1
|
Liu X, Reigle J, Prasath VBS, Dhaliwal J. Artificial intelligence image-based prediction models in IBD exhibit high risk of bias: A systematic review. Comput Biol Med 2024; 171:108093. [PMID: 38354499 DOI: 10.1016/j.compbiomed.2024.108093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 01/04/2024] [Accepted: 01/30/2024] [Indexed: 02/16/2024]
Abstract
BACKGROUND There has been an increase in the development of both machine learning (ML) and deep learning (DL) prediction models in Inflammatory Bowel Disease. We aim in this systematic review to assess the methodological quality and risk of bias of ML and DL IBD image-based prediction studies. METHODS We searched three databases, PubMed, Scopus and Embase, to identify ML and DL diagnostic or prognostic predictive models using imaging data in IBD, to Dec 31, 2022. We restricted our search to include studies that primarily used conventional imaging data, were undertaken in human participants, and published in English. Two reviewers independently reviewed the abstracts. The methodological quality of the studies was determined, and risk of bias evaluated using the prediction risk of bias assessment tool (PROBAST). RESULTS Forty studies were included, thirty-nine developed diagnostic models. Seven studies utilized ML approaches, six were retrospective and none used multicenter data for model development. Thirty-three studies utilized DL approaches, ten were prospective, and twelve multicenter studies. Overall, all studies demonstrated high risk of bias. ML studies were evaluated in 4 domains all rated as high risk of bias: participants (6/7), predictors (1/7), outcome (3/7), and analysis (7/7), and DL studies evaluated in 3 domains: participants (24/33), outcome (10/33), and analysis (18/33). The majority of image-based studies used colonoscopy images. CONCLUSION The risk of bias was high in AI IBD image-based prediction models, owing to insufficient sample size, unreported missingness and lack of an external validation cohort. Models with a high risk of bias are unlikely to be generalizable and suitable for clinical implementation.
Collapse
Affiliation(s)
- Xiaoxuan Liu
- Department of Biomedical Informatics, College of Medicine, University of Cincinnati, OH, USA; Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, OH, USA
| | - James Reigle
- Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, OH, USA; Cincinnati Children's Hospital Medical Center, Division of Gastroenterology, Hepatology and Nutrition, USA
| | - V B Surya Prasath
- Department of Biomedical Informatics, College of Medicine, University of Cincinnati, OH, USA; Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, OH, USA; Cincinnati Children's Hospital Medical Center, Division of Gastroenterology, Hepatology and Nutrition, USA
| | - Jasbir Dhaliwal
- Department of Biomedical Informatics, College of Medicine, University of Cincinnati, OH, USA; Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, OH, USA; Cincinnati Children's Hospital Medical Center, Division of Gastroenterology, Hepatology and Nutrition, USA.
| |
Collapse
|
2
|
Gaddis N, Fortriede J, Guo M, Bardes EE, Kouril M, Tabar S, Burns K, Ardini-Poleske ME, Loos S, Schnell D, Jin K, Iyer B, Du Y, Huo BX, Bhattacharjee A, Korte J, Munshi R, Smith V, Herbst A, Kitzmiller JA, Clair GC, Carson JP, Adkins J, Morrisey EE, Pryhuber GS, Misra R, Whitsett JA, Sun X, Heathorn T, Paten B, Prasath VBS, Xu Y, Tickle T, Aronow BJ, Salomonis N. LungMAP Portal Ecosystem: Systems-level Exploration of the Lung. Am J Respir Cell Mol Biol 2024; 70:129-139. [PMID: 36413377 PMCID: PMC10848697 DOI: 10.1165/rcmb.2022-0165oc] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 11/21/2022] [Indexed: 11/23/2022] Open
Abstract
An improved understanding of the human lung necessitates advanced systems models informed by an ever-increasing repertoire of molecular omics, cellular imaging, and pathological datasets. To centralize and standardize information across broad lung research efforts, we expanded the LungMAP.net website into a new gateway portal. This portal connects a broad spectrum of research networks, bulk and single-cell multiomics data, and a diverse collection of image data that span mammalian lung development and disease. The data are standardized across species and technologies using harmonized data and metadata models that leverage recent advances, including those from the Human Cell Atlas, diverse ontologies, and the LungMAP CellCards initiative. To cultivate future discoveries, we have aggregated a diverse collection of single-cell atlases for multiple species (human, rhesus, and mouse) to enable consistent queries across technologies, cohorts, age, disease, and drug treatment. These atlases are provided as independent and integrated queryable datasets, with an emphasis on dynamic visualization, figure generation, reanalysis, cell-type curation, and automated reference-based classification of user-provided single-cell genomics datasets (Azimuth). As this resource grows, we intend to increase the breadth of available interactive interfaces, supported data types, data portals and datasets from LungMAP, and external research efforts.
Collapse
Affiliation(s)
- Nathan Gaddis
- RTI International, Research Triangle Park, North Carolina
| | - Joshua Fortriede
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
| | - Minzhe Guo
- Division of Pulmonary Biology, The Perinatal Institute, and
| | - Eric E. Bardes
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
| | - Michal Kouril
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
| | - Scott Tabar
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
| | - Kevin Burns
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
| | | | - Stephanie Loos
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
| | - Daniel Schnell
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
| | - Kang Jin
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
| | - Balaji Iyer
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
- Department of Electrical Engineering and Computer Science, University of Cincinnati, Cincinnati, Ohio
| | - Yina Du
- Division of Pulmonary Biology, The Perinatal Institute, and
| | - Bing-Xing Huo
- Data Sciences Platform, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Anukana Bhattacharjee
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
| | - Jeff Korte
- Data Sciences Platform, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Ruchi Munshi
- Data Sciences Platform, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Victoria Smith
- Data Sciences Platform, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Andrew Herbst
- Data Sciences Platform, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | | | - Geremy C. Clair
- Biological Science Division, Pacific Northwest National Laboratory, Richland, Washington
| | - James P. Carson
- Texas Advanced Computing Center, University of Texas at Austin, Austin, Texas
| | - Joshua Adkins
- Biological Science Division, Pacific Northwest National Laboratory, Richland, Washington
| | - Edward E. Morrisey
- Department of Medicine and
- Penn-CHOP Lung Biology Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Gloria S. Pryhuber
- Department of Pediatrics, University of Rochester Medical Center, Rochester, New York
| | - Ravi Misra
- Department of Pediatrics, University of Rochester Medical Center, Rochester, New York
| | - Jeffrey A. Whitsett
- Division of Pulmonary Biology, The Perinatal Institute, and
- Department of Pediatrics, University of Cincinnati School of Medicine, Cincinnati, Ohio
| | - Xin Sun
- Department of Pediatrics and
- Department of Biological Sciences, University of California, San Diego, San Diego, California; and
| | - Trevor Heathorn
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, California
| | - Benedict Paten
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, California
| | - V. B. Surya Prasath
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
- Department of Electrical Engineering and Computer Science, University of Cincinnati, Cincinnati, Ohio
- Department of Pediatrics, University of Cincinnati School of Medicine, Cincinnati, Ohio
| | - Yan Xu
- Division of Pulmonary Biology, The Perinatal Institute, and
- Department of Pediatrics, University of Cincinnati School of Medicine, Cincinnati, Ohio
| | - Tim Tickle
- Data Sciences Platform, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Bruce J. Aronow
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
- Department of Electrical Engineering and Computer Science, University of Cincinnati, Cincinnati, Ohio
- Department of Pediatrics, University of Cincinnati School of Medicine, Cincinnati, Ohio
| | - Nathan Salomonis
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
- Department of Electrical Engineering and Computer Science, University of Cincinnati, Cincinnati, Ohio
- Department of Pediatrics, University of Cincinnati School of Medicine, Cincinnati, Ohio
| |
Collapse
|
3
|
Van Camp PJ, Prasath VBS, Haslam DB, Porollo A. MGS2AMR: a gene-centric mining of metagenomic sequencing data for pathogens and their antimicrobial resistance profile. Microbiome 2023; 11:223. [PMID: 37833777 PMCID: PMC10571262 DOI: 10.1186/s40168-023-01674-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 09/21/2023] [Indexed: 10/15/2023]
Abstract
BACKGROUND Identification of pathogenic bacteria from clinical specimens and evaluating their antimicrobial resistance (AMR) are laborious tasks that involve in vitro cultivation, isolation, and susceptibility testing. Recently, a number of methods have been developed that use machine learning algorithms applied to the whole-genome sequencing data of isolates to approach this problem. However, making AMR assessments from more easily available metagenomic sequencing data remains a big challenge. RESULTS We present the Metagenomic Sequencing to Antimicrobial Resistance (MGS2AMR) pipeline, which detects antibiotic resistance genes (ARG) and their possible organism of origin within a sequenced metagenomics sample. This in silico method allows for the evaluation of bacterial AMR directly from clinical specimens, such as stool samples. We have developed two new algorithms to optimize and annotate the genomic assembly paths within the raw Graphical Fragment Assembly (GFA): the GFA Linear Optimal Path through seed segments (GLOPS) algorithm and the Adapted Dijkstra Algorithm for GFA (ADAG). These novel algorithms improve the sensitivity of ARG detection and aid in species annotation. Tests based on 1200 microbiome samples show a high ARG recall rate and correct assignment of the ARG origin. The MGS2AMR output can further be used in many downstream applications, such as evaluating AMR to specific antibiotics in samples from emerging intestinal infections. We demonstrate that the MGS2AMR-derived data is as informative for the entailing prediction models as the whole-genome sequencing (WGS) data. The performance of these models is on par with our previously published method (WGS2AMR), which is based on the sequencing data of bacterial isolates. CONCLUSIONS MGS2AMR can provide researchers with valuable insights into the AMR content of microbiome environments and may potentially improve patient care by providing faster quantification of resistance against specific antibiotics, thereby reducing the use of broad-spectrum antibiotics. The presented pipeline also has potential applications in other metagenome analyses focused on the defined sets of genes. Video Abstract.
