20 accepted papers
Large language models (LLMs) have recently empowered multi-agent systems (MAS) to achieve remarkable advances in collaborative reasoning and complex task automation. The effectiveness of these systems fundamentally depends on the design of adaptive communication graphs—the underlying workflows that
Recently, significant progress has been made in protein-ligand docking, especially in deep learning methods, and some benchmarks were proposed, such as PoseBench and PLINDER. However, these studies typically focus on the self-docking scenario, which is less practical in real-world applications. More…
DNA, encoding genetic instructions for almost all living organisms, fuels groundbreaking advances in genomics and synthetic biology. Recently, DNA Language Models have achieved success in designing synthetic functional DNA sequences, even whole genomes of novel bacteriophage, verified with wet lab e…
DNA language models have revolutionized our ability to design and manipulate DNA sequences—the fundamental language of life—with unprecedented precision, enabling transformative applications in therapeutics, synthetic biology, and gene editing. However, this capability also poses significant dual-us…
Structure-based drug design (SBDD) aims to generate 3D ligand molecules that bind to specific protein targets. Existing 3D deep generative models including diffusion models have shown great promise for SBDD. However, it is complex to capture the essential protein-ligand interactions exactly in 3D sp…
Molecular docking, a technique for predicting ligand binding poses, is crucial in structure-based drug design for understanding protein-ligand interactions. Recent advancements in docking methods, particularly those leveraging geometric deep learning (GDL), have demonstrated significant efficiency a…
Structure-based drug design (SBDD), which aims to generate 3D ligand molecules binding to target proteins, is a fundamental task in drug discovery. Existing SBDD methods typically treat protein as rigid and neglect protein structural change when binding with ligand molecules, leading to a big gap wi…
Designing ligand-binding proteins, such as enzymes and biosensors, is essential in bioengineering and protein biology. One critical step in this process involves designing protein pockets, the protein interface binding with the ligand. Current approaches to pocket generation often suffer from time-i…
Graph Transformers, which incorporate self-attention and positional encoding, have recently emerged as a powerful architecture for various graph learning tasks. Despite their impressive performance, the complex non-convex interactions across layers and the recursive graph structure have made it chal…
User modeling, which aims to capture users' characteristics or interests, heavily relies on task-specific labeled data and suffers from the data sparsity issue. Several recent studies tackled this problem by pre-training the user model on massive user behavior sequences with a contrastive learning t…
Deep neural networks (DNNs) are recently shown to be vulnerable to backdoor attacks, where attackers embed hidden backdoors in the DNN model by injecting a few poisoned examples into the training dataset. While extensive efforts have been made to detect and remove backdoors from backdoored DNNs, it…
The design of \emph{de novo} functional proteins that bind with specific ligand molecules is crucial in various domains like therapeutics and bio-engineering. One vital yet challenging step is to design the protein pocket, the cavity region of protein where the ligand binds with. Existing methods su…
Lightweight compressed models are prevalent in Approximate Nearest Neighbor Search (ANNS) and Maximum Inner Product Search (MIPS) owing to their superiority of retrieval efficiency in large-scale datasets. However, results given by compressed methods are less accurate due to the curse of dimension a…
Generating molecules with high binding affinities to target proteins (a.k.a. structure-based drug design) is a fundamental and challenging task in drug discovery. Recently, deep generative models have achieved remarkable success in generating 3D molecules conditioned on the protein pocket. However,…
Designing ligand molecules that bind to specific protein binding sites is a fundamental problem in structure-based drug design. Although deep generative models and geometric deep learning have made great progress in drug design, existing works either sample in the 2D graph space or fail to generate…
Federated recommendation (FedRec) can train personalized recommenders without collecting user data, but the decentralized nature makes it susceptible to poisoning attacks. Most previous studies focus on the targeted attack to promote certain items, while the untargeted attack that aims to degrade th…
The Transformer architecture has achieved remarkable success in a number of domains including natural language processing and computer vision. However, when it comes to graph-structured data, transformers have not achieved competitive performance, especially on large graphs. In this paper, we identi…
Despite the recent progress in Graph Neural Networks (GNNs), it remains challenging to explain the predictions made by GNNs. Existing explanation methods mainly focus on post-hoc explanations where another explanatory model is employed to provide explanations for a trained GNN. The fact that post-h…
As machine learning becomes more widely used for critical applications, the need to study its implications in privacy becomes urgent. Given access to the target model and auxiliary information, model inversion attack aims to infer sensitive features of the training dataset, which leads to great pr…
Predicting molecular properties with data-driven methods has drawn much attention in recent years. Particularly, Graph Neural Networks (GNNs) have demonstrated remarkable success in various molecular generation and prediction tasks. In cases where labeled data is scarce, GNNs can be pre-trained on u…