Related papers: Modeling Biological Problems in Computer Science: …
Imitation learning aims to extract knowledge from human experts' demonstrations or artificially created agents in order to replicate their behaviors. Its success has been demonstrated in areas such as video games, autonomous driving,…
Over the past 30 years many researchers in the field of evolutionary computation have put a lot of effort to introduce various approaches for solving hard problems. Most of these problems have been inspired by major industries so that…
The applicability of computational models to the biological world is an active topic of debate. We argue that a useful path forward results from abandoning hard boundaries between categories and adopting an observer-dependent, pragmatic…
Molecular biology and biochemistry interpret microscopic processes in the living world in terms of molecular structures and their interactions, which are quantum mechanical by their very nature. Whereas the theoretical foundations of these…
Reducing the cost of sequencing genomes provided by next-generation sequencing technologies has greatly increased the number of genomic projects. As a result, there is a growing need for better assembly and assembly validation methods. One…
We investigate the ability of a genetic algorithm to design cellular automata that perform computations. The computational strategies of the resulting cellular automata can be understood using a framework in which ``particles'' embedded in…
We consider the solution of the subset sum problem based on a parallel computer consisting of self-propelled biological agents moving in a nanostructured network that encodes the NP-complete task in its geometry. We develop an approximate…
In recent years, substantial advancements have been achieved in understanding the diversity of the human virome and its intricate roles in human health and diseases. Despite this progress, the field of human virome research remains nascent,…
One of the major challenges in biology concerns the integration of data across length and time scales into a consistent framework: how do macroscopic properties and functionalities arise from the molecular regulatory networks - and how can…
Molecular assembly offers a promising path to detect life beyond Earth, while minimizing assumptions based on terrestrial life. As mass spectrometers will be central to upcoming Solar System missions, predicting molecular assembly from…
This paper investigates the reproducibility of computational science research and identifies key challenges facing the community today. It is the result of the First Summer School on Experimental Methodology in Computational Science…
Gene expression programming, a genotype/phenotype genetic algorithm (linear and ramified), is presented here for the first time as a new technique for the creation of computer programs. Gene expression programming uses character linear…
Recently, computational modelling became a very important research tool that enables us to study problems that for decades evaded scientific analysis. Evolutionary systems are certainly examples of such problems: they are composed of many…
The seriation problem seeks to reorder a set of elements given pairwise similarity information, so that elements with higher similarity are closer in the resulting sequence. When a global ordering consistent with the similarity information…
A difficult step in the process of karyotyping is segmenting chromosomes that touch or overlap. In an attempt to automate the process, previous studies turned to Deep Learning methods, with some formulating the task as a semantic…
Using machine learning, especially deep learning, to facilitate biological research is a fascinating research direction. However, in addition to the standard classification or regression problems, in bioinformatics, we often need to predict…
Quantitative methods and mathematical modeling are playing an increasingly important role across disciplines. As a result, interdisciplinary mathematics courses are increasing in popularity. However, teaching such courses at an advanced…
Understanding the mechanisms of interactions within cells, tissues, and organisms is crucial to driving developments across biology and medicine. Mathematical modeling is an essential tool for simulating biological systems and revealing…
Shape assembly, the process of combining parts into a complete whole, is a crucial robotic skill with broad real-world applications. Among various assembly tasks, geometric assembly--where broken parts are reassembled into their original…
Self-assembly is a phenomenon observed in nature at all scales where autonomous entities build complex structures, without external influences nor centralised master plan. Modelling such entities and programming correct interactions among…