定量方法
Several factors affect the structure of communities, including biological, physical and chemical phenomena, impacting the quantification of biodiversity, measured by diversity indexes such as Shannon's entropy. Then, once a point estimate…
Integration of multi-omics data provides opportunities for revealing biological mechanisms related to certain phenotypes. We propose a novel method of multi-omics integration called supervised deep generalized canonical correlation analysis…
Among the infinite number of possible movements that can be produced, humans are commonly assumed to choose those that optimize criteria such as minimizing movement time, subject to certain movement constraints like signal-dependent and…
Objective: This study illustrates the ambiguity of ROC in evaluating two classifiers of 90-day LVAD mortality. This paper also introduces the precision recall curve (PRC) as a supplemental metric that is more representative of LVAD…
Retrosynthesis prediction is one of the fundamental challenges in organic chemistry and related fields. The goal is to find reactants molecules that can synthesize product molecules. To solve this task, we propose a new graph-to-graph…
Epidemic models are used to analyze the progression or outcome of an epidemic under different control policies like vaccinations, quarantines, lockdowns, use of face-masks, pharmaceutical interventions, etc. When these models accurately…
Modern research in the life sciences is unthinkable without computational methods for extracting, quantifying and visualizing information derived from biological microscopy imaging data. In the past decade, we observed a dramatic increase…
Analysis of longitudinal Electronic Health Record (EHR) data is an important goal for precision medicine. Difficulty in applying Machine Learning (ML) methods, either predictive or unsupervised, stems in part from the heterogeneity and…
Explainable ML for molecular toxicity prediction is a promising approach for efficient drug development and chemical safety. A predictive ML model of toxicity can reduce experimental cost and time while mitigating ethical concerns by…
Objective: Data clustering is a common exploration step in the omics era, notably in genomics and proteomics where many genes or proteins can bequantified from one or more experiments. Bayesian clustering is a powerful algorithm that can…
Motivation: Accurate detection of sequence similarity and homologous recombination are essential parts of many evolutionary analyses. Results: We have developed SimPlot++, an open-source multiplatform application implemented in Python,…
Vaccines are among the most powerful tools used to combat the COVID-19 pandemic. They are highly effective against infection and substantially reduce the risk of severe disease, hospitalization, ICU admission, and death. However, their…
Introduction: Background field removal (BFR) is a critical step required for successful quantitative susceptibility mapping (QSM). However, eliminating the background field in brains containing significant susceptibility sources, such as…
Evaluating the blood-brain barrier (BBB) permeability of drug molecules is a critical step in brain drug development. Traditional methods for the evaluation require complicated in vitro or in vivo testing. Alternatively, in silico…
COVID-19 vaccines have proven to be effective against SARS-CoV-2 infection. However, the dynamics of vaccine-induced immunological memory development and neutralizing antibodies generation are not fully understood, limiting vaccine…
The selection of coarse-grained (CG) mapping operators is a critical step for CG molecular dynamics (MD) simulation. It is still an open question about what is optimal for this choice and there is a need for theory. The current state-of-the…
Despite all the efforts, there is no agreement on how temperature affects soil carbon decay and consequently soil CO2 emission, due to overlapping of environmental constraints. To gain further insight into the driving forces of soil…
A stroke is defined as a neurologic deficit arising from an interruption in blood supply to the brain. According to the World Health Organization, over 15 million people suffer from strokes annually, of which almost 70% die or are…
Mortality displacement is the concept that deaths are moved forward in time (e.g., a few days, several months, and years) by exposure from when they would occur without the exposure, which is common in environmental time-series studies.…
A gene expression compendium is a heterogeneous collection of gene expression experiments assembled from data collected for diverse purposes. The widely varied experimental conditions and genetic backgrounds across samples creates a…