Related papers: Moral Lineage Tracing
Unsupervised image segmentation and denoising are two fundamental tasks in image processing. Usually, graph based models such as multicut are used for segmentation and variational models are employed for denoising. Our approach addresses…
Positive linear programs (LP), also known as packing and covering linear programs, are an important class of problems that bridges computer science, operations research, and optimization. Despite the consistent efforts on this problem, all…
We study the problem of instance segmentation in biological images with crowded and compact cells. We formulate this task as an integer program where variables correspond to cells and constraints enforce that cells do not overlap. To solve…
This paper proposes a novel framework for fluorescence plant video processing. The plant research community is interested in the leaf-level photosynthetic analysis within a plant. A prerequisite for such analysis is to segment all leaves,…
Many annotation problems in computer vision can be phrased as integer linear programs (ILPs). The use of standard industrial solvers does not to exploit the underlying structure of such problems eg, the skeleton in pose estimation. The…
We track the lineage of tuples throughout their database lifetime. That is, we consider a scenario in which tuples (records) that are produced by a query may affect other tuple insertions into the DB, as part of a normal workflow. As time…
An important problem in biological modeling is choosing the right model. Given experimental data, one is supposed to find the best mathematical representation to describe the real-world phenomena. However, there may not be a unique model…
Linear programming describes the problem of optimising a linear objective function over a set of constraints on its variables. In this paper we present a solver for linear programs implemented in the proof assistant Isabelle/HOL. This…
Combinatorial optimisation problems framed as mixed integer linear programmes (MILPs) are ubiquitous across a range of real-world applications. The canonical branch-and-bound algorithm seeks to exactly solve MILPs by constructing a search…
Trees have long been used as a graphical representation of species relationships. However complex evolutionary events, such as genetic reassortments or hybrid speciations which occur commonly in viruses, bacteria and plants, do not fit into…
Mixed Integer Linear Programming (MILP) is a fundamental class of NP-hard problems that has garnered significant attention from both academia and industry. The Branch-and-Bound (B\&B) method is the dominant approach for solving MILPs and…
CRISPR technology has enabled large-scale cell lineage tracing for complex multicellular organisms by mutating synthetic genomic barcodes during organismal development. However, these sophisticated biological tools currently use ad-hoc and…
There has been growing interest in implementing massive MIMO systems by one-bit analog-to-digital converters (ADCs), which have the benefit of reducing the power consumption and hardware complexity. One-bit MIMO detection arises in such a…
Cell tracking is an essential tool in live-cell imaging to determine single-cell features, such as division patterns or elongation rates. Unlike in common multiple object tracking, in microbial live-cell experiments cells are growing,…
A linear graph is a graph whose vertices are totally ordered. Biological and linguistic sequences with interactions among symbols are naturally represented as linear graphs. Examples include protein contact maps, RNA secondary structures…
We solve large-scale mixed-integer linear programs (MILPs) via distributed asynchronous saddle point computation. This is motivated by the MILPs being able to model problems in multi-agent autonomy, e.g., task assignment problems and…
Object parsing -- the task of decomposing an object into its semantic parts -- has traditionally been formulated as a category-level segmentation problem. Consequently, when there are multiple objects in an image, current methods cannot…
Developing and maintaining CLP programs requires visualization and explanation tools. However, existing tools are built in an ad hoc way. Therefore porting tools from one platform to another is very difficult. We have shown in previous work…
Cell segmentation and tracking in microscopy images are of great significance to new discoveries in biology and medicine. In this study, we propose a novel approach to combine cell segmentation and cell tracking into a unified end-to-end…
Multiple sequence alignment is a basic procedure in molecular biology, and it is often treated as being essentially a solved computational problem. However, this is not so, and here I review the evidence for this claim, and outline the…