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  1. AU="Katoch, Mitali"
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  1. Article ; Online: Machine Learning Made Easy (MLme): a comprehensive toolkit for machine learning-driven data analysis.

    Akshay, Akshay / Katoch, Mitali / Shekarchizadeh, Navid / Abedi, Masoud / Sharma, Ankush / Burkhard, Fiona C / Adam, Rosalyn M / Monastyrskaya, Katia / Gheinani, Ali Hashemi

    GigaScience

    2024  Volume 13

    Abstract: Background: Machine learning (ML) has emerged as a vital asset for researchers to analyze and extract valuable information from complex datasets. However, developing an effective and robust ML pipeline can present a real challenge, demanding ... ...

    Abstract Background: Machine learning (ML) has emerged as a vital asset for researchers to analyze and extract valuable information from complex datasets. However, developing an effective and robust ML pipeline can present a real challenge, demanding considerable time and effort, thereby impeding research progress. Existing tools in this landscape require a profound understanding of ML principles and programming skills. Furthermore, users are required to engage in the comprehensive configuration of their ML pipeline to obtain optimal performance.
    Results: To address these challenges, we have developed a novel tool called Machine Learning Made Easy (MLme) that streamlines the use of ML in research, specifically focusing on classification problems at present. By integrating 4 essential functionalities-namely, Data Exploration, AutoML, CustomML, and Visualization-MLme fulfills the diverse requirements of researchers while eliminating the need for extensive coding efforts. To demonstrate the applicability of MLme, we conducted rigorous testing on 6 distinct datasets, each presenting unique characteristics and challenges. Our results consistently showed promising performance across different datasets, reaffirming the versatility and effectiveness of the tool. Additionally, by utilizing MLme's feature selection functionality, we successfully identified significant markers for CD8+ naive (BACH2), CD16+ (CD16), and CD14+ (VCAN) cell populations.
    Conclusion: MLme serves as a valuable resource for leveraging ML to facilitate insightful data analysis and enhance research outcomes, while alleviating concerns related to complex coding scripts. The source code and a detailed tutorial for MLme are available at https://github.com/FunctionalUrology/MLme.
    MeSH term(s) Humans ; Data Analysis ; Machine Learning ; Research Personnel ; Software
    Language English
    Publishing date 2024-01-11
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2708999-X
    ISSN 2047-217X ; 2047-217X
    ISSN (online) 2047-217X
    ISSN 2047-217X
    DOI 10.1093/gigascience/giad111
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Machine Learning Made Easy (MLme): A Comprehensive Toolkit for Machine Learning-Driven Data Analysis.

    Akshay, Akshay / Katoch, Mitali / Shekarchizadeh, Navid / Abedi, Masoud / Sharma, Ankush / Burkhard, Fiona C / Adam, Rosalyn M / Monastyrskaya, Katia / Gheinani, Ali Hashemi

    bioRxiv : the preprint server for biology

    2023  

    Abstract: Background: Machine learning (ML) has emerged as a vital asset for researchers to analyze and extract valuable information from complex datasets. However, developing an effective and robust ML pipeline can present a real challenge, demanding ... ...

    Abstract Background: Machine learning (ML) has emerged as a vital asset for researchers to analyze and extract valuable information from complex datasets. However, developing an effective and robust ML pipeline can present a real challenge, demanding considerable time and effort, thereby impeding research progress. Existing tools in this landscape require a profound understanding of ML principles and programming skills. Furthermore, users are required to engage in the comprehensive configuration of their ML pipeline to obtain optimal performance.
    Results: To address these challenges, we have developed a novel tool called
    Conclusion: MLme serves as a valuable resource for leveraging machine learning (ML) to facilitate insightful data analysis and enhance research outcomes, while alleviating concerns related to complex coding scripts. The source code and a detailed tutorial for MLme are available at https://github.com/FunctionalUrology/MLme.
    Language English
    Publishing date 2023-07-04
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.07.04.546825
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Correction to: The specific DNA methylation landscape in focal cortical dysplasia ILAE type 3D.

    Wang, Dan-Dan / Katoch, Mitali / Jabari, Samir / Blumcke, Ingmar / Blumenthal, David B / Lu, De-Hong / Coras, Roland / Wang, Yu-Jiao / Shi, Jie / Zhou, Wen-Jing / Kobow, Katja / Piao, Yue-Shan

    Acta neuropathologica communications

    2024  Volume 12, Issue 1, Page(s) 49

    Language English
    Publishing date 2024-03-29
    Publishing country England
    Document type Published Erratum
    ZDB-ID 2715589-4
    ISSN 2051-5960 ; 2051-5960
    ISSN (online) 2051-5960
    ISSN 2051-5960
    DOI 10.1186/s40478-024-01752-9
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: SpheroScan: A User-Friendly Deep Learning Tool for Spheroid Image Analysis.

