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It is a common practice in modern medicine to prescribe multiple medications simultaneously to treat diseases. However, these medications could have adverse reactions between them, known as Drug-Drug Interactions (DDI), which have the…
Drug repositioning (DR) refers to identification of novel indications for the approved drugs. The requirement of huge investment of time as well as money and risk of failure in clinical trials have led to surge in interest in drug…
Bridging the past to the future, connecting agents both spatially and temporally, lies at the core of the trajectory prediction task. Despite great efforts, it remains challenging to explicitly learn and predict latencies, i.e., response…
The longitudinal analysis of patient response time course following doses of therapeutics is currently performed using Pharmacokinetic/Pharmacodynamic (PK/PD) methodologies, which requires significant human experience and expertise in the…
Molecular property prediction is essential for drug discovery. In recent years, deep learning methods have been introduced to this area and achieved state-of-the-art performances. However, most of existing methods ignore the intrinsic…
Gene expression represents a fundamental interface between genes and environment in the development and ongoing plasticity of the human organism. Individual differences in gene expression are likely to underpin much of human diversity,…
Retrosynthesis analysis is pivotal yet challenging in drug discovery and organic chemistry. Despite the proliferation of computational tools over the past decade, AI-based systems often fall short in generalizing across diverse reaction…
Generative models can produce synthetic patient records for analytical tasks when real data is unavailable or limited. However, current methods struggle with adhering to domain-specific knowledge and removing invalid data. We present…
The study of high-throughput genomic profiles from a pharmacogenomics viewpoint has provided unprecedented insights into the oncogenic features modulating drug response. A recent screening of ~1,000 cancer cell lines to a collection of…
Accurate prediction of outcomes is crucial for clinical decision-making and personalized patient care. Supervised machine learning algorithms, which are commonly used for outcome prediction in the medical domain, optimize for predictive…
Modeling real-world phenomena is a focus of many science and engineering efforts, such as ecological modeling and financial forecasting, to name a few. Building an accurate model for complex and dynamic systems improves understanding of…
Gene expression analysis aims at identifying the genes able to accurately predict biological parameters like, for example, disease subtyping or progression. While accurate prediction can be achieved by means of many different techniques,…
Despite extensive safety assessments of drugs prior to their introduction to the market, certain adverse drug reactions (ADRs) remain undetected. The primary objective of pharmacovigilance is to identify these ADRs (i.e., signals). In…
Dynamic Positron Emission Tomography (dPET) imaging and Time-Activity Curve (TAC) analyses are essential for understanding and quantifying the biodistribution of radiopharmaceuticals over time and space. Traditional compartmental modeling,…
The reliability of a high-throughput biological experiment relies highly on the settings of the operational factors in its experimental and data-analytic procedures. Understanding how operational factors influence the reproducibility of the…
With the advancements in Artificial intelligence (AI) and the accumulation of healthrelated big data, it has become increasingly feasible and commonplace to leverage machine learning technologies to analyze clinical and omics metadata to…
The modeling of time series is becoming increasingly critical in a wide variety of applications. Overall, data evolves by following different patterns, which are generally caused by different user behaviors. Given a time series, we define…
We describe a fully data driven model that learns to perform a retrosynthetic reaction prediction task, which is treated as a sequence-to-sequence mapping problem. The end-to-end trained model has an encoder-decoder architecture that…
Sequential learning systems are used in a wide variety of problems from decision making to optimization, where they provide a 'belief' (opinion) to nature, and then update this belief based on the feedback (result) to minimize (or maximize)…
In this work we present a deep learning approach to conduct hypothesis-free, transcriptomics-based matching of drugs for diseases. Our proposed neural network architecture is trained on approved drug-disease indications, taking as input the…