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management pillar of Abu Dhabi\u2019s Advanced Technology Research Council (ATRC), via the ASPIRE Precision Medicine Research Institute Abu Dhabi","award":["24010902153"],"award-info":[{"award-number":["24010902153"]}]},{"name":"ASPIRE, the technology program management pillar of Abu Dhabi\u2019s Advanced Technology Research Council (ATRC), via the ASPIRE Precision Medicine Research Institute Abu Dhabi","award":["VRI-20\u201310"],"award-info":[{"award-number":["VRI-20\u201310"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Data"],"abstract":"<jats:p>Inflammatory bowel disease (IBD) is a chronic inflammatory condition of the gastrointestinal tract characterized by the deregulation of immuno-oncology markers. IBD includes ulcerative colitis and Crohn\u2019s disease. Chronic active inflammation is a risk factor for the development of colorectal cancer (CRC). This technical note describes a dataset of histological images of ulcerative colitis, CRC (adenocarcinoma), and colon control. The samples were stained with hematoxylin and eosin (H&amp;E), and immunohistochemically analyzed for LAIR1 and TOX2 markers. The methods used for collecting, processing, and analyzing scientific data, including this dataset, using convolutional neural networks (CNNs) and information about the dataset\u2019s use are also described. 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Med."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1038\/nature10209","article-title":"Genetics and pathogenesis of inflammatory bowel disease","volume":"474","author":"Khor","year":"2011","journal-title":"Nature"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"2131","DOI":"10.1093\/ecco-jcc\/jjab102","article-title":"Inflammatory Bowel Disease-Associated Colorectal Cancer: Translational Risks from Mechanisms to Medicines","volume":"15","author":"Porter","year":"2021","journal-title":"J. Crohn\u2019s Colitis"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"91","DOI":"10.3748\/wjg.v20.i1.91","article-title":"Inflammatory bowel disease: Pathogenesis","volume":"20","author":"Zhang","year":"2014","journal-title":"World J. Gastroenterol."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"1047","DOI":"10.1002\/ueg2.12319","article-title":"Environmental risk factors for inflammatory bowel disease","volume":"10","author":"Singh","year":"2022","journal-title":"United Eur. Gastroenterol. J."},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"Qiu, P., Ishimoto, T., Fu, L., Zhang, J., Zhang, Z., and Liu, Y. (2022). The Gut Microbiota in Inflammatory Bowel Disease. Front. Cell. Infect. Microbiol., 12.","DOI":"10.3389\/fcimb.2022.733992"},{"key":"ref_12","doi-asserted-by":"crossref","unstructured":"Jarmakiewicz-Czaja, S., Zielinska, M., Sokal, A., and Filip, R. (2022). Genetic and Epigenetic Etiology of Inflammatory Bowel Disease: An Update. 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J."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"n1554","DOI":"10.1136\/bmj.n1554","article-title":"Association of ultra-processed food intake with risk of inflammatory bowel disease: Prospective cohort study","volume":"374","author":"Narula","year":"2021","journal-title":"BMJ"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"458","DOI":"10.1016\/S2468-1253(23)00003-1","article-title":"The cost of inflammatory bowel disease in high-income settings: A Lancet Gastroenterology & Hepatology Commission","volume":"8","author":"Burisch","year":"2023","journal-title":"Lancet Gastroenterol. Hepatol."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"2211","DOI":"10.1016\/j.cgh.2022.06.030","article-title":"Global Hospitalization Trends for Crohn\u2019s Disease and Ulcerative Colitis in the 21st Century: A Systematic Review With Temporal Analyses","volume":"21","author":"Buie","year":"2023","journal-title":"Clin. Gastroenterol. Hepatol."