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We propose an automatic 3D segmentation algorithm for multiphoton microscopy images of microglia. Our method is capable of segmenting tubular and blob-like structures from noisy images. Current segmentation techniques and software fail to…
Graph Partitioning is a critical problem in numerous scientific and engineering domains including social network analysis, VLSI design, and many more. Spectral methods are known to produce quality partitions while minimizing edge cuts for a…
Cell tracking enables data extraction from time-lapse "cell movies" and promotes modeling biological processes at the single-cell level. We introduce a new fully automated computational strategy to track accurately cells across frames in…
Mixed-integer linear programming (MILP) is one of the most popular mathematical formulations with numerous applications. In practice, improving the performance of MILP solvers often requires a large amount of high-quality data, which can be…
Accurate segmentation of 3-D cell nuclei in microscopy images is essential for the study of nuclear organization, gene expression, and cell morphodynamics. Current image segmentation methods are challenged by the complexity and variability…
We propose an extended variant of the reformulation and decomposition algorithm for solving a special class of mixed-integer bilevel linear programs (MIBLPs) where continuous and integer variables are involved in both upper- and lower-level…
We perform theoretical and algorithmic studies for the problem of clustering and semi-supervised classification on graphs with both pairwise relational information and single-point feature information, upon a joint stochastic block model…
In this paper, we describe a novel unsupervised learning scheme for accelerating the solution of a family of mixed integer programming (MIP) problems. Distinct substantially from existing learning-to-optimize methods, our proposal seeks to…
Biclustering is an unsupervised machine learning technique that simultaneously clusters rows and columns in a data matrix. Biclustering has emerged as an important approach and plays an essential role in various applications such as…
Editing a graph to obtain a disjoint union of s-clubs is one of the models for correlation clustering, which seeks a partition of the vertex set of a graph so that elements of each resulting set are close enough according to some given…
Segmentation is a key stage in dermoscopic image processing, where the accuracy of the border line that defines skin lesions is of utmost importance for subsequent algorithms (e.g., classification) and computer-aided early diagnosis of…
Due to their capacity to encode rich structural information, labeled graphs are often used for modeling various kinds of objects such as images, molecules, and chemical compounds. If pattern recognition problems such as clustering and…
Mixed Integer Linear Programs (MILP) are well known to be NP-hard (Non-deterministic Polynomial-time hard) problems in general. Even though pure optimization-based methods, such as constraint generation, are guaranteed to provide an optimal…
The submodular function maximization is an attractive optimization model that appears in many real applications. Although a variety of greedy algorithms quickly find good feasible solutions for many instances while guaranteeing…
Automatic segmentation of breast tumors from the ultrasound images is essential for the subsequent clinical diagnosis and treatment plan. Although the existing deep learning-based methods have achieved significant progress in automatic…
Cutting planes (cuts) play an important role in solving mixed-integer linear programs (MILPs), as they significantly tighten the dual bounds and improve the solving performance. A key problem for cuts is when to stop cuts generation, which…
The ever higher complexity of manufacturing systems, continually shortening life cycles of products and their increasing variety, as well as the unstable market situation of the recent years require introducing grater flexibility and…
Recently, single-stage embedding based deep learning algorithms gain increasing attention in cell segmentation and tracking. Compared with the traditional "segment-then-associate" two-stage approach, a single-stage algorithm not only…
Processing very large graphs like social networks, biological and chemical compounds is a challenging task. Distributed graph processing systems process the billion-scale graphs efficiently but incur overheads of efficient partitioning and…
Modern deep neural networks achieved remarkable progress in medical image segmentation tasks. However, it has recently been observed that they tend to produce overconfident estimates, even in situations of high uncertainty, leading to…