相关论文: Assessing Biosimilarity using Functional Metrics

Sequence comparison is a widely used computational technique in modern molecular biology. In spite of the frequent use of sequence comparisons the important problem of assigning statistical significance to a given degree of similarity is…

This paper deals with the derivation of a collective model of cell populations out of an individual-based description of the underlying physical particle system. By looking at the spatial distribution of cells in terms of time-evolving…

Robustness to a wide variety of negative factors and the ability to self-repair is an inherent and natural characteristic of all life forms on earth. As opposed to nature, man-made systems are in most cases not inherently robust and a…

In order to find previously unknown subgroups in biomedical data and generate testable hypotheses, visually guided exploratory analysis can be of tremendous importance. In this paper we propose a new dissimilarity measure that can be used…

Mathematical modelling and computer simulation are increasingly being used alongside experiments to help optimise and guide the design of drug delivery systems. Recent drug delivery research has (i) highlighted the advantages of drug…

Inside living cells are complex mixtures of thousands of components. It is hopeless to try to characterise all the individual interactions in these mixtures. Thus, we develop a statistical approach to approximating them, and examine the…

Atomic-level simulations are widely used to study biomolecules and their dynamics. A common goal in such studies is to compare simulations of a molecular system under several conditions -- for example, with various mutations or bound…

Calculating free energy differences is a topic of substantial interest and has many applications including molecular docking and hydration, solvation, and binding free energies which is used in computational drug discovery. However, in…

Violation of the assumptions underlying classical (Gaussian) limit theory often yields unreliable statistical inference. This paper shows that the bootstrap can detect such violations by delivering simple and powerful diagnostic tests that…

We study distributional similarity measures for the purpose of improving probability estimation for unseen cooccurrences. Our contributions are three-fold: an empirical comparison of a broad range of measures; a classification of similarity…

One of the important challenges facing high resolution molecular dynamics calculations is to reproduce biological functions that occur in the macroscopic world and involve macroscopic variables. Some of these functions can be well described…

Biological molecules, like all active matter, use free energy to generate force and motion which drive them out of thermal equilibrium, and undergo inherent dynamic interconversion between metastable free energy states separated by levels…

Approximate Bayesian computation methods are useful for generative models with intractable likelihoods. These methods are however sensitive to the dimension of the parameter space, requiring exponentially increasing resources as this…

From flocks of birds to biomolecular assemblies, systems in which many individual components independently consume energy to perform mechanical work exhibit a wide array of striking behaviors. Methods to quantify the dynamics of these so…

Estimating causal networks from biological data is a critical step in systems biology. When evaluating the inferred network, assessing the networks based on their intervention effects is particularly important for downstream probabilistic…

You measure the value of a quantity x for a number of systems (cells, molecules, people, chunks of metal, DNA vectors, etc.). You repeat the whole set of measures in different occasions or assays, which you try to design as equal to one…

Compartmentalised biochemical reactions are a ubiquitous building block of biological systems. The interplay between chemical and compartmental dynamics can drive rich and complex dynamical behaviors that are difficult to analyse…

Systems that answer questions by reviewing the scientific literature are becoming increasingly feasible. To draw reliable conclusions, these systems should take into account the quality of available evidence from different studies, placing…

The predominant method for evaluating the quality of causal models is to measure the graphical accuracy of the learned model structure. We present an alternative method for evaluating causal models that directly measures the accuracy of…

In biomanufacturing, developing an accurate model to simulate the complex dynamics of bioprocesses is an important yet challenging task. This is partially due to the uncertainty associated with bioprocesses, high data acquisition cost, and…