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   Articles with "persistent homology" as a keyword



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Integration of element specific persistent homology and machine learning for protein-ligand binding affinity prediction.

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recommendations! Published in 2018 at "International journal for numerical methods in biomedical engineering"

DOI: 10.1002/cnm.2914

Abstract: Protein-ligand binding is a fundamental biological process that is paramount to many other biological processes, such as signal transduction, metabolic pathways, enzyme construction, cell secretion, and gene expression. Accurate prediction of protein-ligand binding affinities is… read more here.

Keywords: persistent homology; topology; protein ligand; ligand binding ... See more keywords

Relative-perfectness of discrete gradient vector fields and multi-parameter persistent homology

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recommendations! Published in 2021 at "Journal of Combinatorial Optimization"

DOI: 10.1007/s10878-021-00729-x

Abstract: The combination of persistent homology and discrete Morse theory has proven very effective in visualizing and analyzing big and heterogeneous data. Indeed, topology provides computable and coarse summaries of data independently from specific coordinate systems… read more here.

Keywords: gradient vector; perfectness; discrete gradient; homology ... See more keywords

Fractal dimension and the persistent homology of random geometric complexes

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recommendations! Published in 2020 at "Advances in Mathematics"

DOI: 10.1016/j.aim.2020.107291

Abstract: We prove that the fractal dimension of a metric space equipped with an Ahlfors regular measure can be recovered from the persistent homology of random samples. Our main result is that if $x_1,\ldots, x_n$ are… read more here.

Keywords: ldots right; persistent homology; fractal dimension; left ldots ... See more keywords
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Quantification of LSS using the persistent homology in the SDSS fields

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recommendations! Published in 2017 at "Advances in Space Research"

DOI: 10.1016/j.asr.2017.04.020

Abstract: Abstract Using galaxy samples from the Sloan Digital Sky Survey (SDSS) Data Release 12 (DR12), we first estimate the topology of cosmic large-scale structure (LSS) by means of a new method of persistent homology which… read more here.

Keywords: quantification lss; persistent homology; topology; lss using ... See more keywords

Adsorbate Organization Characterized by Sublevelset Persistent Homology.

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recommendations! Published in 2023 at "Journal of chemical theory and computation"

DOI: 10.1021/acs.jctc.3c00090

Abstract: Interfacial adsorbate organization influences a variety physicochemical properties and reactivity. Surfaces that are rough, defect laden, or have large fluctuations (as in soft matter interfaces) can lead to complex adsorbate structures. This is amplified if… read more here.

Keywords: sublevelset persistent; adsorbate; liquid; persistent homology ... See more keywords

Weighted persistent homology for osmolyte molecular aggregation and hydrogen-bonding network analysis

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recommendations! Published in 2020 at "Scientific Reports"

DOI: 10.1038/s41598-020-66710-6

Abstract: It has long been observed that trimethylamine N-oxide (TMAO) and urea demonstrate dramatically different properties in a protein folding process. Even with the enormous theoretical and experimental research work on these two osmolytes, various aspects… read more here.

Keywords: aggregation hydrogen; network; molecular aggregation; persistent homology ... See more keywords
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Higher-order structure of polymer melt described by persistent homology

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recommendations! Published in 2021 at "Scientific Reports"

DOI: 10.1038/s41598-021-80975-5

Abstract: The optimal method of the polymer Materials Informatics (MI) has not been developed because the amorphous nature of the higher-order structure affects these properties. We have now tried to develop the polymer MI’s descriptor of… read more here.

Keywords: order; polymer; higher order; persistent homology ... See more keywords
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Flow estimation solely from image data through persistent homology analysis

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recommendations! Published in 2021 at "Scientific Reports"

DOI: 10.1038/s41598-021-97222-6

Abstract: Topological data analysis is an emerging concept of data analysis for characterizing shapes. A state-of-the-art tool in topological data analysis is persistent homology, which is expected to summarize quantified topological and geometric features. Although persistent… read more here.

Keywords: persistent homology; image data; homology; homology analysis ... See more keywords

Identifying key genes in cancer networks using persistent homology

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recommendations! Published in 2024 at "Scientific Reports"

DOI: 10.1038/s41598-025-87265-4

Abstract: Identifying driver genes is crucial for understanding oncogenesis and developing targeted cancer therapies. Driver discovery methods using protein or pathway networks rely on traditional network science measures, focusing on nodes, edges, or community metrics. These… read more here.

Keywords: cancer; persistent homology; using persistent; cancer networks ... See more keywords

Selecting embedding delays: An overview of embedding techniques and a new method using persistent homology.

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recommendations! Published in 2023 at "Chaos"

DOI: 10.1063/5.0137223

Abstract: Delay embedding methods are a staple tool in the field of time series analysis and prediction. However, the selection of embedding parameters can have a big impact on the resulting analysis. This has led to… read more here.

Keywords: time; selecting embedding; embedding methods; method ... See more keywords

Cosmology with persistent homology: parameter inference via machine learning

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recommendations! Published in 2024 at "Journal of Cosmology and Astroparticle Physics"

DOI: 10.1088/1475-7516/2025/09/064

Abstract: Building upon previous work [1], we investigate the constraining power of persistent homology on cosmological parameters and primordial non-Gaussianity in a likelihood-free inference pipeline utilizing machine learning. We evaluate the ability of Persistence Images (PIs)… read more here.

Keywords: inference; cosmology; persistent homology; machine learning ... See more keywords