Collapse
Affiliation(s)
- Pieter-Jan Van Camp
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - V B Surya Prasath
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH, 45267, USA
| | - David B Haslam
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH, 45267, USA
- Division of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Aleksey Porollo
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA.
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH, 45267, USA.
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA.
| |
Collapse
|
4
|
Gundawar A, Lodha S, Vijayarajan V, Iyer B, Prasath VBS. On the Performance of new Higher Order Transformation Functions for Highly Efficient Dense Layers. Neural Process Lett 2023. [DOI: 10.1007/s11063-023-11343-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/25/2023] [Indexed: 09/24/2023]
|
5
|
Diop EHS, Ngom A, Prasath VBS. Signal Approximations Based on Nonlinear and Optimal Piecewise Affine Functions. Circuits Syst Signal Process 2023; 42:2366-2384. [DOI: 10.1007/s00034-022-02224-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 10/18/2022] [Accepted: 10/19/2022] [Indexed: 09/24/2023]
|
6
|
Boopathiraja S, Kalavathi P, Deoghare S, Prasath VBS. Near Lossless Compression for 3D Radiological Images Using Optimal Multilinear Singular Value Decomposition (3D-VOI-OMLSVD). J Digit Imaging 2023; 36:259-275. [PMID: 36038701 PMCID: PMC9422948 DOI: 10.1007/s10278-022-00687-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 07/14/2022] [Accepted: 07/18/2022] [Indexed: 11/03/2022] Open
Abstract
Storage and transmission of high-compression 3D radiological images that create high-quality reconstruction upon decompression are critical necessities for effective and efficient teleradiology. To cater to this need, we propose a near lossless 3D image volume compression method based on optimal multilinear singular value decomposition called "3D-VOI-OMLSVD." The proposed strategy first eliminates any blank 2D image slices from the 3D image volume and uses the selective bounding volume (SBV) to identify and extract the volume of Interest (VOI). Following this, the VOI is decomposed with an optimal multilinear singular value decomposition (OMLSVD) to obtain the corresponding core tensor, factor matrices, and singular values that are compressed with adaptive binary range coder (ABRC), integrated as an entropy encoder. The compressed file can be transferred or transmitted and then decompressed in order to reconstruct the original image. The resultant decompressed VOI is acquired by reversing the above process and then fusing it with the background, using the bound volume coordinates associated with the compressed 3D image. The proposed method performance was tested on a variety of 3D radiological images with different imaging modalities and dimensions using quantitative evaluation metrics such as the compression rate (CR), bit rate (BR), peak signal to noise ratio (PSNR), and structural similarity index (SSIM). Furthermore, we also investigate the impact of VOI extraction on the model performance, before comparing it with two popular compression methods, namely JPEG and JPEG2000. Our proposed method, 3D-VOI-OMLSVD, displayed a high CR value, with a maximum of 37.31, and a low BR, with the lowest reported to be 0.21. The SSIM score was consistently high, with an average performance of 0.9868, while using < 1 second for decoding the image. We observe that with VOI extraction, the compression rate increases manifold, and bit rate drops significantly, and thus reduces the encoding and decoding time to a great extent. Compared to JPEG and JPEG2000, our method consistently performs better in terms of higher CR and lower BR. The results indicate that the proposed compression methodology performs consistently to create high-quality image compressions, and overall gives a better outcome when compared against two state-of-the-art and widely used methods, JPEG and JPEG2000.
Collapse
Affiliation(s)
- S. Boopathiraja
- Department of Computer Science and Applications, The Gandhigram Rural Institute (Deemed to Be University), Gandhigram, 624 302 Tamil Nadu India
| | - P. Kalavathi
- Department of Computer Science and Applications, The Gandhigram Rural Institute (Deemed to Be University), Gandhigram, 624 302 Tamil Nadu India
| | - S. Deoghare
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229 USA
- Department of Biomedical Informatics, College of Medicine, University of Cincinnati, Cincinnati, OH 45267 USA
| | - V. B. Surya Prasath
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229 USA
- Department of Biomedical Informatics, College of Medicine, University of Cincinnati, Cincinnati, OH 45267 USA
- Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH 45257 USA
- Department of Electrical Engineering and Computer Science, College of Engineering and Applied Science, University of Cincinnati, Cincinnati, OH 45221 USA
| |
Collapse
|
7
|
Li G, Song B, Singh H, Surya Prasath VB, Leighton Grimes H, Salomonis N. Decision level integration of unimodal and multimodal single cell data with scTriangulate. Nat Commun 2023; 14:406. [PMID: 36697445 PMCID: PMC9876931 DOI: 10.1038/s41467-023-36016-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 01/10/2023] [Indexed: 01/27/2023] Open
Abstract
Decisively delineating cell identities from uni- and multimodal single-cell datasets is complicated by diverse modalities, clustering methods, and reference atlases. We describe scTriangulate, a computational framework to mix-and-match multiple clustering results, modalities, associated algorithms, and resolutions to achieve an optimal solution. Rather than ensemble approaches which select the "consensus", scTriangulate picks the most stable solution through coalitional iteration. When evaluated on diverse multimodal technologies, scTriangulate outperforms alternative approaches to identify high-confidence cell-populations and modality-specific subtypes. Unlike existing integration strategies that rely on modality-specific joint embedding or geometric graphs, scTriangulate makes no assumption about the distributions of raw underlying values. As a result, this approach can solve unprecedented integration challenges, including the ability to automate reference cell-atlas construction, resolve clonal architecture within molecularly defined cell-populations and subdivide clusters to discover splicing-defined disease subtypes. scTriangulate is a flexible strategy for unified integration of single-cell or multimodal clustering solutions, from nearly unlimited sources.
Collapse
Affiliation(s)
- Guangyuan Li
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.,Department of Biomedical Informatics, College of Medicine, University of Cincinnati, Cincinnati, OH, 45267, USA
| | - Baobao Song
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.,Immunology Graduate Program, College of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA
| | - Harinder Singh
- Center for Systems Immunology and the Department of Immunology, University of Pittsburgh, Pittsburgh, PA, USA
| | - V B Surya Prasath
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.,Department of Biomedical Informatics, College of Medicine, University of Cincinnati, Cincinnati, OH, 45267, USA.,Department of Pediatrics, University of Cincinnati School of Medicine, Cincinnati, OH, USA.,Department of Computer Science, University of Cincinnati, Cincinnati, OH 45221, USA
| | - H Leighton Grimes
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA. .,Immunology Graduate Program, College of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA. .,Department of Pediatrics, University of Cincinnati School of Medicine, Cincinnati, OH, USA.
| | - Nathan Salomonis
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA. .,Department of Biomedical Informatics, College of Medicine, University of Cincinnati, Cincinnati, OH, 45267, USA. .,Immunology Graduate Program, College of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA. .,Department of Pediatrics, University of Cincinnati School of Medicine, Cincinnati, OH, USA. .,Department of Computer Science, University of Cincinnati, Cincinnati, OH 45221, USA.
