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Drug discovery is a complex process that involves sequentially screening and examining a vast array of molecules to identify those with the target properties. This process, also referred to as sequential experimentation, faces challenges…
Delays in protein synthesis cause a confounding effect when constructing Gene Regulatory Networks (GRNs) from RNA-sequencing time-series data. Accurate GRNs can be very insightful when modelling development, disease pathways, and drug…
Drug-drug interaction prediction is a crucial issue in molecular biology. Traditional methods of observing drug-drug interactions through medical experiments require significant resources and labor. This paper presents a medical knowledge…
We present a novel classification-based method for learning to predict gene regulatory response. Our approach is motivated by the hypothesis that in simple organisms such as Saccharomyces cerevisiae, we can learn a decision rule for…
Network science is already making an impact on the study of complex systems and offers a promising variety of tools to understand their formation and evolution (1-4) in many disparate fields from large communication networks (5,6),…
Identification of drug-target interactions is an indispensable part of drug discovery. While conventional shallow machine learning and recent deep learning methods based on chemogenomic properties of drugs and target proteins have pushed…
Neural Temporal Point Processes (TPPs) have emerged as the primary framework for predicting sequences of events that occur at irregular time intervals, but their sequential nature can hamper performance for long-horizon forecasts. To…
Motivation: Cell-biological processes are regulated through a complex network of interactions between genes and their products. The processes, their activating conditions, and the associated transcriptional responses are often unknown.…
Motivation: Measurements of gene expression over time enable the reconstruction of transcriptional networks. However, Bayesian networks and many other current reconstruction methods rely on assumptions that conflict with the differential…
Introduction: Approximately 23 million or 30% of epilepsy patients worldwide suffer from drug-resistant epilepsy (DRE). The unpredictability of seizure occurrences, which causes safety issues as well as social concerns, restrict the…
Minimizing adverse reactions caused by drug-drug interactions has always been a momentous research topic in clinical pharmacology. Detecting all possible interactions through clinical studies before a drug is released to the market is a…
Designing new chemical compounds with desired pharmaceutical properties is a challenging task and takes years of development and testing. Still, a majority of new drugs fail to prove efficient. Recent success of deep generative modeling…
Substances of abuse are known to activate and disrupt neuronal circuits in the brain reward system. We propose a simple and easily interpretable dynamical systems model to describe the neurobiology of drug addiction that incorporates the…
Drug repurposing has attracted increasing attention from both the pharmaceutical industry and the research community. Many existing computational drug repurposing methods rely on preclinical data (e.g., chemical structures, drug targets),…
In realistic scenarios, multivariate timeseries evolve over case-by-case time-scales. This is particularly clear in medicine, where the rate of clinical events varies by ward, patient, and application. Increasingly complex models have been…
In the dynamic hospital setting, decision support can be a valuable tool for improving patient outcomes. Data-driven inference of future outcomes is challenging in this dynamic setting, where long sequences such as laboratory tests and…
In microarray experiments, it is often of interest to identify genes which have a pre-specified gene expression profile with respect to time. Methods available in the literature are, however, typically not stringent enough in identifying…
The contributions of model complexity, data volume, and feature modalities to knowledge graph-based drug repurposing remain poorly quantified under rigorous temporal validation. We constructed a pharmacology knowledge graph from ChEMBL 36…
Predicting clinical outcomes to anti-cancer drugs on a personalized basis is challenging in cancer treatment due to the heterogeneity of tumors. Traditional computational efforts have been made to model the effect of drug response on…
There is an abundance of complex dynamic systems that are critical to our daily lives and our society but that are hardly understood, and even with today's possibilities to sense and collect large amounts of experimental data, they are so…