20 accepted papers
Protein design is revolutionizing biotechnology, yet existing approaches struggle to balance structural foldability with functional performance. Structure-based models excel at generating stable protein backbones but often overlook critical functional properties, while protein language models captur
Molecular structure generation from mass spectrometry is fundamental for understanding cellular metabolism and discovering novel compounds. Although tandem mass spectrometry (MS/MS) enables the high-throughput acquisition of fragment fingerprints, these spectra often reflect higher-order interaction
Understanding genotype-phenotype relationships is pivotal for advancing biomedical research, drug discovery, and precision medicine. With the rise of high-throughput cellular imaging, it is essential to tightly integrate high-content cellular morphology with structured biological knowledge to extrac
Reasoning Large Multi-modality Models (LMMs) have become the de facto choice for many applications. However, these models rely on a Chain-of-Thought (CoT) process that is lengthy and unpredictable at runtime, often resulting in inefficient use of computational resources (due to memory fragmentation)
Drug-drug interaction (DDI) prediction is pivotal for drug safety and clinical decision-making. Recently, subgraph-based methods utilizing knowledge graphs (KGs) and domain information have achieved promising results by extracting informative subgraphs for DDI prediction. However, existing subgraph
Spatial transcriptomics (ST) links gene expression to tissue architecture and enables predicting spatial expression from H&E-stained whole-slide images (WSIs). However, existing spot- or slide-level predictors focus on single-spot features or pairwise relations, failing to capture high-order, many-t
Predicting changes in binding free energy ($\Delta\Delta G$) is essential for understanding protein-protein interactions, which are critical in drug design and protein engineering. However, existing methods often rely on pre-trained knowledge and heuristic features, limiting their ability to accurat…
Diffusion-based molecular graph generative models have achieved significant success in template-free, single-step retrosynthesis prediction. However, these models typically generate reactants from scratch, often overlooking the fact that the scaffold of a product molecule typically remains unchanged…
While Graph Neural Networks and Transformers have shown promise in predicting molecular properties, they struggle with directly modeling complex many-body interactions. Current methods often approximate interactions like three- and four-body terms in message passing, while attention-based models, de…
Virtual Screening (VS) is vital for drug discovery but struggles with low hit rates and high computational costs. While Active Learning (AL) has shown promise in improving the efficiency of VS, traditional methods rely on inflexible and handcrafted heuristics, limiting adaptability in complex chemic…
Automatic radiology report generation can provide substantial advantages to clinical physicians by effectively reducing their workload and improving efficiency. Despite the promising potential of current methods challenges persist in effectively extracting and preventing degradation of prominent fea…
The increasing scale of vision transformers (ViT) has made the efficient fine-tuning of these large models for specific needs a significant challenge in various applications. This issue originates from the computationally demanding matrix multiplications required during the backpropagation process t…
Despite its importance for federated learning, continuous learning and many other applications, on-device training remains an open problem for EdgeAI. The problem stems from the large number of operations (e.g., floating point multiplications and additions) and memory consumption required during tra…
Anytime neural networks (AnytimeNNs) are a promising solution to adaptively adjust the model complexity at runtime under various hardware resource constraints. However, the manually-designed AnytimeNNs are biased by designers' prior experience and thus provide sub-optimal solutions. To address the l…
Neural Architecture Search (NAS) is widely used to automatically obtain the neural network with the best performance among a large number of candidate architectures. To reduce the search time, zero-shot NAS aims at designing training-free proxies that can predict the test performance of a given arch…
Illuminating the interconnections between drugs and genes is an important topic in drug development and precision medicine. Currently, computational predictions of drug-gene interactions mainly focus on the binding interactions without considering other relation types like agonist, antagonist, etc.…
Depth estimation is a safety critical and energy sensitive method for environment sensing. However, in real applications, the depth estimation may be halted at any time, due to the random interruptions or low energy capacity of battery when using powerful sensors like 3D LiDAR. To address this probl…
Relation prediction for knowledge graphs aims at predicting missing relationships between entities. Despite the importance of inductive relation prediction, most previous works are limited to a transductive setting and cannot process previously unseen entities. The recent proposed subgraph-based rel…
Constructing appropriate representations of molecules lies at the core of numerous tasks such as material science, chemistry, and drug designs. Recent researches abstract molecules as attributed graphs and employ graph neural networks (GNN) for molecular representation learning, which have made rema…
Constructing proper representations of molecules lies at the core of numerous tasks such as molecular property prediction and drug design. Graph neural networks, especially message passing neural network (MPNN) and its variants, have recently made remarkable achievements in molecular graph modeling.…