| |
Collapse
|
8
|
Cazares TA, Rizvi FW, Iyer B, Chen X, Kotliar M, Bejjani AT, Wayman JA, Donmez O, Wronowski B, Parameswaran S, Kottyan LC, Barski A, Weirauch MT, Prasath VBS, Miraldi ER. maxATAC: Genome-scale transcription-factor binding prediction from ATAC-seq with deep neural networks. PLoS Comput Biol 2023; 19:e1010863. [PMID: 36719906 PMCID: PMC9917285 DOI: 10.1371/journal.pcbi.1010863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 02/10/2023] [Accepted: 01/10/2023] [Indexed: 02/01/2023] Open
Abstract
Transcription factors read the genome, fundamentally connecting DNA sequence to gene expression across diverse cell types. Determining how, where, and when TFs bind chromatin will advance our understanding of gene regulatory networks and cellular behavior. The 2017 ENCODE-DREAM in vivo Transcription-Factor Binding Site (TFBS) Prediction Challenge highlighted the value of chromatin accessibility data to TFBS prediction, establishing state-of-the-art methods for TFBS prediction from DNase-seq. However, the more recent Assay-for-Transposase-Accessible-Chromatin (ATAC)-seq has surpassed DNase-seq as the most widely-used chromatin accessibility profiling method. Furthermore, ATAC-seq is the only such technique available at single-cell resolution from standard commercial platforms. While ATAC-seq datasets grow exponentially, suboptimal motif scanning is unfortunately the most common method for TFBS prediction from ATAC-seq. To enable community access to state-of-the-art TFBS prediction from ATAC-seq, we (1) curated an extensive benchmark dataset (127 TFs) for ATAC-seq model training and (2) built "maxATAC", a suite of user-friendly, deep neural network models for genome-wide TFBS prediction from ATAC-seq in any cell type. With models available for 127 human TFs, maxATAC is the largest collection of high-performance TFBS prediction models for ATAC-seq. maxATAC performance extends to primary cells and single-cell ATAC-seq, enabling improved TFBS prediction in vivo. We demonstrate maxATAC's capabilities by identifying TFBS associated with allele-dependent chromatin accessibility at atopic dermatitis genetic risk loci.
Collapse
Affiliation(s)
- Tareian A. Cazares
- Immunology Graduate Program, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Faiz W. Rizvi
- Systems Biology and Physiology Graduate Program, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Balaji Iyer
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Department of Electrical Engineering and Computer Science, University of Cincinnati, Cincinnati, Ohio, United States of America
| | - Xiaoting Chen
- The Center for Autoimmune Genetics and Etiology (CAGE), Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Michael Kotliar
- Division of Allergy and Immunology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Anthony T. Bejjani
- Molecular and Developmental Biology Graduate Program, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Joseph A. Wayman
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Omer Donmez
- The Center for Autoimmune Genetics and Etiology (CAGE), Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Benjamin Wronowski
- Division of Allergy and Immunology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Sreeja Parameswaran
- The Center for Autoimmune Genetics and Etiology (CAGE), Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Leah C. Kottyan
- The Center for Autoimmune Genetics and Etiology (CAGE), Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Artem Barski
- Division of Allergy and Immunology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Matthew T. Weirauch
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- The Center for Autoimmune Genetics and Etiology (CAGE), Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - V. B. Surya Prasath
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Department of Electrical Engineering and Computer Science, University of Cincinnati, Cincinnati, Ohio, United States of America
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Emily R. Miraldi
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Department of Electrical Engineering and Computer Science, University of Cincinnati, Cincinnati, Ohio, United States of America
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| |
Collapse
|
9
|
Salamat N, Arif AH, Mustahsan M, Missen MMS, Prasath VBS. On compacton traveling wave solutions of Zakharov-Kuznetsov-Benjamin-Bona-Mahony (ZK-BBM) equation. Comp Appl Math 2022; 41:365. [DOI: 10.1007/s40314-022-02082-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 07/25/2022] [Accepted: 09/29/2022] [Indexed: 09/24/2023]
|
10
|
Jin K, Schnell D, Li G, Salomonis N, Prasath VBS, Szczesniak R, Aronow BJ. CellDrift: inferring perturbation responses in temporally sampled single-cell data. Brief Bioinform 2022; 23:6673850. [PMID: 35998893 PMCID: PMC9487655 DOI: 10.1093/bib/bbac324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 06/27/2022] [Accepted: 07/18/2022] [Indexed: 11/13/2022] Open
Abstract
Cells and tissues respond to perturbations in multiple ways that can be sensitively reflected in the alterations of gene expression. Current approaches to finding and quantifying the effects of perturbations on cell-level responses over time disregard the temporal consistency of identifiable gene programs. To leverage the occurrence of these patterns for perturbation analyses, we developed CellDrift (https://github.com/KANG-BIOINFO/CellDrift), a generalized linear model-based functional data analysis method that is capable of identifying covarying temporal patterns of various cell types in response to perturbations. As compared to several other approaches, CellDrift demonstrated superior performance in the identification of temporally varied perturbation patterns and the ability to impute missing time points. We applied CellDrift to multiple longitudinal datasets, including COVID-19 disease progression and gastrointestinal tract development, and demonstrated its ability to identify specific gene programs associated with sequential biological processes, trajectories and outcomes.
Collapse
Affiliation(s)
- Kang Jin
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Department of Biomedical Informatics, University of Cincinnati, Cincinnati, OH 45229, USA
| | - Daniel Schnell
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Guangyuan Li
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Department of Biomedical Informatics, University of Cincinnati, Cincinnati, OH 45229, USA
| | - Nathan Salomonis
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Department of Biomedical Informatics, University of Cincinnati, Cincinnati, OH 45229, USA.,Department of Pediatrics, University of Cincinnati School of Medicine, Cincinnati, OH 45256, USA
| | - V B Surya Prasath
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Department of Biomedical Informatics, University of Cincinnati, Cincinnati, OH 45229, USA.,Department of Electrical Engineering and Computer Science, University of Cincinnati, OH 45256, USA
| | - Rhonda Szczesniak
- Division of Biostatistics and Epidemiology, Cincinnati Children's Hospital Medical Center, OH 45229, USA
| | - Bruce J Aronow
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Department of Biomedical Informatics, University of Cincinnati, Cincinnati, OH 45229, USA.,Department of Pediatrics, University of Cincinnati School of Medicine, Cincinnati, OH 45256, USA.,Department of Electrical Engineering and Computer Science, University of Cincinnati, OH 45256, USA
| |
Collapse
|
11
|
Katsuma D, Kawanaka H, Prasath VBS, Aronow BJ. Data Augmentation Using Generative Adversarial Networks for Multi-Class Segmentation of Lung Confocal IF Images. JACIII 2022. [DOI: 10.20965/jaciii.2022.p0138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The human lung is a complex organ with high cellular heterogeneity, and its development and maintenance require interactive gene networks and dynamic cross-talk among multiple cell types. We focus on the confocal immunofluorescent (IF) images of lung tissues from the LungMAP database to reveal lung development. Using the current state-of-the-art deep learning-based model, the authors consider obtaining accurate multi-class segmentation of lung confocal IF images. One of the primary bottlenecks in using deep Convolutional Neural Network (CNN) models is the lack of availability of large-scale training or ground-truth segmentation labels. Then, we implement the multi-class segmentation with Generative Adversarial Network (GAN) models to expand the training dataset, improve overall segmentation accuracy, and discuss the effectiveness of created synthetic images in the segmentation of IF images. Consequently, experimental results indicated that 15.1% increased the accuracy of six-class segmentation using Mask R-CNN. In particular, the accuracy of our few data was mainly improved by using our proposed method. Therefore, the synthetic dataset can moderate the imbalanced data and be used for expanding the dataset.
Collapse
|
12
|
Abstract
In this world of big data, the development and exploitation of medical technology is vastly increasing and especially in big biomedical imaging modalities available across medicine. At the same instant, acquisition, processing, storing and transmission of such huge medical data requires efficient and robust data compression models. Over the last two decades, numerous compression mechanisms, techniques and algorithms were proposed by many researchers. This work provides a detailed status of these existing computational compression methods for medical imaging data. Appropriate classification, performance metrics, practical issues and challenges in enhancing the two dimensional (2D) and three dimensional (3D) medical image compression arena are reviewed in detail.
