Related papers: Phylotrack: C++ and Python libraries for in silico…
The complex dynamicity of open-world objects presents non-negligible challenges for multi-object tracking (MOT), often manifested as severe deformations, fast motion, and occlusions. Most methods that solely depend on coarse-grained object…
Reproducibility is an important requirement in evolutionary computation, where results largely depend on computational experiments. In practice, reproducibility relies on how algorithms, experimental protocols, and artifacts are documented…
Flow cytometry (FC) is a single-cell profiling platform for measuring the phenotypes of individual cells from millions of cells in biological samples. FC employs high-throughput technologies and generates high-dimensional data, and hence…
Visual tracking has made significant improvements in the past few decades. Most existing state-of-the-art trackers 1) merely aim for performance in ideal conditions while overlooking the real-world conditions; 2) adopt the…
Phylogenies are commonly used to represent the evolutionary relationships between species, and often these phylogenies are equipped with edge lengths that indicate degrees of evolutionary difference. Given such a phylogeny, a popular…
This paper presents the case study of a non-intrusive porting of a monolithic C++ library for real-time 3D hand tracking, to the domain of edge-based computation. Towards a proof of concept, the case study considers a pair of workstations,…
Despite the importance of sparse matrices in numerous fields of science, software implementations remain difficult to use for non-expert users, generally requiring the understanding of underlying details of the chosen sparse matrix storage…
As high-performance computing systems scale in size and computational power, the danger of silent errors, i.e., errors that can bypass hardware detection mechanisms and impact application state, grows dramatically. Consequently,…
A semantic gap separates how users describe tasks from how tools are documented. As API ecosystems scale to tens of thousands of endpoints, static retrieval from the initial query alone cannot bridge this gap: the agent's understanding of…
Phylogenetically decisive collections of taxon sets have the property that if trees are chosen for each of their elements, as long as these trees are compatible, the resulting supertree is unique. This means that as long as the trees…
Lifemapper (http://www.lifemapper.org) is a predictive electronic atlas of the Earth's biological biodiversity. Using a screensaver version of the GARP genetic algorithm for modeling species distributions, Lifemapper harnesses vast…
Computing systems form the backbone of many aspects of our life, hence they are becoming as vital as water, electricity, and road infrastructures for our society. Yet, engineering long running computing systems that achieve their goals in…
One way to understand the role history plays on evolutionary trajectories is by giving ancient life a second opportunity to evolve. Our ability to empirically perform such an experiment, however, is limited by current experimental designs.…
Analyzing the dynamical properties of mobile objects requires to extract trajectories from recordings, which is often done by tracking movies. We compiled a database of two-dimensional movies for very different biological and physical…
In a seminal paper, Valiant (2006) introduced a computational model for evolution to address the question of complexity that can arise through Darwinian mechanisms. Valiant views evolution as a restricted form of computational learning,…
Object-oriented programming languages such as Java and Objective C have become popular for implementing agent-based and other object-based simulations since objects in those languages can {\em reflect} (i.e. make runtime queries of an…
Building a virtual cell capable of accurately simulating cellular behaviors in silico has long been a dream in computational biology. We introduce CellFlux, an image-generative model that simulates cellular morphology changes induced by…
Epigenetic Tracking (ET) is an Artificial Embryology system which allows for the evolution and development of large complex structures built from artificial cells. In terms of the number of cells, the complexity of the bodies generated with…
The statistical estimation of phylogenies is always associated with uncertainty, and accommodating this uncertainty is an important component of modern phylogenetic comparative analysis. The birth-death polytomy resolver is a method of…
We introduce a data-driven epistatic model of protein evolution, capable of generating evolutionary trajectories spanning very different time scales reaching from individual mutations to diverged homologs. Our in silico evolution…