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The ability of deep learning (DL) to improve the practice of medicine and its clinical outcomes faces a looming obstacle: model interpretation. Without description of how outputs are generated, a collaborating physician can neither resolve…

Molecular property prediction has gained significant attention due to its transformative potential in multiple scientific disciplines. Conventionally, a molecule graph can be represented either as a graph-structured data or a SMILES text.…

Since the advent of machine learning, interpretability has remained a persistent challenge, becoming increasingly urgent as generative models support high-stakes applications in drug and material discovery. Recent advances in large language…

Molecular Representation Learning (MRL) has proven impactful in numerous biochemical applications such as drug discovery and enzyme design. While Graph Neural Networks (GNNs) are effective at learning molecular representations from a 2D…

Advanced computational methods are being actively sought for addressing the challenges associated with discovery and development of new combinatorial material such as formulations. A widely adopted approach involves domain informed…

In this paper, we present a novel diagnostic framework that integrates Knowledge Graphs (KGs) and Large Language Models (LLMs) to support system diagnostics in high-reliability systems such as nuclear power plants. Traditional diagnostic…

Advances in deep learning have greatly improved structure prediction of molecules. However, many macroscopic observations that are important for real-world applications are not functions of a single molecular structure, but rather…

Graph neural networks (GNNs) have been used extensively for addressing problems in drug design and discovery. Both ligand and target molecules are represented as graphs with node and edge features encoding information about atomic elements…

There is a perceived dichotomy between structure-based and descriptor-based molecular representations used for predictive chemistry tasks. Here, we study the performance, generalizability, and interpretability of the recently proposed…

Chemical representation learning has gained increasing interest due to the limited availability of supervised data in fields such as drug and materials design. This interest particularly extends to chemical language representation learning,…

With the development of computer-assisted techniques, research communities including biochemistry and deep learning have been devoted into the drug discovery field for over a decade. Various applications of deep learning have drawn great…

The success of machine learning (ML) in materials property prediction depends heavily on how the materials are represented for learning. Two dominant families of material descriptors exist, one that encodes crystal structure in the…

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…

In recent years, Large Language Models (LLMs) have achieved significant success in natural language processing (NLP) and various interdisciplinary areas. However, applying LLMs to chemistry is a complex task that requires specialized domain…

Deep learning-based molecular generation models have shown great potential in efficiently exploring vast chemical spaces by generating potential drug candidates with desired properties. However, these models often produce chemically invalid…

Contemporary graph learning algorithms are not well-defined for large molecules since they do not consider the hierarchical interactions among the atoms, which are essential to determine the molecular properties of macromolecules. In this…

Structural biology relies on accurate three-dimensional biomolecular structures to advance our understanding of biological functions, disease mechanisms, and therapeutics. While recent advances in deep learning have enabled the development…

Large language models (LLMs) have demonstrated broad utility across molecular domains, spanning drug discovery and materials design. Analyzing LLMs' latent representations is crucial for elucidating their underlying mechanisms, improving…

The perceptual-based grouping process produces a hierarchical and compositional image representation that helps both human and machine vision systems recognize heterogeneous visual concepts. Examples can be found in the classical…

Accurate and efficient prediction of polymer properties is of key importance for polymer design. Traditional experimental tools and density function theory (DFT)-based simulations for polymer property evaluation, are both expensive and…