resolution images with text conditions, there are still several open problems to be solved, which limits the further improvement of i…
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…
Recent years have witnessed the rise and success of pre-training techniques in visually-rich document understanding. However, most existing methods lack the systematic mining and utilization of layout-centered knowledge, leading to sub-optimal performances. In this paper, we propose ERNIE-Layout, a…
Relational graph neural networks have garnered particular attention to encode graph context in knowledge graphs (KGs). Although they achieved competitive performance on small KGs, how to efficiently and effectively utilize graph context for large KGs remains an open problem. To this end, we propose…
Graph neural network (GNN) and label propagation algorithm (LPA) are both message passing algorithms, which have achieved superior performance in semi-supervised classification. GNN performs feature propagation by a neural network to make predictions, while LPA uses label propagation across graph ad…