Related papers: Moral Lineage Tracing
Lineage tracing, the joint segmentation and tracking of living cells as they move and divide in a sequence of light microscopy images, is a challenging task. Jug et al. have proposed a mathematical abstraction of this task, the moral…
Determining the trajectories of cells and their lineages or ancestries in live-cell experiments are fundamental to the understanding of how cells behave and divide. This paper proposes novel online algorithms for jointly tracking and…
Cell segmentation and tracking allow us to extract a plethora of cell attributes from bacterial time-lapse cell movies, thus promoting computational modeling and simulation of biological processes down to the single-cell level. However, to…
Rapid advance of experimental techniques provides an unprecedented in-depth view into complex developmental processes. Still, little is known on how the complexity of multicellular organisms evolved by elaborating developmental programs and…
We consider the problem of drawing multiple gene trees inside a single species tree in order to visualize multispecies coalescent trees. Specifically, the drawing of the species tree fills a rectangle in which each of its edges is…
Integer Linear Programming (ILP) can be seen as the archetypical problem for NP-complete optimization problems, and a wide range of problems in artificial intelligence are solved in practice via a translation to ILP. Despite its huge range…
This dissertation investigates integer linear programming (ILP) formulation of Bayesian Network structure learning problem. We review the definition and key properties of Bayesian network and explain score metrics used to measure how well…
Lineage tracing, the determination and mapping of progeny arising from single cells, is an important approach enabling the elucidation of mechanisms underlying diverse biological processes ranging from development to disease. We developed a…
In transmission networks, power flows and network topology are deeply intertwined due to power flow physics. Recent literature shows that a specific more hierarchical network structure can effectively inhibit the propagation of line…
Tracking of plant cells in images obtained by microscope is a challenging problem due to biological phenomena such as large number of cells, non-uniform growth of different layers of the tightly packed plant cells and cell division.…
Storyline drawings are a popular visualization of interactions of a set of characters over time, e.g., to show participants of scenes in a book or movie. Characters are represented as $x$-monotone curves that converge vertically for…
Reconciliation methods aim at recovering macro evolutionary events and at localizing them in the species history, by observing discrepancies between gene family trees and species trees. In this article we introduce an Integer Linear…
Given experimental data, one of the main objectives of biological modeling is to construct a model which best represents the real world phenomena. In some cases, there could be multiple distinct models exhibiting the exact same dynamics,…
Integer Linear Programming (ILP) has a broad range of applications in various areas of artificial intelligence. Yet in spite of recent advances, we still lack a thorough understanding of which structural restrictions make ILP tractable.…
Cell tracking and segmentation assist biologists in extracting insights from large-scale microscopy time-lapse data. Driven by local accuracy metrics, current tracking approaches often suffer from a lack of long-term consistency and the…
Joint object matching, also known as multi-image matching, namely, the problem of finding consistent partial maps among all pairs of objects within a collection, is a crucial task in many areas of computer vision. This problem subsumes…
Given a collection $L$ of line segments, we consider its arrangement and study the problem of covering all cells with line segments of $L$. That is, we want to find a minimum-size set $L'$ of line segments such that every cell in the…
Integer linear programming (ILP) encompasses a very important class of optimization problems that are of great interest to both academia and industry. Several algorithms are available that attempt to explore the solution space of this class…
For clustering of an undirected graph, this paper presents an exact algorithm for the maximization of modularity density, a more complicated criterion to overcome drawbacks of the well-known modularity. The problem can be interpreted as the…
Tracking all nuclei of an embryo in noisy and dense fluorescence microscopy data is a challenging task. We build upon a recent method for nuclei tracking that combines weakly-supervised learning from a small set of nuclei center point…