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"612","DOI":"10.1002\/ueg2.12426","article-title":"Smoking and colorectal neoplasia in patients with inflammatory bowel disease: Dose-effect relationship","volume":"11","author":"Wijnands","year":"2023","journal-title":"United Eur. Gastroenterol. J."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"587","DOI":"10.1007\/s10620-020-06207-4","article-title":"Influence of Severe Vitamin D Deficiency on the Clinical Course of Inflammatory Bowel Disease","volume":"66","author":"Ham","year":"2021","journal-title":"Dig. Dis. Sci."},{"key":"ref_24","unstructured":"Kane, S.V. (2025). Definitions, Epidemiology, and Risk Factors for Inflammatory Bowel Disease. UpToDate, Wolters Kluwer. Available online: https:\/\/www.uptodate.com\/."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"1756","DOI":"10.1016\/S0140-6736(16)32126-2","article-title":"Ulcerative colitis","volume":"389","author":"Ungaro","year":"2017","journal-title":"Lancet"},{"key":"ref_26","doi-asserted-by":"crossref","unstructured":"Gomez-Bris, R., Saez, A., Herrero-Fernandez, B., Rius, C., Sanchez-Martinez, H., and Gonzalez-Granado, J.M. (2023). CD4 T-Cell Subsets and the Pathophysiology of Inflammatory Bowel Disease. Int. J. Mol. Sci., 24.","DOI":"10.3390\/ijms24032696"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"11795549241301358","DOI":"10.1177\/11795549241301358","article-title":"Th9 and Th17 Cells in Human Ulcerative Colitis-Associated Dysplastic Lesions","volume":"18","author":"Cui","year":"2024","journal-title":"Clin. Med. Insights Oncol."},{"key":"ref_28","doi-asserted-by":"crossref","unstructured":"Gerlach, K., Lechner, K., Popp, V., Offensperger, L., Zundler, S., Wiendl, M., Becker, E., Atreya, R., Rath, T., and Neurath, M.F. (2020). The JAK1\/3 inhibitor tofacitinib suppresses T cell homing and activation in chronic intestinal inflammation. J. Crohn\u2019s Colitis, online ahead of print.","DOI":"10.1093\/ecco-jcc\/jjaa162"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"591","DOI":"10.1053\/j.gastro.2020.04.074","article-title":"Single-Cell Analyses of Colon and Blood Reveal Distinct Immune Cell Signatures of Ulcerative Colitis and Crohn\u2019s Disease","volume":"159","author":"Mitsialis","year":"2020","journal-title":"Gastroenterology"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"1137","DOI":"10.1016\/j.immuni.2021.05.008","article-title":"Dysbiosis exacerbates colitis by promoting ubiquitination and accumulation of the innate immune adaptor STING in myeloid cells","volume":"54","author":"Humphries","year":"2021","journal-title":"Immunity"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"1137","DOI":"10.1097\/MIB.0000000000000750","article-title":"Current Understanding of Dysbiosis in Disease in Human and Animal Models","volume":"22","author":"DeGruttola","year":"2016","journal-title":"Inflamm. Bowel Dis."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"1625","DOI":"10.1056\/NEJM198712243172603","article-title":"Coated oral 5-aminosalicylic acid therapy for mildly to moderately active ulcerative colitis. A randomized study","volume":"317","author":"Schroeder","year":"1987","journal-title":"N. Engl. J. Med."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"5A","DOI":"10.1155\/2005\/269076","article-title":"Toward an integrated clinical, molecular and serological classification of inflammatory bowel disease: Report of a Working Party of the 2005 Montreal World Congress of Gastroenterology","volume":"19","author":"Silverberg","year":"2005","journal-title":"Can. J. Gastroenterol."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"1041","DOI":"10.1136\/bmj.2.4947.1041","article-title":"Cortisone in ulcerative colitis; final report on a therapeutic trial","volume":"2","author":"Truelove","year":"1955","journal-title":"Br. Med. J."