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Biomarker measurements can be relatively easy and quick to obtain and they are useful to investigate whether a compound works as intended on a mechanistic, pharmacological level. In some situations, it is realistic to assume that patients,…

Alchemical binding free energy (BFE) calculations offer an efficient and thermodynamically rigorous approach to in silico binding affinity predictions. As a result of decades of methodological improvements and recent advances in computer…

Maximum likelihood or restricted maximum likelihood (REML) estimates of the parameters in linear mixed-effects models can be determined using the lmer function in the lme4 package for R. As for most model-fitting functions in R, the model…

Recent advances in experimental methods have enabled researchers to collect data on thousands of analytes simultaneously. This has led to correlational studies that associated molecular measurements with diseases such as Alzheimer's, Liver,…

In this paper, a nonparametric maximum likelihood (ML) estimator for band-limited (BL) probability density functions (pdfs) is proposed. The BLML estimator is consistent and computationally efficient. To compute the BLML estimator, three…

Deep learning (DL) and machine learning (ML) models have shown promise in drug response prediction (DRP), yet their ability to generalize across datasets remains an open question, raising concerns about their real-world applicability. Due…

We demonstrate the application of mixture density networks (MDNs) in the context of automated radiation therapy treatment planning. It is shown that an MDN can produce good predictions of dose distributions as well as reflect uncertain…

The problem of optimal dosage estimation arises in diverse scientific domains, from pharmacology and toxicology to aquaculture and environmental studies. Statistical modeling of nonlinear dose-response relationships is essential to quantify…

State-of-the-art neural networks can be trained to become remarkable solutions to many problems. But while these architectures can express symbolic, perfect solutions, trained models often arrive at approximations instead. We show that the…

Analogy completion has been a popular task in recent years for evaluating the semantic properties of word embeddings, but the standard methodology makes a number of assumptions about analogies that do not always hold, either in recent…

Inference in hierarchical nonlinear models needs careful consideration about targeting parameters that have either a conditional or population-average interpretation. For the special case of mixed-effects nonlinear sigmoidal models we…

This paper considers the problem of estimating a power-law degree distribution of an undirected network using sampled data. Although power-law degree distributions are ubiquitous in nature, the widely used parametric methods for estimating…

Although much of the success of Deep Learning builds on learning good representations, a rigorous method to evaluate their quality is lacking. In this paper, we treat the evaluation of representations as a model selection problem and…

Key processes in biological and chemical systems are described by networks of chemical reactions. From molecular biology to biotechnology applications, computational models of reaction networks are used extensively to elucidate their…

In recent years, machine learning has been proposed as a promising strategy to build accurate scoring functions for computational docking finalized to numerically empowered drug discovery. However, the latest studies have suggested that…

We consider the problem of estimating a dose-response curve. Continuous treatments arise often in practice, e.g. in the form of time spent on an operation, distance traveled to a location or dosage of a drug. Letting $A$ denote a continuous…

The analysis of tabular datasets is highly prevalent both in scientific research and real-world applications of Machine Learning (ML). Unlike many other ML tasks, Deep Learning (DL) models often do not outperform traditional methods in this…

In observational studies, weighting methods that directly optimize the balance between treatment and covariates have received much attention lately; however these have mainly focused on binary treatments. Inspired by domain adaptation, we…

Detection of anomalous situations for complex mission-critical systems hold paramount importance when their service continuity needs to be ensured. A major challenge in detecting anomalies from the operational data arises due to the…

Deep learning (DL) models have become core modules for many applications. However, deploying these models without careful performance benchmarking that considers both hardware and software's impact often leads to poor service and costly…