Analysis and Estimation of Pathological Data and Findings with Deep Learning Methods

Year 2022, Volume: 7 Issue: 3, 175 - 187, 31.12.2022

Ahmet Anıl Şakır , Ali Hakan Işık , Özlem Özmen , Volkan İpek

https://doi.org/10.24880/maeuvfd.1121112

Abstract

As in human diseases, rapid diagnosis of animal diseases is of great importance. In order for the disease treatments to be carried out properly, the diagnosis must be of high accuracy, as well as the rapid diagnosis. In this study, the disease types in the data set consisting of the data examined between the years 2000-2020 belonging to the Department of Pathology of the Faculty of Veterinary Medicine of Burdur Mehmet Akif Ersoy University were estimated by using the decision tree classification model and the KNN classification model. Categories such as age, type, city, and gender in the data set were analyzed in graphics. For the estimation and analysis processes to give accurate results, the data set was corrected by going through some pre-processes and the missing data in the data set was completed. It is thought that the results obtained from the estimation and analysis will allow rapid and accurate diagnosis in animal disease diagnoses.

Keywords

Pathology, classification, decision tree, KNN, deep learning

Supporting Institution

Burdur Mehmet Akif Ersoy Üniversitesi Bilimsel Araştırma Projeleri Koordinatörlüğü

Project Number

0671-YL-20

Thanks

The present M.Sc. Thesis was supported by Burdur Mehmet Akif Ersoy University Scientific Research Projects Under the Project number of 0671-YL-20

