Related papers: DRExplainer: Quantifiable Interpretability in Drug…

Accurate prediction of CB2 receptor ligand activity is pivotal for advancing drug discovery targeting this receptor, which is implicated in inflammation, pain management, and neurodegenerative conditions. Although conventional machine…

Cancer drug response varies widely across tumors due to multi-layer molecular heterogeneity, motivating computational decision support for precision oncology. Despite recent progress in deep CDR models, robust alignment between…

How can we find interpretable, domain-appropriate models of natural phenomena given some complex, raw data such as images? Can we use such models to derive scientific insight from the data? In this paper, we propose some methods for…

Cancer is a primary cause of human death, but discovering drugs and tailoring cancer therapies are expensive and time-consuming. We seek to facilitate the discovery of new drugs and treatment strategies for cancer using variational…

Deep convolutional neural networks (CNNs) have achieved breakthrough performance in many pattern recognition tasks such as image classification. However, the development of high-quality deep models typically relies on a substantial amount…

Deep learning based methods hold state-of-the-art results in image denoising, but remain difficult to interpret due to their construction from poorly understood building blocks such as batch-normalization, residual learning, and feature…

Deep convolutional neural networks (DCNN) have enjoyed great successes in many signal processing applications because they can learn complex, non-linear causal relationships from input to output. In this light, DCNNs are well suited for the…

Machine learning models that offer excellent predictive performance often lack the interpretability necessary to support integrated human machine decision-making. In clinical medicine and other high-risk settings, domain experts may be…

Deep neural networks have been well-known for their superb handling of various machine learning and artificial intelligence tasks. However, due to their over-parameterized black-box nature, it is often difficult to understand the prediction…

Molecular property prediction constitutes a cornerstone of drug discovery and materials science, necessitating models capable of disentangling complex structure-property relationships across diverse molecular modalities. Existing approaches…

Convolutional neural networks (CNNs) have shown exceptional performance for a range of medical imaging tasks. However, conventional CNNs are not able to explain their reasoning process, therefore limiting their adoption in clinical…

In structure-based drug design, accurately estimating the binding affinity between a candidate ligand and its protein receptor is a central challenge. Recent advances in artificial intelligence, particularly deep learning, have demonstrated…

A key goal of computational personalized medicine is to systematically utilize genomic and other molecular features of samples to predict drug responses for a previously unseen sample. Such predictions are valuable for developing hypotheses…

Human cancers present a significant public health challenge and require the discovery of novel drugs through translational research. Transcriptomics profiling data that describes molecular activities in tumors and cancer cell lines are…

We develop a novel convolutional architecture tailored for learning from data defined over directed acyclic graphs (DAGs). DAGs can be used to model causal relationships among variables, but their nilpotent adjacency matrices pose unique…

Deep learning has achieved tremendous success in designing novel chemical compounds with desirable pharmaceutical properties. In this work, we focus on a new type of drug design problem -- generating a small "linker" to physically attach…

Drug-Target Interaction (DTI) prediction is vital for drug discovery, yet challenges persist in achieving model interpretability and optimizing performance. We propose a novel transformer-based model, FragXsiteDTI, that aims to address…

Deep Neural Networks have achieved huge success at a wide spectrum of applications from language modeling, computer vision to speech recognition. However, nowadays, good performance alone is not sufficient to satisfy the needs of practical…

Accurate prediction of drug molecule solubility is crucial for therapeutic effectiveness and safety. Traditional methods often miss complex molecular structures, leading to inaccuracies. We introduce the YZS-Model, a deep learning framework…

Given the increasing volume and quality of genomics data, extracting new insights requires interpretable machine-learning models. This work presents Genomic Interpreter: a novel architecture for genomic assay prediction. This model…