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"404","DOI":"10.1136\/gut.47.3.404","article-title":"A reproducible grading scale for histological assessment of inflammation in ulcerative colitis","volume":"47","author":"Geboes","year":"2000","journal-title":"Gut"},{"key":"ref_36","first-page":"27","article-title":"Morphology of inflammatory bowel diseases (IBD)","volume":"58","author":"Fabian","year":"2022","journal-title":"Cesk Patol."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"317","DOI":"10.1111\/his.12263","article-title":"Ulcerative colitis or Crohn\u2019s disease? Pitfalls and problems","volume":"64","author":"Feakins","year":"2014","journal-title":"Histopathology"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"767","DOI":"10.1093\/ecco-jcc\/jjac178","article-title":"Beyond Neutrophils for Predicting Relapse and Remission in Ulcerative Colitis","volume":"17","author":"Shaffer","year":"2023","journal-title":"J. Crohn\u2019s Colitis"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"1099","DOI":"10.1053\/j.gastro.2007.08.001","article-title":"Histologic inflammation is a risk factor for progression to colorectal neoplasia in ulcerative colitis: A cohort study","volume":"133","author":"Gupta","year":"2007","journal-title":"Gastroenterology"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"951","DOI":"10.1001\/jama.2023.15389","article-title":"Ulcerative Colitis in Adults: A Review","volume":"330","author":"Gros","year":"2023","journal-title":"JAMA"},{"key":"ref_41","unstructured":"Kane, S.V. (2025). Management of Moderate to Severe Ulcerative Colitis in Adults. UpToDate, Wolters Kluwer. Available online: https:\/\/www.uptodate.com\/contents\/management-of-moderate-to-severe-ulcerative-colitis-in-adults."},{"key":"ref_42","unstructured":"Meyer, C., and Kane, S.V. (2025). Medical Management of Low-Risk Adult Patients with Mild to Moderate Ulcerative Colitis. UpToDate, Wolters Kluwer. Available online: https:\/\/www.uptodate.com\/contents\/medical-management-of-low-risk-adult-patients-with-mild-to-moderate-ulcerative-colitis."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"571","DOI":"10.1016\/S0140-6736(23)00966-2","article-title":"Ulcerative colitis","volume":"402","author":"Honap","year":"2023","journal-title":"Lancet"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"20406223241239168","DOI":"10.1177\/20406223241239168","article-title":"Patient preferences for active ulcerative colitis treatments and fecal microbiota transplantation","volume":"15","author":"Marshall","year":"2024","journal-title":"Ther. Adv. Chronic Dis."},{"key":"ref_45","unstructured":"Global Cancer Observatory, International Agency for Research on Cancer, and World Health Organization (2023, December 13). Available online: https:\/\/gco.iarc.fr\/."},{"key":"ref_46","unstructured":"Goldberg, R.M., and Seres, D. (2025). Epidemiology and Risk Factors for Colorectal Cancer. UpToDate, Wolters Kluwer. Available online: https:\/\/www.uptodate.com\/contents\/epidemiology-and-risk-factors-for-colorectal-cancer."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"998","DOI":"10.2174\/18735592MTEx9NTk2y","article-title":"Colorectal Cancer Epidemiology: Recent Trends and Impact on Outcomes","volume":"22","author":"Baidoun","year":"2021","journal-title":"Curr. Drug Targets"},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"1467","DOI":"10.1016\/S0140-6736(19)32319-0","article-title":"Colorectal cancer","volume":"394","author":"Dekker","year":"2019","journal-title":"Lancet"},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"262","DOI":"10.1016\/S2468-1253(21)00426-X","article-title":"The rising tide of early-onset colorectal cancer: A comprehensive review of epidemiology, clinical features, biology, risk factors, prevention, and early detection","volume":"7","author":"Patel","year":"2022","journal-title":"Lancet Gastroenterol. Hepatol."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"177","DOI":"10.1016\/j.giec.2021.12.001","article-title":"Cause, Epidemiology, and Histology of Polyps and Pathways to Colorectal Cancer","volume":"32","author":"Sullivan","year":"2022","journal-title":"Gastrointest. Endosc. Clin. N. Am."