定量方法
Immune cells have evolved to recognize and eliminate pathogens, and the efficiency of this process can be measured in a Petri dish. Yet, even if the cells are time-lapse recorded and tracked with high resolution, it is difficult to judge…
Diffusion weighted MRI (dMRI) provides a non invasive virtual reconstruction of the brain's white matter structures through tractography. Analyzing dMRI measures along the trajectory of white matter bundles can provide a more specific…
This paper asks whether integrating multimodal EEG and fMRI data offers a better characterisation of functional brain architectures than either modality alone. This evaluation rests upon a dynamic causal model that generates both EEG and…
Metabolomics is becoming a mature part of analytical chemistry as evidenced by the growing number of publications and attendees of international conferences dedicated to this topic. Yet, a systematic treatment of the fundamental structure…
Artificial intelligence (AI) classification holds promise as a novel and affordable screening tool for clinical management of ocular diseases. Rural and underserved areas, which suffer from lack of access to experienced ophthalmologists may…
Recent large cancer studies have measured somatic alterations in an unprecedented number of tumours. These large datasets allow the identification of cancer-related sets of genetic alterations by identifying relevant combinatorial patterns.…
In our recent article (Tu et al., Warnings and caveats in brain controllability, arXiv:1705.08261) we provided quantitative evidence to show that there are warnings and caveats in the way Gu and collaborators (Gu et al. Controllability of…
An agent's actions can be influenced by external factors through the inputs it receives from the environment, as well as internal factors, such as memories or intrinsic preferences. The extent to which an agent's actions are "caused from…
Fragment-based assembly has been widely used in Ab initio protein folding simulation which can effectively reduce the conformational space and thus accelerate sampling. The efficiency of fragment-based movement as well as the quality of…
The cause-specific cumulative incidence function (CIF) quantifies the subject-specific disease risk with competing risk outcome. With longitudinally collected biomarker data, it is of interest to dynamically update the predicted CIF by…
Stochastic simulation is a widely used method for estimating quantities in models of chemical reaction networks where uncertainty plays a crucial role. However, reducing the statistical uncertainty of the corresponding estimators requires…
Resource Balance Analysis (RBA) is a computational method based on resource allocation, which performs accurate quantitative predictions of whole-cell states (i.e. growth rate, meta-bolic fluxes, abundances of molecular machines including…
Equilibrium and nonequilibrium systems exhibit power-law singularities close to their critical and bifurcation points respectively. A recent study has shown that biochemical nonequilibrium models with positive feedback belong to the…
Connectivity across landscapes influences a wide range of conservation-relevant ecological processes, including species movements, gene flow, and the spread of wildfire, pests, and diseases. Recent improvements in remote sensing data…
Alzheimer's disease (AD) and Parkinson's disease (PD) are the two most common neurodegenerative disorders in humans. Because a significant percentage of patients have clinical and pathological features of both diseases, it has been…
Background: A large number of neurology case reports have been published, but it is a challenging task for human medical experts to explore all of these publications. Text mining offers a computational approach to investigate neurology…
In this chapter, we present a strategy and the technics to approach a scientific field from a set of articles gathered from the bibliographic database, Web of Science. The strategy is based on methods developed to analyze social networks.…
Revealing the functional sites of biological sequences, such as evolutionary conserved, structurally interacting or co-evolving protein sites, is a fundamental, and yet challenging task. Different frameworks and models were developed to…
We present an attention-based Transformer model for automatic retrosynthesis route planning. Our approach starts from reactants prediction of single-step organic reactions for given products, followed by Monte Carlo tree search-based…
As biomedical sciences discover new layers of complexity in the mechanisms of life and disease, mathematical models trying to catch up with these developments become mathematically intractable. As a result, in the grand scheme of things,…