定量方法
In computational neuroscience, there has been an increased interest in developing machine learning algorithms that leverage brain imaging data to provide estimates of "brain age" for an individual. Importantly, the discordance between brain…
We address the issue of structure changes of a canola protein gel (as a solid food model) during gastrointestinal digestion. We present a method for synchrotron Small-Angle X-ray Scattering analysis of the digestion of a gel in a capillary.…
The skin microbiome plays an important role in the maintenance of a healthy skin. It is an ecosystem, composed of several species, competing for resources and interacting with the skin cells. Imbalance in the cutaneous microbiome, also…
In this paper, we outline the theory of epidemic percolation networks and their use in the analysis of stochastic SIR epidemic models on undirected contact networks. We then show how the same theory can be used to analyze stochastic SIR…
In an important paper, M.E.J. Newman claimed that a general network-based stochastic Susceptible-Infectious-Removed (SIR) epidemic model is isomorphic to a bond percolation model, where the bonds are the edges of the contact network and the…
Although bulk transcriptomic analyses have significantly contributed to an enhanced comprehension of multifaceted diseases, their exploration capacity is impeded by the heterogeneous compositions of biological samples. Indeed, by averaging…
The Turing completeness of continuous Chemical Reaction Networks (CRNs) states that any computable real function can be computed by a continuous CRN on a finite set of molecular species, possibly restricted to elementary reactions, i.e.…
Single-cell RNA sequencing (scRNA-seq) is widely used to reveal heterogeneity in cells, which has given us insights into cell-cell communication, cell differentiation, and differential gene expression. However, analyzing scRNA-seq data is a…
The combination of Deep Learning techniques and Raman spectroscopy shows great potential offering precise and prompt identification of pathogenic bacteria in clinical settings. However, the traditional closed-set classification approaches…
While tumor dynamic modeling has been widely applied to support the development of oncology drugs, there remains a need to increase predictivity, enable personalized therapy, and improve decision-making. We propose the use of Tumor Dynamic…
Chemical formula annotation for tandem mass spectrometry (MS/MS) data is the first step toward structurally elucidating unknown metabolites. While great strides have been made toward solving this problem, the current state-of-the-art method…
Spatial transcriptomic (ST) clustering employs spatial and transcription information to group spots spatially coherent and transcriptionally similar together into the same spatial domain. Graph convolution network (GCN) and graph attention…
Rapid, sensitive detection of biomolecules is important for improved testing methods for viruses as well as biomarkers and environmental hormones. For example, testing for SARS-CoV-2 is essential in the fight against the COVID-19 pandemic.…
The household secondary attack risk (SAR), often called the secondary attack rate or secondary infection risk, is the probability of infectious contact from an infectious household member A to a given household member B, where we define…
Recent work has attempted to use whole-genome sequence data from pathogens to reconstruct the transmission trees linking infectors and infectees in outbreaks. However, transmission trees from one outbreak do not generalize to future…
The generation interval is the time between the infection time of an infected person and the infection time of his or her infector. Probability density functions for generation intervals have been an important input for epidemic models and…
Levenshtein distance is a commonly used edit distance metric, typically applied in language processing, and to a lesser extent, in molecular biology analysis. Biological nucleic acid sequences are often embedded in longer sequences and are…
The segmentation of cells and neurites in microscopy images of neuronal networks provides valuable quantitative information about neuron growth and neuronal differentiation, including the number of cells, neurites, neurite length and…
How do the same mechanisms that faithfully regenerate complex developmental programs in spite of environmental and genetic perturbations also permit responsiveness to environmental signals, adaptation, and genetic evolution? Using the…
To obtain explicit understanding of the behavior of dynamical systems, geometrical methods and slow-fast analysis have proved to be highly useful. Such methods are standard for smooth dynamical systems, and increasingly used for continuous,…