定量方法

A retinal trait, or phenotype, summarises a specific aspect of a retinal image in a single number. This can then be used for further analyses, e.g. with statistical methods. However, reducing an aspect of a complex image to a single,…

Freely and openly shared low-cost electronic applications, known as open electronics, have sparked a new open-source movement, with much un-tapped potential to advance scientific research. Initially designed to appeal to electronic…

Fundamental differences between natural and medical images have recently favored the use of self-supervised learning (SSL) over ImageNet transfer learning for medical image applications. Differences between image types are primarily due to…

In this paper, we investigate phase retrieval algorithm for the single particle X-ray imaging data. We present a variance-reduced randomized Kaczmarz (VR-RK) algorithm for phase retrieval. The VR-RK algorithm is inspired by the randomized…

Capturing intricate biological phenomena often requires multiscale modeling where coarse and inexpensive models are developed using limited components of expensive and high-fidelity models. Here, we consider such a multiscale framework in…

Coral reef science is a fast-growing field propelled by the need to better understand coral health and resilience to devise strategies to slow reef loss resulting from environmental stresses. Key to coral resilience are the symbiotic…

Whole slide imaging (WSI) has become the primary modality for digital pathology data. However, due to the size and high-resolution nature of these images, they are generally only accessed in smaller sections or tiles via specialized…

In this study we derive the governing equations for mesoscopic collective activity in the cortex, starting from the generic Hodgkin-Huxley equations for microscopic cell dynamics. For simplicity, and to maintain focus on the essential…

Living cell segmentation from bright-field light microscopy images is challenging due to the image complexity and temporal changes in the living cells. Recently developed deep learning (DL)-based methods became popular in medical and…

Recent years have seen substantial advances in the development of biofunctional materials using synthetic polymers. The growing problem of elusive sequence-functionality relations for most biomaterials has driven researchers to seek more…

Detailed dynamical systems models used in life sciences may include dozens or even hundreds of state variables. Models of large dimension are not only harder from the numerical perspective (e.g., for parameter estimation or simulation), but…

Modern high-throughput single-cell immune profiling technologies, such as flow and mass cytometry and single-cell RNA sequencing can readily measure the expression of a large number of protein or gene features across the millions of cells…

Due to the redundancy of our motor system, movements can be performed in many ways. While multiple motor control strategies can all lead to the desired behavior, they result in different joint and muscle forces. This creates opportunities…

OpenSim is a widely used biomechanics simulator with several anatomically accurate human musculo-skeletal models. While OpenSim provides useful tools to analyse human movement, it is not fast enough to be routinely used for emerging…

Synthetic biologists have made great progress over the past decade in developing methods for modular assembly of genetic sequences and in engineering biological systems with a wide variety of functions in various contexts and organisms.…

Visual neuroprostheses are the only FDA-approved technology for the treatment of retinal degenerative blindness. Although recent work has demonstrated a systematic relationship between electrode location and the shape of the elicited visual…

Gene expression is a stochastic process in which cells produce biomolecules essential to the function of life. Modern experimental methods allow for the measurement of biomolecules at single-cell and single-molecule resolution over time.…

Evapotranspiration (ET) represents the largest water loss flux in drylands, but ET and its partition into plant transpiration (T) and soil evaporation (E) are poorly quantified, especially at fine temporal scales. Physically-based remote…

The increasingly pressing demand of novel drugs (e.g., gene therapies for personalized cancer care, ever evolving vaccines) with unprecedented levels of personalization, has put a remarkable pressure on the traditionally long time required…

One key task in virtual screening is to accurately predict the binding affinity ($\triangle$$G$) of protein-ligand complexes. Recently, deep learning (DL) has significantly increased the predicting accuracy of scoring functions due to the…