    Akshay, Akshay / Katoch, Mitali / Abedi, Masoud / Besic, Mustafa / Shekarchizadeh, Navid / Burkhard, Fiona C / Bigger-Allen, Alex / Adam, Rosalyn M / Monastyrskaya, Katia / Gheinani, Ali Hashemi

    bioRxiv : the preprint server for biology

    2023  

    Abstract: Background: In recent years, three-dimensional (3D) spheroid models have become increasingly popular in scientific research as they provide a more physiologically relevant microenvironment that mimics in vivo conditions. The use of 3D spheroid assays ... ...

    Abstract Background: In recent years, three-dimensional (3D) spheroid models have become increasingly popular in scientific research as they provide a more physiologically relevant microenvironment that mimics in vivo conditions. The use of 3D spheroid assays has proven to be advantageous as it offers a better understanding of the cellular behavior, drug efficacy, and toxicity as compared to traditional two-dimensional cell culture methods. However, the use of 3D spheroid assays is impeded by the absence of automated and user-friendly tools for spheroid image analysis, which adversely affects the reproducibility and throughput of these assays.
    Results: To address these issues, we have developed a fully automated, web-based tool called SpheroScan, which uses the deep learning framework called Mask Regions with Convolutional Neural Networks (R-CNN) for image detection and segmentation. To develop a deep learning model that could be applied to spheroid images from a range of experimental conditions, we trained the model using spheroid images captured using IncuCyte Live-Cell Analysis System and a conventional microscope. Performance evaluation of the trained model using validation and test datasets shows promising results.
    Conclusion: SpheroScan allows for easy analysis of large numbers of images and provides interactive visualization features for a more in-depth understanding of the data. Our tool represents a significant advancement in the analysis of spheroid images and will facilitate the widespread adoption of 3D spheroid models in scientific research. The source code and a detailed tutorial for SpheroScan are available at https://github.com/FunctionalUrology/SpheroScan.
    Language English
    Publishing date 2023-06-28
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2023.06.28.533479
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  5. Article ; Online: The specific DNA methylation landscape in focal cortical dysplasia ILAE type 3D.

    Wang, Dan-Dan / Katoch, Mitali / Jabari, Samir / Blumcke, Ingmar / Blumenthal, David B / Lu, De-Hong / Coras, Roland / Wang, Yu-Jiao / Shi, Jie / Zhou, Wen-Jing / Kobow, Katja / Piao, Yue-Shan

    Acta neuropathologica communications

    2023  Volume 11, Issue 1, Page(s) 129

    Abstract: Focal Cortical Dysplasia (FCD) is a frequent cause of drug-resistant focal epilepsy in children and young adults. The international FCD classifications of 2011 and 2022 have identified several clinico-pathological subtypes, either occurring isolated, i.e. ...

    Abstract Focal Cortical Dysplasia (FCD) is a frequent cause of drug-resistant focal epilepsy in children and young adults. The international FCD classifications of 2011 and 2022 have identified several clinico-pathological subtypes, either occurring isolated, i.e., FCD ILAE Type 1 or 2, or in association with a principal cortical lesion, i.e., FCD Type 3. Here, we addressed the DNA methylation signature of a previously described new subtype of FCD 3D occurring in the occipital lobe of very young children and microscopically defined by neuronal cell loss in cortical layer 4. We studied the DNA methylation profile using 850 K BeadChip arrays in a retrospective cohort of 104 patients with FCD 1 A, 2 A, 2B, 3D, TLE without FCD, and 16 postmortem specimens without neurological disorders as controls, operated in China or Germany. DNA was extracted from formalin-fixed paraffin-embedded tissue blocks with microscopically confirmed lesions, and DNA methylation profiles were bioinformatically analyzed with a recently developed deep learning algorithm. Our results revealed a distinct position of FCD 3D in the DNA methylation map of common FCD subtypes, also different from non-FCD epilepsy surgery controls or non-epileptic postmortem controls. Within the FCD 3D cohort, the DNA methylation signature separated three histopathology subtypes, i.e., glial scarring around porencephalic cysts, loss of layer 4, and Rasmussen encephalitis. Differential methylation in FCD 3D with loss of layer 4 mapped explicitly to biological pathways related to neurodegeneration, biogenesis of the extracellular matrix (ECM) components, axon guidance, and regulation of the actin cytoskeleton. Our data suggest that DNA methylation signatures in cortical malformations are not only of diagnostic value but also phenotypically relevant, providing the molecular underpinnings of structural and histopathological features associated with epilepsy. Further studies will be necessary to confirm these results and clarify their functional relevance and epileptogenic potential in these difficult-to-treat children.
    MeSH term(s) Child ; Young Adult ; Humans ; Child, Preschool ; Retrospective Studies ; Focal Cortical Dysplasia ; Malformations of Cortical Development/diagnostic imaging ; Malformations of Cortical Development/genetics ; DNA Methylation ; Epilepsy/genetics ; Drug Resistant Epilepsy/pathology ; Magnetic Resonance Imaging
    Language English
    Publishing date 2023-08-09
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2715589-4
    ISSN 2051-5960 ; 2051-5960
    ISSN (online) 2051-5960
    ISSN 2051-5960
    DOI 10.1186/s40478-023-01618-6
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: SpheroScan: a user-friendly deep learning tool for spheroid image analysis.

