A bibliography of the ABS methods

Nicolai, Silvia; Spedocatq, Emilio

doi:10.1080/10556789708805674

Cited by 4 publications

(3 citation statements)

References 23 publications

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“…All data are uploaded in the following repositories: Imaging data: https://doi.org/10.5281/zenodo.10820761 Code: https://github.com/mariaclaudianicolai/ADeS (copy archived at Nicolai, 2024 ).…”

Section: Data Availabilitymentioning

confidence: 99%

Transformer-based spatial–temporal detection of apoptotic cell death in live-cell imaging

Pulfer,

Pizzagalli,

Gagliardi

et al. 2024

eLife

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Intravital microscopy has revolutionized live cell imaging by allowing the study of spatial-temporal cell dynamics in living animals. However, the complexity of the data generated by this technology has limited the development of effective computational tools to identify and quantify cell processes. Amongst them, apoptosis is a crucial form of regulated cell death involved in tissue homeostasis and host defense. Live-cell imaging enabled the study of apoptosis at the cellular level, enhancing our understanding of its spatial-temporal regulation. However, at present, no computational method can deliver label-free detection of apoptosis in microscopy time-lapses. To overcome this limitation, we developed ADeS, a deep learning-based apoptosis detection system that employs the principle of activity recognition. We trained ADeS on extensive datasets containing more than 10,000 apoptotic instances collected both in vitro and in vivo, achieving a classification accuracy above 98% and outperforming state-of-the-art solutions. ADeS is the first method capable of detecting the location and duration of multiple apoptotic events in full microscopy time-lapses, surpassing human performance in the same task. We demonstrated the effectiveness and robustness of ADeS across various imaging modalities, cell types, and staining techniques. Finally, we employed ADeS to quantify cell survival in vitro and tissue damage in vivo, demonstrating its potential application in toxicity assays, treatment evaluation, and inflammatory dynamics. Our findings suggest that ADeS is a valuable tool for the accurate detection and quantification of apoptosis in live-cell imaging and, in particular, intravital microscopy data, providing insights into the complex spatial-temporal regulation of this process.

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Section: Data Availabilitymentioning

confidence: 99%

Transformer-based spatial–temporal detection of apoptotic cell death in live-cell imaging

Pulfer,

Pizzagalli,

Gagliardi

et al. 2024

eLife

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“…There are important methods to solve systems of linear equations, such as, the ABS methods, which solve systems of linear equations with a number of constraints smaller or equal to the number of unknowns and full rank matrices; see, for example, [9][10][11], or [12,13], which contain interesting reviews and a bibliography on ABS methods.…”

Section: Some Software Availablementioning

confidence: 99%

“…However, there are also other methods that transform the initial problem into other simpler methods and then recover the initial problem; see, for example, the ABS methods in [9,12,13,27,29], in which they obtain non-negative solutions of linear systems of equations, a particular case of linear inequalities, that permits solving the general case using slackness variables.…”

Section: Some Software Availablementioning

confidence: 99%

A State of the Art Review of Systems of Linear Inequalities and Related Observability Problems

Castillo

2023

Algorithms

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This work is a short review of the state of the art aiming to contribute to the use, disclosure, and propagation of systems of linear inequalities in real life, teaching, and research. It shows that the algebraic structure of their solutions consists of the sum of a linear subspace, an acute cone, and a polytope, and that adequate software exists to obtain, in their simplest forms, these three components. The work describes, based on orthogonality and polarity, homogeneous and complete systems of inequalities, the associated compatibility problems, and their relations with convex polyhedra and polytopes, which are the only possible solution for bounded problems, the most common in real practice. The compatibility and the observability problems, including their symbolic forms, are analyzed and solved, identifying the subsets of unknowns with unique solutions and those unbounded, important items of information with practical relevance in artificial intelligence and automatic learning. Having infinitely many solutions of a given problem allows us to find solutions when some of the assumptions fail and unexpected constraints come into play, a common situation for engineers. The linear programming problem becomes trivial when the set of all solutions is available and all solutions are obtained, contrary to the case of standard programs that provide only one solution. Several examples of applications to several areas of knowledge are presented, illustrating the advantages of solving these systems of inequalities.

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New solutions of LR fuzzy linear systems using ranking functions and ABS algorithms

Ghanbari¹,

Mahdavi–Amiri²

2010

Applied Mathematical Modelling

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A bibliography of the ABS methods

Cited by 4 publications

References 23 publications

Transformer-based spatial–temporal detection of apoptotic cell death in live-cell imaging

Transformer-based spatial–temporal detection of apoptotic cell death in live-cell imaging

A State of the Art Review of Systems of Linear Inequalities and Related Observability Problems

New solutions of LR fuzzy linear systems using ranking functions and ABS algorithms

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