Collapse
Affiliation(s)
- S. Boopathiraja
- Department of Computer Science and Applications, The Gandhigram Rural Institute (Deemed to be University), Gandhigram, 624 302 Tamil Nadu, India
| | - V. Punitha
- Department of Computer Science and Applications, The Gandhigram Rural Institute (Deemed to be University), Gandhigram, 624 302 Tamil Nadu, India
| | - P. Kalavathi
- Department of Computer Science and Applications, The Gandhigram Rural Institute (Deemed to be University), Gandhigram, 624 302 Tamil Nadu, India
| | - V. B. Surya Prasath
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, OH 45229 USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45257, USA
- Department of Biomedical Informatics, College of Medicine, University of Cincinnati, OH 45267 USA
- Department of Electrical Engineering and Computer Science, University of Cincinnati, OH 45221 USA
- , ,
| |
Collapse
|
13
|
Li G, Iyer B, Prasath VBS, Ni Y, Salomonis N. DeepImmuno: deep learning-empowered prediction and generation of immunogenic peptides for T-cell immunity. Brief Bioinform 2021; 22:bbab160. [PMID: 34009266 PMCID: PMC8135853 DOI: 10.1093/bib/bbab160] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 03/26/2021] [Accepted: 04/05/2021] [Indexed: 02/07/2023] Open
Abstract
Cytolytic T-cells play an essential role in the adaptive immune system by seeking out, binding and killing cells that present foreign antigens on their surface. An improved understanding of T-cell immunity will greatly aid in the development of new cancer immunotherapies and vaccines for life-threatening pathogens. Central to the design of such targeted therapies are computational methods to predict non-native peptides to elicit a T-cell response, however, we currently lack accurate immunogenicity inference methods. Another challenge is the ability to accurately simulate immunogenic peptides for specific human leukocyte antigen alleles, for both synthetic biological applications, and to augment real training datasets. Here, we propose a beta-binomial distribution approach to derive peptide immunogenic potential from sequence alone. We conducted systematic benchmarking of five traditional machine learning (ElasticNet, K-nearest neighbors, support vector machine, Random Forest and AdaBoost) and three deep learning models (convolutional neural network (CNN), Residual Net and graph neural network) using three independent prior validated immunogenic peptide collections (dengue virus, cancer neoantigen and SARS-CoV-2). We chose the CNN as the best prediction model, based on its adaptivity for small and large datasets and performance relative to existing methods. In addition to outperforming two highly used immunogenicity prediction algorithms, DeepImmuno-CNN correctly predicts which residues are most important for T-cell antigen recognition and predicts novel impacts of SARS-CoV-2 variants. Our independent generative adversarial network (GAN) approach, DeepImmuno-GAN, was further able to accurately simulate immunogenic peptides with physicochemical properties and immunogenicity predictions similar to that of real antigens. We provide DeepImmuno-CNN as source code and an easy-to-use web interface.
Collapse
Affiliation(s)
- Guangyuan Li
- University of Cincinnati, 3333 Burnet Ave, MLC7024, Cincinnati, OH 45267, USA
| | | | - V B Surya Prasath
- Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, USA
| | - Yizhao Ni
- Cincinnati Children’s Hospital Medical Center, USA
| | | |
Collapse
|
14
|
Subramanian B, Palanisamy K, Prasath VBS. On a hybrid lossless compression technique for three-dimensional medical images. J Appl Clin Med Phys 2021; 22:191-203. [PMID: 33960632 PMCID: PMC8364287 DOI: 10.1002/acm2.12960] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 11/29/2019] [Accepted: 06/02/2020] [Indexed: 02/05/2023] Open
Abstract
In the last two decades, incredible progress in various medical imaging modalities and sensing techniques have been made, leading to the proliferation of three-dimensional (3D) imagery. Byproduct of such great progress is the production of huge volume of medical images and this big data place a burden on automatic image processing methods for diagnostic assistance processes. Moreover, large amount of medical imaging data needs to be transmitted with no loss of information for the purpose of telemedicine, remote diagnosis etc. In this work, we consider a hybrid lossless compression technique with object-based features for three-dimensional (3D) medical images. Our approach utilizes two phases as follows: first we determine the volume of interest (VOI) for a given 3D medical imagery using selective bounding volume (SBV) method, and second the obtained VOI is encoded using a hybrid lossless algorithm using Lembel-Ziv-Welch Coding (LZW) followed by arithmetic coding (L to A). Experimental results show that our proposed 3D medical image compression method is comparable with other existing standard lossless encoding methods such as Huffman Coding, Run Length Coding, LZW, and Arithmetic Coding and obtains superior results overall.
Collapse
Affiliation(s)
- Boopathiraja Subramanian
- Department of Computer Science and ApplicationsThe Gandhigram Rural InstituteGandhigramTamil NaduIndia
| | - Kalavathi Palanisamy
- Department of Computer Science and ApplicationsThe Gandhigram Rural InstituteGandhigramTamil NaduIndia
| | - V. B. Surya Prasath
- Division of Biomedical InformaticsCincinnati Children's Hospital Medical CenterCincinnatiOH45229USA
- Department of PediatricsUniversity of CincinnatiCincinnatiOHUSA
- Department of Biomedical InformaticsCollege of MedicineUniversity of CincinnatiCincinnatiOHUSA
- Department of Electrical Engineering and Computer ScienceUniversity of CincinnatiOH45221USA
| |
Collapse
|
15
|
Shah M, Shu D, Prasath VBS, Ni Y, Schapiro AH, Dufendach KR. Machine Learning for Detection of Correct Peripherally Inserted Central Catheter Tip Position from Radiology Reports in Infants. Appl Clin Inform 2021; 12:856-863. [PMID: 34496420 PMCID: PMC8426077 DOI: 10.1055/s-0041-1735178] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND In critically ill infants, the position of a peripherally inserted central catheter (PICC) must be confirmed frequently, as the tip may move from its original position and run the risk of hyperosmolar vascular damage or extravasation into surrounding spaces. Automated detection of PICC tip position holds great promise for alerting bedside clinicians to noncentral PICCs. OBJECTIVES This research seeks to use natural language processing (NLP) and supervised machine learning (ML) techniques to predict PICC tip position based primarily on text analysis of radiograph reports from infants with an upper extremity PICC. METHODS Radiographs, containing a PICC line in infants under 6 months of age, were manually classified into 12 anatomical locations based on the radiologist's textual report of the PICC line's tip. After categorization, we performed a 70/30 train/test split and benchmarked the performance of seven different (neural network, support vector machine, the naïve Bayes, decision tree, random forest, AdaBoost, and K-nearest neighbors) supervised ML algorithms. After optimization, we calculated accuracy, precision, and recall of each algorithm's ability to correctly categorize the stated location of the PICC tip. RESULTS A total of 17,337 radiographs met criteria for inclusion and were labeled manually. Interrater agreement was 99.1%. Support vector machines and neural networks yielded accuracies as high as 98% in identifying PICC tips in central versus noncentral position (binary outcome) and accuracies as high as 95% when attempting to categorize the individual anatomical location (12-category outcome). CONCLUSION Our study shows that ML classifiers can automatically extract the anatomical location of PICC tips from radiology reports. Two ML classifiers, support vector machine (SVM) and a neural network, obtained top accuracies in both binary and multiple category predictions. Implementing these algorithms in a neonatal intensive care unit as a clinical decision support system may help clinicians address PICC line position.
Collapse
Affiliation(s)
- Manan Shah
- Division of Neonatal and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, United States
- Address for correspondence Manan Shah, MD Division of Neonatal and Pulmonary Biology, Cincinnati Children's Hospital Medical Center3333 Burnet Avenue MLC 7009, Cincinnati, OH 45229United States
| | - Derek Shu
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States
| | - V. B. Surya Prasath
- Division of Bioinformatics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, United States
| | - Yizhao Ni
- Division of Bioinformatics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, United States
- Department of Biomedical Informatics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States
| | - Andrew H. Schapiro
- Department of Radiology and Medical Imaging, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, United States
- Department of Radiology, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States
| | - Kevin R. Dufendach
- Division of Neonatal and Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, United States
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States
- Division of Bioinformatics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, United States
| |
Collapse
|
16
|
Abstract
Having control over your data is a right and a duty that every citizen has in our digital society. It is often that users skip entire policies of applications or websites to save time and energy without realizing the potential sticky points in these policies. Due to obscure language and verbose explanations majority of users of hypermedia do not bother to read them. Further, sometimes digital media companies do not spend enough effort in stating their policies clearly which often time can also be incomplete. A summarized version of these privacy policies that can be categorized into the useful information can help the users. To solve this problem, in this work we propose to use machine learning based models for policy categorizer that classifies the policy paragraphs under the attributes proposed like security, contact etc. By benchmarking different machine learning based classifier models, we show that artificial neural network model performs with higher accuracy on a challenging dataset of textual privacy policies. We thus show that machine learning can help summarize the relevant paragraphs under the various attributes so that the user can get the gist of that topic within a few lines.