    Akshay, Akshay / Katoch, Mitali / Abedi, Masoud / Shekarchizadeh, Navid / Besic, Mustafa / Burkhard, Fiona C / Bigger-Allen, Alex / Adam, Rosalyn M / Monastyrskaya, Katia / Gheinani, Ali Hashemi

    GigaScience

    2023  Volume 12

    Abstract: Background: In recent years, 3-dimensional (3D) spheroid models have become increasingly popular in scientific research as they provide a more physiologically relevant microenvironment that mimics in vivo conditions. The use of 3D spheroid assays has ... ...

    Abstract Background: In recent years, 3-dimensional (3D) spheroid models have become increasingly popular in scientific research as they provide a more physiologically relevant microenvironment that mimics in vivo conditions. The use of 3D spheroid assays has proven to be advantageous as it offers a better understanding of the cellular behavior, drug efficacy, and toxicity as compared to traditional 2-dimensional cell culture methods. However, the use of 3D spheroid assays is impeded by the absence of automated and user-friendly tools for spheroid image analysis, which adversely affects the reproducibility and throughput of these assays.
    Results: To address these issues, we have developed a fully automated, web-based tool called SpheroScan, which uses the deep learning framework called Mask Regions with Convolutional Neural Networks (R-CNN) for image detection and segmentation. To develop a deep learning model that could be applied to spheroid images from a range of experimental conditions, we trained the model using spheroid images captured using IncuCyte Live-Cell Analysis System and a conventional microscope. Performance evaluation of the trained model using validation and test datasets shows promising results.
    Conclusion: SpheroScan allows for easy analysis of large numbers of images and provides interactive visualization features for a more in-depth understanding of the data. Our tool represents a significant advancement in the analysis of spheroid images and will facilitate the widespread adoption of 3D spheroid models in scientific research. The source code and a detailed tutorial for SpheroScan are available at https://github.com/FunctionalUrology/SpheroScan.
    MeSH term(s) Deep Learning ; Reproducibility of Results ; Image Processing, Computer-Assisted/methods ; Neural Networks, Computer ; Software
    Language English
    Publishing date 2023-10-27
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
    ZDB-ID 2708999-X
    ISSN 2047-217X ; 2047-217X
    ISSN (online) 2047-217X
    ISSN 2047-217X
    DOI 10.1093/gigascience/giad082
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: MLcps: machine learning cumulative performance score for classification problems.

    Akshay, Akshay / Abedi, Masoud / Shekarchizadeh, Navid / Burkhard, Fiona C / Katoch, Mitali / Bigger-Allen, Alex / Adam, Rosalyn M / Monastyrskaya, Katia / Gheinani, Ali Hashemi

    GigaScience

    2023  Volume 12

    Abstract: Background: Assessing the performance of machine learning (ML) models requires careful consideration of the evaluation metrics used. It is often necessary to utilize multiple metrics to gain a comprehensive understanding of a trained model's performance, ...

    Abstract Background: Assessing the performance of machine learning (ML) models requires careful consideration of the evaluation metrics used. It is often necessary to utilize multiple metrics to gain a comprehensive understanding of a trained model's performance, as each metric focuses on a specific aspect. However, comparing the scores of these individual metrics for each model to determine the best-performing model can be time-consuming and susceptible to subjective user preferences, potentially introducing bias.
    Results: We propose the Machine Learning Cumulative Performance Score (MLcps), a novel evaluation metric for classification problems. MLcps integrates several precomputed evaluation metrics into a unified score, enabling a comprehensive assessment of the trained model's strengths and weaknesses. We tested MLcps on 4 publicly available datasets, and the results demonstrate that MLcps provides a holistic evaluation of the model's robustness, ensuring a thorough understanding of its overall performance.
    Conclusions: By utilizing MLcps, researchers and practitioners no longer need to individually examine and compare multiple metrics to identify the best-performing models. Instead, they can rely on a single MLcps value to assess the overall performance of their ML models. This streamlined evaluation process saves valuable time and effort, enhancing the efficiency of model evaluation. MLcps is available as a Python package at https://pypi.org/project/MLcps/.
    MeSH term(s) Machine Learning ; Benchmarking
    Language English
    Publishing date 2023-12-13
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2708999-X
    ISSN 2047-217X ; 2047-217X
    ISSN (online) 2047-217X
    ISSN 2047-217X
    DOI 10.1093/gigascience/giad108
    Database MEDical Literature Analysis and Retrieval System OnLINE

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