},{"key":"ref_51","doi-asserted-by":"crossref","unstructured":"Yokoyama, S., Watanabe, T., Fujita, Y., Matsumura, S., Ueda, K., Nagano, S., Kinoshita, I., Murakami, D., Tabata, H., and Tsuji, T. (2023). Histology of metastatic colorectal cancer in a lymph node. PLoS ONE, 18.","DOI":"10.1371\/journal.pone.0284536"},{"key":"ref_52","first-page":"259","article-title":"The Increasing Relevance of Tumour Histology in Determining Oncological Outcomes in Colorectal Cancer","volume":"11","author":"Nagtegaal","year":"2015","journal-title":"Curr. Color. Cancer Rep."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"125553","DOI":"10.1016\/j.eswa.2024.125553","article-title":"FocalNeXt: A ConvNeXt augmented FocalNet architecture for lung cancer classification from CT-scan images","volume":"261","author":"Gulsoy","year":"2025","journal-title":"Expert Syst. Appl."},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1007\/s00418-019-01783-7","article-title":"Quantitative pixel intensity- and color-based image analysis on minimally compressed files: Implications for whole-slide imaging","volume":"152","author":"Taatjes","year":"2019","journal-title":"Histochem. Cell Biol."},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1016\/j.compmedimag.2018.08.010","article-title":"Deep learning nuclei detection: A simple approach can deliver state-of-the-art results","volume":"70","author":"Hofener","year":"2018","journal-title":"Comput. Med. Imaging Graph."},{"key":"ref_56","unstructured":"MathWorks (2024, December 12). MATLAB for Artificial Intelligence. Design AI Models and AI-Driven Systems. Available online: https:\/\/www.mathworks.com\/."},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"21","DOI":"10.37934\/araset.50.1.2133","article-title":"Detecting and Classifying Household Insects in Iraq by using Transfer Learning Models","volume":"50","author":"Ewaeed","year":"2025","journal-title":"J. Adv. Res. Appl. Sci. Eng. Technol."},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"181","DOI":"10.1038\/s41586-024-07441-w","article-title":"A whole-slide foundation model for digital pathology from real-world data","volume":"630","author":"Xu","year":"2024","journal-title":"Nature"},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"102129","DOI":"10.1016\/j.cpcardiol.2023.102129","article-title":"Attention-UNet architectures with pretrained backbones for multi-class cardiac MR image segmentation","volume":"49","author":"Das","year":"2024","journal-title":"Curr. Probl. Cardiol."},{"key":"ref_60","doi-asserted-by":"crossref","unstructured":"Jiang, X., Hu, Z., Wang, S., and Zhang, Y. (2023). Deep Learning for Medical Image-Based Cancer Diagnosis. Cancers, 15.","DOI":"10.3390\/cancers15143608"},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"161592","DOI":"10.1016\/j.jpedsurg.2024.06.001","article-title":"Artificial Intelligence vs. Doctors: Diagnosing Necrotizing Enterocolitis on Abdominal Radiographs","volume":"59","author":"Weller","year":"2024","journal-title":"J. Pediatr. Surg."},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"6203","DOI":"10.3934\/mbe.2020328","article-title":"Brain tumor classification in MRI image using convolutional neural network","volume":"17","author":"Khan","year":"2020","journal-title":"Math. Biosci. Eng."},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"29322","DOI":"10.1109\/ACCESS.2022.3156894","article-title":"Medical Image Segmentation Using Transformer Networks","volume":"10","author":"Karimi","year":"2022","journal-title":"IEEE Access"},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"102559","DOI":"10.1016\/j.media.2022.102559","article-title":"Transformer-based unsupervised contrastive learning for histopathological image classification","volume":"81","author":"Wang","year":"2022","journal-title":"Med. Image Anal."