Collapse
Affiliation(s)
- Rushikesh Deotale
- School of Computer Science and Engineering, Vellore Institute of Technology, Vellore, India
| | - Shreyash Rawat
- School of Computer Science and Engineering, Vellore Institute of Technology, Vellore, India
| | - V Vijayarajan
- School of Computer Science and Engineering, Vellore Institute of Technology, Vellore, India
| | - V B Surya Prasath
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati OH 45229 USA. Departments of Pediatrics, Biomedical Informatics, Electrical Engineering and Computer Science, University of Cincinnati College of Medicine, Cincinnati, OH USA
| |
Collapse
|
17
|
Zhang J, Wu Q, Johnson CB, Pham G, Kinder JM, Olsson A, Slaughter A, May M, Weinhaus B, D'Alessandro A, Engel JD, Jiang JX, Kofron JM, Huang LF, Prasath VBS, Way SS, Salomonis N, Grimes HL, Lucas D. In situ mapping identifies distinct vascular niches for myelopoiesis. Nature 2021; 590:457-462. [PMID: 33568812 PMCID: PMC8020897 DOI: 10.1038/s41586-021-03201-2] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 12/24/2020] [Indexed: 02/07/2023]
Abstract
In contrast to nearly all other tissues, the anatomy of cell differentiation in the bone marrow remains unknown. This is owing to a lack of strategies for examining myelopoiesis-the differentiation of myeloid progenitors into a large variety of innate immune cells-in situ in the bone marrow. Such strategies are required to understand differentiation and lineage-commitment decisions, and to define how spatial organizing cues inform tissue function. Here we develop approaches for imaging myelopoiesis in mice, and generate atlases showing the differentiation of granulocytes, monocytes and dendritic cells. The generation of granulocytes and dendritic cells-monocytes localizes to different blood-vessel structures known as sinusoids, and displays lineage-specific spatial and clonal architectures. Acute systemic infection with Listeria monocytogenes induces lineage-specific progenitor clusters to undergo increased self-renewal of progenitors, but the different lineages remain spatially separated. Monocyte-dendritic cell progenitors (MDPs) map with nonclassical monocytes and conventional dendritic cells; these localize to a subset of blood vessels expressing a major regulator of myelopoiesis, colony-stimulating factor 1 (CSF1, also known as M-CSF)1. Specific deletion of Csf1 in endothelium disrupts the architecture around MDPs and their localization to sinusoids. Subsequently, there are fewer MDPs and their ability to differentiate is reduced, leading to a loss of nonclassical monocytes and dendritic cells during both homeostasis and infection. These data indicate that local cues produced by distinct blood vessels are responsible for the spatial organization of definitive blood cell differentiation.
Collapse
Affiliation(s)
- Jizhou Zhang
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Medical Center, Cincinnati, OH, USA
| | - Qingqing Wu
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Medical Center, Cincinnati, OH, USA
| | - Courtney B Johnson
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Medical Center, Cincinnati, OH, USA
| | - Giang Pham
- Division of Infectious Diseases, Center for Inflammation and Tolerance, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Jeremy M Kinder
- Division of Infectious Diseases, Center for Inflammation and Tolerance, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Andre Olsson
- Division of Immunobiology and Center for Systems Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Anastasiya Slaughter
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Medical Center, Cincinnati, OH, USA
- Immunology Graduate Program, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Margot May
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Medical Center, Cincinnati, OH, USA
| | - Benjamin Weinhaus
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Medical Center, Cincinnati, OH, USA
- Immunology Graduate Program, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Angelo D'Alessandro
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver-Anschutz Medical Campus, Aurora, CO, USA
| | - James Douglas Engel
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Jean X Jiang
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center, San Antonio, TX, USA
| | - J Matthew Kofron
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - L Frank Huang
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Brain Tumor Center, Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Medical Center, Cincinnati, OH, USA
| | - V B Surya Prasath
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Sing Sing Way
- Division of Infectious Diseases, Center for Inflammation and Tolerance, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Nathan Salomonis
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - H Leighton Grimes
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Medical Center, Cincinnati, OH, USA
- Division of Immunobiology and Center for Systems Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Daniel Lucas
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Medical Center, Cincinnati, OH, USA.
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA.
| |
Collapse
|
18
|
Li G, Iyer B, Prasath VBS, Ni Y, Salomonis N. DeepImmuno: Deep learning-empowered prediction and generation of immunogenic peptides for T cell immunity. bioRxiv 2020:2020.12.24.424262. [PMID: 33398286 PMCID: PMC7781330 DOI: 10.1101/2020.12.24.424262] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
T-cells play an essential role in the adaptive immune system by seeking out, binding and destroying foreign antigens presented on the cell surface of diseased cells. An improved understanding of T-cell immunity will greatly aid in the development of new cancer immunotherapies and vaccines for life threatening pathogens. Central to the design of such targeted therapies are computational methods to predict non-native epitopes to elicit a T cell response, however, we currently lack accurate immunogenicity inference methods. Another challenge is the ability to accurately simulate immunogenic peptides for specific human leukocyte antigen (HLA) alleles, for both synthetic biological applications and to augment real training datasets. Here, we proposed a beta-binomial distribution approach to derive epitope immunogenic potential from sequence alone. We conducted systematic benchmarking of five traditional machine learning (ElasticNet, KNN, SVM, Random Forest, AdaBoost) and three deep learning models (CNN, ResNet, GNN) using three independent prior validated immunogenic peptide collections (dengue virus, cancer neoantigen and SARS-Cov-2). We chose the CNN model as the best prediction model based on its adaptivity for small and large datasets, and performance relative to existing methods. In addition to outperforming two highly used immunogenicity prediction algorithms, DeepHLApan and IEDB, DeepImmuno-CNN further correctly predicts which residues are most important for T cell antigen recognition. Our independent generative adversarial network (GAN) approach, DeepImmuno-GAN, was further able to accurately simulate immunogenic peptides with physiochemical properties and immunogenicity predictions similar to that of real antigens. We provide DeepImmuno-CNN as source code and an easy-to-use web interface. DATA AVAILABILITY DeepImmuno Python3 code is available at https://github.com/frankligy/DeepImmuno . The DeepImmuno web portal is available from https://deepimmuno.herokuapp.com . The data in this article is available in GitHub and supplementary materials.
Collapse
Affiliation(s)
- Guangyuan Li
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- Department of Biomedical Informatics, College of Medicine, University of Cincinnati, OH, 45267 USA
| | - Balaji Iyer
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- Department of Electrical Engineering and Computer Science, University of Cincinnati, OH 45221 USA
| | - V. B. Surya Prasath
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati School of Medicine, Cincinnati, Ohio, USA
- Department of Biomedical Informatics, College of Medicine, University of Cincinnati, OH, 45267 USA
- Department of Electrical Engineering and Computer Science, University of Cincinnati, OH 45221 USA
| | - Yizhao Ni
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati School of Medicine, Cincinnati, Ohio, USA
- Department of Biomedical Informatics, College of Medicine, University of Cincinnati, OH, 45267 USA
| | - Nathan Salomonis
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati School of Medicine, Cincinnati, Ohio, USA
- Department of Biomedical Informatics, College of Medicine, University of Cincinnati, OH, 45267 USA
- Department of Electrical Engineering and Computer Science, University of Cincinnati, OH 45221 USA
| |
Collapse
|
19
|
Prasath VBS, Thanh DNH, Thanh LT, San NQ, Dvoenko S. Human Visual System Consistent Model for Wireless Capsule Endoscopy Image Enhancement and Applications. Pattern Recognit Image Anal 2020. [DOI: 10.1134/s1054661820030219] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
|
20
|
Missen MMS, Naeem A, Asmat H, Salamat N, Akhtar N, Coustaty M, Prasath VBS. Improving seller–customer communication process using word embeddings. J Ambient Intell Human Comput 2020. [DOI: 10.1007/s12652-020-02323-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|
21
|
Hieu LM, Thanh DNH, Surya Prasath VB. Second Order Monotone Difference Schemes with Approximation on Non-Uniform Grids for Two-Dimensional Quasilinear Parabolic Convection-Diffusion Equations. Vestnik St Petersb Univ Math 2020. [DOI: 10.1134/s1063454120020107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
|
22
|
Thanh DNH, Prasath VBS, Hieu LM, Hien NN. Melanoma Skin Cancer Detection Method Based on Adaptive Principal Curvature, Colour Normalisation and Feature Extraction with the ABCD Rule. J Digit Imaging 2020; 33:574-585. [PMID: 31848895 PMCID: PMC7256173 DOI: 10.1007/s10278-019-00316-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
According to statistics of the American Cancer Society, in 2015, there are about 91,270 American adults diagnosed with melanoma of the skin. For the European Union, there are over 90,000 new cases of melanoma annually. Although melanoma only accounts for about 1% of all skin cancers, it causes most of the skin cancer deaths. Melanoma is considered one of the fastest-growing forms of skin cancer, and hence the early detection is crucial, as early detection is helpful and can provide strong recommendations for specific and suitable treatment regimens. In this work, we propose a method to detect melanoma skin cancer with automatic image processing techniques. Our method includes three stages: pre-process images of skin lesions by adaptive principal curvature, segment skin lesions by the colour normalisation and extract features by the ABCD rule. We provide experimental results of the proposed method on the publicly available International Skin Imaging Collaboration (ISIC) skin lesions dataset. The acquired results on melanoma skin cancer detection indicates that the proposed method has high accuracy, and overall, a good performance: for the segmentation stage, the accuracy, Dice, Jaccard scores are 96.6%, 93.9% and 88.7%, respectively; and for the melanoma detection stage, the accuracy is up to 100% for a selected subset of the ISIC dataset.