References

• Abels, E., Pantanowitz, L., Aeffner, F., Zarella, M. D., van der Laak, J., Bui, M. M., Vemuri, V. N., Parwani, A. V., Gibbs, J., Agosto-Arroyo, E., Beck, A. H., Kozlowski, C. (2019). Computational pathology definitions, best practices, and recommendations for regulatory guidance: a white paper from the Digital Pathology Association. The Journal of Pathology, 249(3), 286-294. https://doi.org/10.1002/path.5331
• Barisoni, L., Gimpel, C., Kain, R., Laurinavicius, A., Bueno, G., Zeng, C., Liu, Z., Schaefer, F., Kretzler, M., Holzman, L. B., Hewitt, S. M. (2017). Digital pathology imaging as a novel platform for standardization and globalization of quantitative nephropathology. Clinical Kidney Journal, 10(2), 176-187. https://doi.org/10.1093/ckj/sfw129
• Bera, K., Schalper, K.A., Rimm, D.L., Velcheti, V., Madabhushi, A. (2019). Artificial intelligence in digital pathology - new tools for diagnosis and precision oncology. Nature Reviews Clinical Oncology, 16, 703-715. https://doi.org/10.1038/s41571-019-0252-y
• Bounsaythip, C., & Rinta-Runsala, E. (2001). Overview of Data Mining for Customer Behavior Modeling, Research Report TTE1-2001-18, VTT Information Technology.
• Nakhleh, R. E., & Volmar, K.E. (2015). Error Reduction and Prevention in Surgical Pathology (2nd Edition), Springer.
• Carlton, W. W., McGavin, M. D. (1995). Thomson’s Special Veterinary Pathology, Mosby-Yearbook, Inc., Missouri.
• Chang, H.Y., Jung, C.K., Woo, J.I., Lee, S., Cho, J., Kim, S.W., Kwak, T., Y. (2019). Artificial intelligence in pathology. Journal of Pathology and Translational Medicine, 53(1), 1-12. https://doi.org/10.4132/jptm.2018.12.16
• Cheville, N.F. (1999). Introduction to Veterinary Pathology, 2nd Ed. Iowa State University Pres.
• Emel G., & Taşkın Ç. (2005). Veri Madenciliğinde Karar Ağaçları ve Bir Satış Analizi Uygulaması. Eskişehir Osman Gazi Üniversitesi Sosyal Bilimler Dergisi, 6(2), 221-239.
• Euclidian Distance. (2021). Öklid Uzaklığı. Retrieved December 23, 2021, from https://tr.wikipedia.org/wiki/Öklid_uzaklığı
• Jones, T.C., & R.D. Hunt. (1993). Veterinary Pathology, Lea & Febiger, Philadelphia.
• Kahraman, M.M. (1996). Genel Patoloji Ders Notları, Uludağ Üniversitesi Veteriner Fakültesi.
• McCarty, J., Minsky, M.L., Rochester, N., Shannon, C.E. (2006). A proposal for the Dartmouth Summer Research Project on Artificial Intelligence. AI Magazine, 27(4), 12-14. https://doi.org/10.1609/aimag.v27i4.1904
• Mean Absolute Error. (2021). Mean Absolute Error. Retrieved December 25, 2021, from https://en.wikipedia.org/wiki/Mean_absolute_error
• Mean Squared Error. (2021). Mean Squared Error. Retrieved December 25, 2021, from https://en.wikipedia.org/wiki/Mean_squared_error
• Niazi, M. K. K., Parwani, A. V., Gürcan, M. N. (2019). Digital pathology and artificial intelligence. The Lancet Oncology, 20(5), e253-e261. https://doi.org/10.1016/S1470-2045(19)30154-8
• Numpy-a. (2021). NumPy. Retrieved December 20, 2021, from https://numpy.org
• Numpy-b. (2021). NumPy. Retrieved December 20, 2021, from https://tr.wikipedia.org/wiki/NumPy
• Özmen, Ö. (2006). Veteriner Genel Patoloji Ders Notları, Mehmet Akif Ersoy Üniversitesi Veteriner Fakültesi.
• Özmen, Ö. (2016). 2000-2015 Yılları Arasında Burdur’daki Rutin Patoloji Teşhisleri. VIII. Ulusal Veteriner Patoloji Kongresi, 1-3 Eylül 2016, Samsun.
• Özmen, Ö. (2021). Veteriner Fakültesi Öğrencilerinin Uygulamalı Patoloji Laboratuvar Eğitimleri ile Bilgi Düzeylerinin Arttırılması ve Çağdaş Yaklaşımlar ile Mesleğe Hazırlanması, Bilimsel Araştırma Projeleri Komisyonu, Mehmet Akif Ersoy Üniversitesi Veteriner Fakültesi.
• Pandas-a. (2021). pandas – Python Data Analysis Library. Retrieved December 21, 2021, from https://pandas.pydata.org
• Pandas-b. (2021). pandas: powerful Python data analysis toolkit. Retrieved December 21, 2021, from https://github.com/pandas-dev/pandas
• Pandas-c. (2021). Pandas. Retrieved December 21, 2021, from https://tr.wikipedia.org/wiki/Pandas
• Pandas-d. (2021). pandas.get_dummies. Retrieved December 23, 2021, from https://pandas.pydata.org/docs/reference/api/ pandas.get_dummies.html
• Root Mean Squared Error. (2021). Root Mean Squared Error. Retrieved December 25, 2021, from https://en.wikipedia.org/wiki/Root-mean-square_deviation
• Scikit Learn-a. (2021). sklearn.impute.SimpleImputer. Retrieved December 22, 2021, from, https://scikit-learn.org/stable/modules/generated/sklearn.impute.SimpleImputer.html
• Scikit Learn-b. (2021). sklearn.tree.DecisionTreeClassifier. Retrieved December 23, 2021, from https://scikit-learn.org/stable/modules/ generated/sklearn.tree.DecisionTreeClassifier.html
• Scikit Learn-c. (2021). sklearn.model_selection.train_test_split. Retrieved December 24, 2021, from https://scikit-learn.org/stable/modules/generated/sklearn.model_selection.train_test_split.html
• Scikit Learn-d. (2021). sklearn.metrics.accuracy_score. Retrieved December 26, 2021, from https://scikit-learn.org/stable/modules/generated/sklearn.metrics.accuracy_score.html
• Scikit Learn-e. (2021). sklearn.neighbors.KNeighborsClassifier. Retrieved December 24, 2021, from https://scikit-learn.org/stable/modules/generated/sklearn.neighbors.KNeighborsClassifier.html#sklearn.neighbors.KNeighborsClassifier
• Scikit Learn-f. (2021). Nearest Neighbors. Retrieved December 23, 2021, from https://scikit-learn.org/stable/modules/neighbors.html
• Scikit Learn-g. (2021). sklearn.metrics.mean_squared_error. Retrieved December 24, 2021, from https://scikit-learn.org/stable/modules/generated/sklearn.metrics.mean_squared_error.html
• Scikit Learn-h. (2021). sklearn.metrics.mean_absolute_error. Retrieved December 24, 2021, from https://scikit-learn.org/stable/modules/generated/sklearn.metrics.mean_absolute_error.html
• Slauson, D.O., Cooper, B.J. (1990). Mechanisms of Disease A Textbook of Comparative General Pathology, 2nd Ed., Williams & Wilkins.
• Sütcü C., & Aytekin Ç. (2018). Veri Bilimi, Paloma Yayınevi.
• Zorman, M., Vili, P., Kokol, P., Peterson, M., Sprogar, M., Ojstersek, M. (2001). Finding The Right Decision Tree’s Induction Strategy for a Hard Real World Problem, International Journal of Medical Informatics, 63(1-2), 109-121. https://doi.org/10.1016/S1386-5056(01)00176-9