},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"526","DOI":"10.1007\/s10278-022-00740-6","article-title":"ChimeraNet: U-Net for Hair Detection in Dermoscopic Skin Lesion Images","volume":"36","author":"Lama","year":"2023","journal-title":"J. Digit. Imaging"},{"key":"ref_66","unstructured":"(2024, December 12). TensorFlow. Available online: https:\/\/www.tensorflow.org\/."},{"key":"ref_67","unstructured":"(2024, December 12). TensorFlow Keras Basic Image Classification. Available online: https:\/\/www.tensorflow.org\/tutorials\/keras\/classification."},{"key":"ref_68","unstructured":"(2024, December 12). PyTorch, Get Started. Available online: https:\/\/pytorch.org\/."},{"key":"ref_69","unstructured":"(2024, December 12). ONNX, Open Neural Network Exchange. Available online: https:\/\/onnx.ai\/."},{"key":"ref_70","doi-asserted-by":"crossref","unstructured":"He, K., Zhang, X., Ren, S., and Sun, J. (2015). Deep Residual Learning for Image Recognition. arXiv.","DOI":"10.1109\/CVPR.2016.90"},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"223","DOI":"10.1186\/s12943-024-02140-6","article-title":"Artificial intelligence alphafold model for molecular biology and drug discovery: A machine-learning-driven informatics investigation","volume":"23","author":"Guo","year":"2024","journal-title":"Mol. Cancer"},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"e126","DOI":"10.1016\/S1470-2045(25)00008-7","article-title":"AI model using clinical images for genomic prediction and tailored treatment in patients with cancer","volume":"26","author":"Guo","year":"2025","journal-title":"Lancet Oncol."},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"1180","DOI":"10.1053\/j.gastro.2023.02.031","article-title":"Artificial Intelligence Enabled Histological Prediction of Remission or Activity and Clinical Outcomes in Ulcerative Colitis","volume":"164","author":"Iacucci","year":"2023","journal-title":"Gastroenterology"},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"100124","DOI":"10.1016\/j.modpat.2023.100124","article-title":"Artificial Intelligence Enables Quantitative Assessment of Ulcerative Colitis Histology","volume":"36","author":"Najdawi","year":"2023","journal-title":"Mod. Pathol."},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"1630","DOI":"10.1093\/ibd\/izae204","article-title":"Deployment of an Artificial Intelligence Histology Tool to Aid Qualitative Assessment of Histopathology Using the Nancy Histopathology Index in Ulcerative Colitis","volume":"31","author":"Rubin","year":"2024","journal-title":"Inflamm. Bowel Dis."},{"key":"ref_76","doi-asserted-by":"crossref","unstructured":"Selvaraju, R.R., Cogswell, M., Das, A., Vedantam, R., Parikh, D., and Batra, D. (2017, January 22\u201329). Grad-CAM: Visual Explanations from Deep Networks via Gradient-Based Localization. Proceedings of the IEEE International Conference on Computer Vision (ICCV), Venice, Italy.","DOI":"10.1109\/ICCV.2017.74"},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"D523","DOI":"10.1093\/nar\/gkac1052","article-title":"UniProt: The Universal Protein Knowledgebase in 2023","volume":"51","author":"UniProt","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"ref_78","doi-asserted-by":"crossref","first-page":"4520","DOI":"10.1038\/s41467-020-18298-8","article-title":"Collagen promotes anti-PD-1\/PD-L1 resistance in cancer through LAIR1-dependent CD8(+) T cell exhaustion","volume":"11","author":"Peng","year":"2020","journal-title":"Nat. Commun."},{"key":"ref_79","doi-asserted-by":"crossref","unstructured":"Van Laethem, F., Donaty, L., Tchernonog, E., Lacheretz-Szablewski, V., Russello, J., Buthiau, D., Almeras, M., Moreaux, J., and Bret, C. (2022). LAIR1, an ITIM-Containing Receptor Involved in Immune Disorders and in Hematological Neoplasms. Int. J. Mol. Sci., 23.","DOI":"10.3390\/ijms232416136"},{"key":"ref_80","doi-asserted-by":"crossref","first-page":"826","DOI":"10.1016\/j.immuni.2019.10.006","article-title":"The Transcription Factor Tox2 Drives T Follicular Helper Cell Development via Regulating Chromatin