Collapse
Affiliation(s)
- Dang N H Thanh
- Department of Information Technology, Hue College of Industry, Hue, Vietnam.
| | - V B Surya Prasath
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH, USA
- Department of Biomedical Informatics, College of Medicine, University of Cincinnati, Cincinnati, OH, USA
- Department of Electrical Engineering and Computer Science, University of Cincinnati, Cincinnati, OH, USA
| | - Le Minh Hieu
- Department of Economics, University of Economics, The University of Danang, Danang, Vietnam
| | - Nguyen Ngoc Hien
- Centre of occupational skills development, Dong Thap University, Cao Lanh, Vietnam
| |
Collapse
|
23
|
Thanh DNH, Hai NH, Prasath VBS, Hieu LM, Tavares JMRS. A two-stage filter for high density salt and pepper denoising. Multimed Tools Appl 2020. [DOI: 10.1007/s11042-020-08887-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|
24
|
Prasath VBS, Thanh DNH, Hung NQ, Hieu LM. Multiscale Gradient Maps Augmented Fisher Information-Based Image Edge Detection. IEEE Access 2020. [DOI: 10.1109/access.2020.3013888] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
|
25
|
Bidani S, Priya RP, Vijayarajan V, Prasath VBS. Automatic body mass index detection using correlation of face visual cues. Technol Health Care 2020; 28:107-112. [PMID: 31658072 DOI: 10.3233/thc-191850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Body mass index (BMI) is used widely as an indicator in general health. Determination of BMI using non-intrusive measurements are of interest and recent advancements in the availability of digital imaging sensors have paved the way for performing quick and automatic measurements. In this work, we consider automatic computation of BMI using correlation features from face images. We show that using face detection based facial fiducial points analysis provides good BMI prediction. Experimental results on comparing the correlation coefficients of facial ratios along with the colour feature has higher significance in BMI of a person.
Collapse
Affiliation(s)
- Shiv Bidani
- School of Computing Science and Engineering, VIT University, Vellore, India
| | - R Padma Priya
- School of Computing Science and Engineering, VIT University, Vellore, India
| | - V Vijayarajan
- School of Computing Science and Engineering, VIT University, Vellore, India
| | - V B Surya Prasath
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH, USA
- Department of Biomedical Informatics, College of Medicine, University of Cincinnati, Cincinnati, OH, USA
- Department of Electrical Engineering and Computer Science, University of Cincinnati, Cincinnati, OH, USA
| |
Collapse
|
26
|
Prasath VBS, Pelapur R, Seetharaman G, Palaniappan K. Multiscale Structure Tensor for Improved Feature Extraction and Image Regularization. IEEE Trans Image Process 2019; 28:6198-6210. [PMID: 31265398 DOI: 10.1109/tip.2019.2924799] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Regularization methods are used widely in image selective smoothing and edge preserving restoration of noisy images. Traditional methods utilize image gradients within regularization function for controlling the smoothing and can produce artifacts when noise levels are higher. In this paper, we consider a robust image adaptive exponent driven regularization for filtering noisy images with salient feature preservation. Our spatially adaptive variable exponent function depends on a continuous switch based on the eigenvalues of structure tensor which identifies noisy edges, and corners with higher accuracy. Structure tensor eigenvalues encode various image features and we consider a spatially varying continuous map which provides multiscale edge maps of natural images. By embedding the structure tensor-based exponent in a well-defined regularization model, we obtain denoising filters which are capable of obtaining good feature preserving image restoration. The GPU-based implementation computes the edge map in real time at 45-60 frames/s depending on the GPU card. Multiscale structure tensor-based spatially adaptive variable exponent provides reliable edge maps and compared with standard edge detectors it is robust under various noisy conditions. Moreover, filtering based on the multiscale variable exponent map method outperforms L0 sparse gradient-based image smoothing and related filters.
Collapse
|
27
|
Abu Alfeilat HA, Hassanat ABA, Lasassmeh O, Tarawneh AS, Alhasanat MB, Eyal Salman HS, Prasath VBS. Effects of Distance Measure Choice on K-Nearest Neighbor Classifier Performance: A Review. Big Data 2019; 7:221-248. [PMID: 31411491 DOI: 10.1089/big.2018.0175] [Citation(s) in RCA: 113] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The K-nearest neighbor (KNN) classifier is one of the simplest and most common classifiers, yet its performance competes with the most complex classifiers in the literature. The core of this classifier depends mainly on measuring the distance or similarity between the tested examples and the training examples. This raises a major question about which distance measures to be used for the KNN classifier among a large number of distance and similarity measures available? This review attempts to answer this question through evaluating the performance (measured by accuracy, precision, and recall) of the KNN using a large number of distance measures, tested on a number of real-world data sets, with and without adding different levels of noise. The experimental results show that the performance of KNN classifier depends significantly on the distance used, and the results showed large gaps between the performances of different distances. We found that a recently proposed nonconvex distance performed the best when applied on most data sets comparing with the other tested distances. In addition, the performance of the KNN with this top performing distance degraded only ∼20% while the noise level reaches 90%, this is true for most of the distances used as well. This means that the KNN classifier using any of the top 10 distances tolerates noise to a certain degree. Moreover, the results show that some distances are less affected by the added noise comparing with other distances.
Collapse
Affiliation(s)
| | - Ahmad B A Hassanat
- Department of Computer Science, Faculty of Information Technology, Mutah University, Karak, Jordan
| | - Omar Lasassmeh
- Department of Computer Science, Faculty of Information Technology, Mutah University, Karak, Jordan
| | - Ahmad S Tarawneh
- Department of Algorithm and Their Applications, Eötvös Loránd University, Budapest, Hungary
| | - Mahmoud Bashir Alhasanat
- Department of Geomatics, Faculty of Environmental Design, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Civil Engineering, Faculty of Engineering, Al-Hussein Bin Talal University, Maan, Jordan
| | - Hamzeh S Eyal Salman
- Department of Computer Science, Faculty of Information Technology, Mutah University, Karak, Jordan
| | - V B Surya Prasath
- Department of Pediatrics, Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
- Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, Ohio
- Department of Biomedical Informatics, College of Medicine, University of Cincinnati, Cincinnati, Ohio
- Department of Electrical Engineering and Computer Science, University of Cincinnati, Cincinnati, Ohio
| |
Collapse
|
28
|
Missen MMS, Javed A, Asmat H, Nosheen M, Coustaty M, Salamat N, Prasath VBS. Systematic review and usability evaluation of writing mobile apps for children. NEW REV HYPERMEDIA M 2019. [DOI: 10.1080/13614568.2019.1677787] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Malik M. Saad Missen
- Department of Computer Science and IT, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Amna Javed
- Department of Computer Science and IT, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Hina Asmat
- Department of Computer Science and IT, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Mariam Nosheen
- Department of Computer Science, Lahore College for Women University, Lahore, Pakistan
| | - Mickaël Coustaty
- Laboratoire Informatique, Image et Interaction (L3i), Facultés des Sciences et Technologies, University of La Rochelle, La Rochelle, France
| | - Nadeem Salamat
- Department of Mathematics, Khawaja Fareed University of Engineering and Information Technology (KFUIT), Rahim Yar Khan, Pakistan
| | - V. B. Surya Prasath
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Department of Biomedical Informatics, College of Medicine, University of Cincinnati, Cincinnati, OH, USA
- Department of Electrical Engineering and Computer Science, University of Cincinnati, Cincinnati, OH, USA
| |
Collapse
|
29
|
Diop EHS, Boudraa AO, Prasath VBS. Optimal Nonlinear Signal Approximations Based on Piecewise Constant Functions. Circuits Syst Signal Process 2019. [DOI: 10.1007/s00034-019-01285-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|
30
|
Pranav A, Rajeshkannan R, Vijayarajan V, Prasath VBS. BREAK, MAKE and TAKE: an information retrieval approach. Sādhanā 2019; 44:204. [DOI: 10.1007/s12046-019-1187-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 06/28/2019] [Accepted: 07/09/2019] [Indexed: 09/24/2023]
|
31
|
Hassanat ABA, Prasath VBS, Al-kasassbeh M, Tarawneh AS, Al-shamailh AJ. Magnetic energy-based feature extraction for low-quality fingerprint images. SIViP 2018; 12:1471-1478. [DOI: 10.1007/s11760-018-1302-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Revised: 03/28/2018] [Accepted: 05/07/2018] [Indexed: 09/24/2023]
|
32
|
Yonekura A, Kawanaka H, Prasath VBS, Aronow BJ, Takase H. Automatic disease stage classification of glioblastoma multiforme histopathological images using deep convolutional neural network. Biomed Eng Lett 2018; 8:321-327. [PMID: 30603216 PMCID: PMC6208537 DOI: 10.1007/s13534-018-0077-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 05/28/2018] [Accepted: 06/17/2018] [Indexed: 02/07/2023] Open
Abstract
In the field of computational histopathology, computer-assisted diagnosis systems are important in obtaining patient-specific diagnosis for various diseases and help precision medicine. Therefore, many studies on automatic analysis methods for digital pathology images have been reported. In this work, we discuss an automatic feature extraction and disease stage classification method for glioblastoma multiforme (GBM) histopathological images. In this paper, we use deep convolutional neural networks (Deep CNNs) to acquire feature descriptors and a classification scheme simultaneously. Further, comparisons with other popular CNNs objectively as well as quantitatively in this challenging classification problem is undertaken. The experiments using Glioma images from The Cancer Genome Atlas shows that we obtain 96.5 % average classification accuracy for our network and for higher cross validation folds other networks perform similarly with a higher accuracy of 98.0 % . Deep CNNs could extract significant features from the GBM histopathology images with high accuracy. Overall, the disease stage classification of GBM from histopathological images with deep CNNs is very promising and with the availability of large scale histopathological image data the deep CNNs are well suited in tackling this challenging problem.
Collapse
Affiliation(s)
- Asami Yonekura
- Graduate School of Engineering, Mie University, 1577 Kurima-machiya, Tsu, Mie 514-8507 Japan
| | - Hiroharu Kawanaka
- Graduate School of Engineering, Mie University, 1577 Kurima-machiya, Tsu, Mie 514-8507 Japan
| | - V. B. Surya Prasath
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229 USA
- Department of Biomedical Informatics, College of Medicine, University of Cincinnati, Cincinnati, OH 45267 USA
- Department of Electrical Engineering and Computer Science, University of Cincinnati, Cincinnati, OH 45221 USA
| | - Bruce J. Aronow
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229 USA
- Department of Biomedical Informatics, College of Medicine, University of Cincinnati, Cincinnati, OH 45267 USA
| | - Haruhiko Takase
- Graduate School of Engineering, Mie University, 1577 Kurima-machiya, Tsu, Mie 514-8507 Japan
| |
Collapse
|
33
|
Prasath VBS, Moreno JC. On convergent finite difference schemes for variational–PDE-based image processing. Comp Appl Math 2018; 37:1562-1580. [DOI: 10.1007/s40314-016-0414-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/24/2023]
|
34
|
Affiliation(s)
- Malik M. Saad Missen
- Department of Computer Science and IT, The Islamia University of Bahawalpur, Pakistan
| | - Mickaël Coustaty
- Laboratoire Informatique, Image et Interaction (L3i), Facultés des Sciences et Technologies, University of La Rochelle, France
| | - Nadeem Salamat
- Department of Mathematics, Khawaja Fareed University of Engineering and Information Technology (KFUIT), Rahim Yar Khan, Pakistan
| | - V. B. Surya Prasath
- Department of Computer Science, University of Missouri-Columbia, MO, USA
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Biomedical Informatics, College of Medicine, University of Cincinnati, OH, USA
| |
Collapse
|
35
|
|
36
|
|
37
|
|
38
|
Aliakbarpour H, Ferreira JF, Prasath VBS, Palaniappan K, Seetharaman G, Dias J. A Probabilistic Fusion Framework for 3-D Reconstruction Using Heterogeneous Sensors. IEEE Sensors J 2017. [DOI: 10.1109/jsen.2017.2679187] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
|
39
|
Prasath VBS. App Review Series: Radiology Pocket Game. J Digit Imaging 2017; 30:127-129. [PMID: 27844214 PMCID: PMC5359209 DOI: 10.1007/s10278-016-9924-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Affiliation(s)
- V B Surya Prasath
- Computational Imaging and VisAnalysis (CIVA) Lab, Department of Computer Science, University of Missouri, Columbia, MO, 65211, USA.
| |
Collapse
|
40
|
Sarmiento CI, San-Juan D, Prasath VBS. Letter to the Editor: Brief history of transcranial direct current stimulation (tDCS): from electric fishes to microcontrollers. Psychol Med 2016; 46:3259-3261. [PMID: 27572999 DOI: 10.1017/s0033291716001926] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- C I Sarmiento
- Biomedical Engineering Laboratory, Division of Basic Sciences and Engineering,Metropolitan Autonomous University at Iztapalapa,Mexico City,Mexico
| | - D San-Juan
- Department of Clinical Research,National Institute of Neurology and Neurosurgery,Mexico City,Mexico
| | - V B S Prasath
- Computational Imaging and VisAnalysis (CIVA) Laboratory,Department of Computer Science,University of Missouri,Columbia, MO,USA
| |
Collapse
|
41
|
Kassim YM, Surya Prasath VB, Glinskii OV, Glinsky VV, Huxley VH, Palaniappan K. Confocal Vessel Structure Segmentation with Optimized Feature Bank and Random Forests. IEEE Appl Imag Pattern Recognit Workshop 2016; 2016:10.1109/AIPR.2016.8010580. [PMID: 29152413 PMCID: PMC5690568 DOI: 10.1109/aipr.2016.8010580] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
In this paper, we consider confocal microscopy based vessel segmentation with optimized features and random forest classification. By utilizing multi-scale vessel-specific features tuned to capture curvilinear structures such as Frobenius norm of the Hessian eigenvalues, Laplacian of Gaussians (LoG), oriented second derivative, line detector and intensity masked with LoG scale map. we obtain better segmentation results in challenging imaging conditions. We obtain binary segmentations using random forest classifier trained on physiologists marked ground-truth. Experimental results on mice dura mater confocal microscopy vessel segmentations indicate that we obtain better results compared to global segmentation approaches.
Collapse
Affiliation(s)
- Yasmin M Kassim
- Computational Imaging and VisAnalysis (CIVA) Lab Department of Computer Science, University of Missouri-Columbia, Columbia, MO 65211 USA
| | - V B Surya Prasath
- Computational Imaging and VisAnalysis (CIVA) Lab Department of Computer Science, University of Missouri-Columbia, Columbia, MO 65211 USA
| | - Olga V Glinskii
- Research Service, Harry S. Truman Memorial Veterans Hospital, Columbia, MO 65201 USA
- Department of Medical Pharmacology and Physiology, University of Missouri-Columbia, Columbia, MO 65211 USA
| | - Vladislav V Glinsky
- Research Service, Harry S. Truman Memorial Veterans Hospital, Columbia, MO 65201 USA
- Department of Pathology and Anatomical Sciences, University of Missouri-Columbia, Columbia, MO 65211 USA
| | - Virginia H Huxley
- Department of Medical Pharmacology and Physiology, University of Missouri-Columbia, Columbia, MO 65211 USA
- National Center for Gender Physiology, University of Missouri-Columbia, MO 65211 USA
| | - Kannappan Palaniappan
- Computational Imaging and VisAnalysis (CIVA) Lab Department of Computer Science, University of Missouri-Columbia, Columbia, MO 65211 USA
| |
Collapse
|
42
|
Kassim YM, Surya Prasath VB, Pelapur R, Glinskii OV, Maude RJ, Glinsky VV, Huxley VH, Palaniappan K. Random Forests for Dura Mater Microvasculature Segmentation Using Epifluorescence Images. Annu Int Conf IEEE Eng Med Biol Soc 2016; 2016:2901-2904. [PMID: 28261007 PMCID: PMC5324830 DOI: 10.1109/embc.2016.7591336] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Automatic segmentation of microvascular structures is a critical step in quantitatively characterizing vessel remodeling and other physiological changes in the dura mater or other tissues. We developed a supervised random forest (RF) classifier for segmenting thin vessel structures using multiscale features based on Hessian, oriented second derivatives, Laplacian of Gaussian and line features. The latter multiscale line detector feature helps in detecting and connecting faint vessel structures that would otherwise be missed. Experimental results on epifluorescence imagery show that the RF approach produces foreground vessel regions that are almost 20 and 25 percent better than Niblack and Otsu threshold-based segmentations respectively.