Accessibility","volume":"51","author":"Xu","year":"2019","journal-title":"Immunity"},{"key":"ref_81","doi-asserted-by":"crossref","unstructured":"Carreras, J., Roncador, G., and Hamoudi, R. (2024). Ulcerative Colitis, LAIR1 and TOX2 expression and Colorectal Cancer Deep Learning Image Classification Using Convolutional Neural Networks. Cancers, 16.","DOI":"10.20944\/preprints202411.0211.v1"},{"key":"ref_82","doi-asserted-by":"crossref","first-page":"595","DOI":"10.1111\/his.13106","article-title":"Clinicopathological characteristics and genomic profile of primary sinonasal tract diffuse large B cell lymphoma (DLBCL) reveals gain at 1q31 and RGS1 encoding protein; high RGS1 immunohistochemical expression associates with poor overall survival in DLBCL not otherwise specified (NOS)","volume":"70","author":"Carreras","year":"2017","journal-title":"Histopathology"},{"key":"ref_83","doi-asserted-by":"crossref","first-page":"334","DOI":"10.1111\/cas.15179","article-title":"High PTX3 expression is associated with a poor prognosis in diffuse large B-cell lymphoma","volume":"113","author":"Carreras","year":"2022","journal-title":"Cancer Sci."},{"key":"ref_84","doi-asserted-by":"crossref","first-page":"936","DOI":"10.1097\/PAS.0000000000001071","article-title":"Genomic Profile and Pathologic Features of Diffuse Large B-Cell Lymphoma Subtype of Methotrexate-associated Lymphoproliferative Disorder in Rheumatoid Arthritis Patients","volume":"42","author":"Carreras","year":"2018","journal-title":"Am. J. Surg. Pathol."},{"key":"ref_85","doi-asserted-by":"crossref","first-page":"18","DOI":"10.3390\/biomedinformatics1010003","article-title":"High Expression of Caspase-8 Associated with Improved Survival in Diffuse Large B-Cell Lymphoma: Machine Learning and Artificial Neural Networks Analyses","volume":"1","author":"Carreras","year":"2021","journal-title":"BioMedInformatics"},{"key":"ref_86","doi-asserted-by":"crossref","unstructured":"Carreras, J. (2024). Celiac Disease Deep Learning Image Classification Using Convolutional Neural Networks. J. Imaging, 10.","DOI":"10.3390\/jimaging10080200"},{"key":"ref_87","unstructured":"MathWorks (2024, July 28). Batch Normalization Layer. Available online: https:\/\/www.mathworks.com\/help\/deeplearning\/ref\/nnet.cnn.layer.batchnormalizationlayer.html."},{"key":"ref_88","doi-asserted-by":"crossref","first-page":"182","DOI":"10.3390\/hemato2020011","article-title":"Integrative Statistics, Machine Learning and Artificial Intelligence Neural Network Analysis Correlated CSF1R with the Prognosis of Diffuse Large B-Cell Lymphoma","volume":"2","author":"Carreras","year":"2021","journal-title":"Hemato"},{"key":"ref_89","doi-asserted-by":"crossref","first-page":"119","DOI":"10.3390\/hemato5020011","article-title":"Artificial Intelligence, Lymphoid Neoplasms, and Prediction of MYC, BCL2, and BCL6 Gene Expression Using a Pan-Cancer Panel in Diffuse Large B-Cell Lymphoma","volume":"5","author":"Carreras","year":"2024","journal-title":"Hemato"},{"key":"ref_90","doi-asserted-by":"crossref","first-page":"295","DOI":"10.3390\/biomedinformatics4010017","article-title":"Artificial Intelligence Analysis and Reverse Engineering of Molecular Subtypes of Diffuse Large B-Cell Lymphoma Using Gene Expression Data","volume":"4","author":"Carreras","year":"2024","journal-title":"BioMedInformatics"}],"container-title":["Data"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2306-5729\/10\/7\/99\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,9]],"date-time":"2025-10-09T17:57:52Z","timestamp":1760032672000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2306-5729\/10\/7\/99"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,6,24]]},"references-count":90,"journal-issue":{"issue":"7","published-online":{"date-parts":[[2025,7]]}},"alternative-id":["data10070099"],"URL":"https:\/\/doi.org\/10.3390\/data10070099","relation":{},"ISSN":["2306-5729"],"issn-type":[{"value":"2306-5729","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,6,24]]}}}