Collapse
Affiliation(s)
- Yasmin M Kassim
- Computational Imaging and VisAnalysis (CIVA) Lab, Department of Computer Science, Columbia, MO 65201 USA
| | - V B Surya Prasath
- Computational Imaging and VisAnalysis (CIVA) Lab, Department of Computer Science, Columbia, MO 65201 USA
| | - Rengarajan Pelapur
- Computational Imaging and VisAnalysis (CIVA) Lab, Department of Computer Science, Columbia, MO 65201 USA
| | - Olga V Glinskii
- Research Service, Harry S. Truman Memorial Veterans Hospital, Columbia, MO 65201 USA; Department of Medical Pharmacology and Physiology, University of Missouri-Columbia, MO 65211 USA
| | - Richard J Maude
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand; Harvard TH Chan School of Public Health, Harvard University, Boston, USA
| | - Vladislav V Glinsky
- Research Service, Harry S. Truman Memorial Veterans Hospital, Columbia, MO 65201 USA; Department of Pathology and Anatomical Sciences, University of Missouri-Columbia, MO 65211 USA
| | - Virginia H Huxley
- Department of Medical Pharmacology and Physiology, University of Missouri-Columbia, MO 65211 USA; National Center for Gender Physiology, University of Missouri-Columbia, MO 65211 USA
| | - Kannappan Palaniappan
- Computational Imaging and VisAnalysis (CIVA) Lab, Department of Computer Science, Columbia, MO 65201 USA
| |
Collapse
|
43
|
Meena S, Surya Prasath VB, Kassim YM, Maude RJ, Glinskii OV, Glinsky VV, Huxley VH, Palaniappan K. Multiquadric Spline-Based Interactive Segmentation of Vascular Networks. Annu Int Conf IEEE Eng Med Biol Soc 2016; 2016:5913-5916. [PMID: 28261011 PMCID: PMC5324779 DOI: 10.1109/embc.2016.7592074] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Commonly used drawing tools for interactive image segmentation and labeling include active contours or boundaries, scribbles, rectangles and other shapes. Thin vessel shapes in images of vascular networks are difficult to segment using automatic or interactive methods. This paper introduces the novel use of a sparse set of user-defined seed points (supervised labels) for precisely, quickly and robustly segmenting complex biomedical images. A multiquadric spline-based binary classifier is proposed as a unique approach for interactive segmentation using as features color values and the location of seed points. Epifluorescence imagery of the dura mater microvasculature are difficult to segment for quantitative applications due to challenging tissue preparation, imaging conditions, and thin, faint structures. Experimental results based on twenty epifluorescence images is used to illustrate the benefits of using a set of seed points to obtain fast and accurate interactive segmentation compared to four interactive and automatic segmentation approaches.
Collapse
Affiliation(s)
- Sachin Meena
- Computational Imaging and VisAnalysis Lab, Department of Computer Science, Columbia, MO 65201 USA
| | - V B Surya Prasath
- Computational Imaging and VisAnalysis Lab, Department of Computer Science, Columbia, MO 65201 USA
| | - Yasmin M Kassim
- Computational Imaging and VisAnalysis Lab, Department of Computer Science, Columbia, MO 65201 USA
| | - Richard J Maude
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand; Harvard TH Chan School of Public Health, Harvard University, Boston, USA
| | - Olga V Glinskii
- Research Service, Harry S. Truman Memorial Veterans Hospital, Columbia, MO 65201 USA; Department of Medical Pharmacology and Physiology, University of Missouri-Columbia, MO 65211 USA
| | - Vladislav V Glinsky
- Research Service, Harry S. Truman Memorial Veterans Hospital, Columbia, MO 65201 USA; Department of Pathology and Anatomical Sciences, University of Missouri-Columbia, MO 65211 USA
| | - Virginia H Huxley
- Department of Medical Pharmacology and Physiology, University of Missouri-Columbia, MO 65211 USA; National Center for Gender Physiology, University of Missouri-Columbia, MO 65211 USA
| | - Kannappan Palaniappan
- Computational Imaging and VisAnalysis Lab, Department of Computer Science, Columbia, MO 65201 USA
| |
Collapse
|
44
|
Abstract
The high resolution magnetic resonance (MR) brain images contain some non-brain tissues such as skin, fat, muscle, neck, and eye balls compared to the functional images namely positron emission tomography (PET), single photon emission computed tomography (SPECT), and functional magnetic resonance imaging (fMRI) which usually contain relatively less non-brain tissues. The presence of these non-brain tissues is considered as a major obstacle for automatic brain image segmentation and analysis techniques. Therefore, quantitative morphometric studies of MR brain images often require a preliminary processing to isolate the brain from extra-cranial or non-brain tissues, commonly referred to as skull stripping. This paper describes the available methods on skull stripping and an exploratory review of recent literature on the existing skull stripping methods.
Collapse
Affiliation(s)
- P. Kalavathi
- />Department of Computer Science and Applications, Gandhigram Rural Institute - Deemed University, Gandhigram, Tamil Nadu 624302 India
| | - V. B. Surya Prasath
- />Computational Imaging and VisAnalysis (CIVA) Lab, Department of Computer Science, University of Missouri-Columbia, Columbia, MO 65211 USA
| |
Collapse
|
45
|
Moreno JC, Prasath VBS, Neves JC. Color image processing by vectorial total variation with gradient channels coupling. IPI 2016. [DOI: 10.3934/ipi.2016008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
|
46
|
Affiliation(s)
- P. Kalavathi
- Department of Computer Science and Applications; Gandhigram Rural-Institute Deemed University; Gandhigram 624 302 Tamil Nadu India
| | - V. B. Surya Prasath
- Computational Imaging and VisAnalysis (CIVA) Lab, Department of Computer Science, University of Missouri-Columbia; Columbia MO 65211 USA
| |
Collapse
|
47
|
Aliakbarpour H, Prasath VBS, Palaniappan K, Seetharaman G, Dias J. Heterogeneous Multi-View Information Fusion: Review of 3-D Reconstruction Methods and a New Registration with Uncertainty Modeling. IEEE Access 2016. [DOI: 10.1109/access.2016.2629987] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
|
48
|
Prasath VBS, Vorotnikov D, Pelapur R, Jose S, Seetharaman G, Palaniappan K. Multiscale Tikhonov-Total Variation Image Restoration Using Spatially Varying Edge Coherence Exponent. IEEE Trans Image Process 2015; 24:5220-35. [PMID: 26394419 DOI: 10.1109/tip.2015.2479471] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Edge preserving regularization using partial differential equation (PDE)-based methods although extensively studied and widely used for image restoration, still have limitations in adapting to local structures. We propose a spatially adaptive multiscale variable exponent-based anisotropic variational PDE method that overcomes current shortcomings, such as over smoothing and staircasing artifacts, while still retaining and enhancing edge structures across scale. Our innovative model automatically balances between Tikhonov and total variation (TV) regularization effects using scene content information by incorporating a spatially varying edge coherence exponent map constructed using the eigenvalues of the filtered structure tensor. The multiscale exponent model we develop leads to a novel restoration method that preserves edges better and provides selective denoising without generating artifacts for both additive and multiplicative noise models. Mathematical analysis of our proposed method in variable exponent space establishes the existence of a minimizer and its properties. The discretization method we use satisfies the maximum-minimum principle which guarantees that artificial edge regions are not created. Extensive experimental results using synthetic, and natural images indicate that the proposed multiscale Tikhonov-TV (MTTV) and dynamical MTTV methods perform better than many contemporary denoising algorithms in terms of several metrics, including signal-to-noise ratio improvement and structure preservation. Promising extensions to handle multiplicative noise models and multichannel imagery are also discussed.
Collapse
|
49
|
Prasath VBS, Urbano JM, Vorotnikov D. Analysis of adaptive forward-backward diffusion flows with applications in image processing. Inverse Problems 2015. [DOI: 10.1088/0266-5611/31/10/105008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|
50
|
Moreno JC, Surya Prasath VB, Santos G, Proença H. Robust Periocular Recognition by Fusing Sparse Representations of Color and Geometry Information. J Sign Process Syst 2015. [DOI: 10.1007/s11265-015-1023-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|