Abstract
The Alzheimer’s disease Drug Development Pipeline [1, 2] delivers updates on potential AD-treatment, as well as drug development ongoing in clinical trials. To create these reports, researchers manually extract information from several resources like ClinicalTrials.gov and drug manufacturer websites; however, some of these items require expert review, such as when predicting a drug’s Mechanism of Action (MOA). In this paper, we aim to assist researchers by predicting and suggesting a drug’s MOA using Machine Learning. We test Random Forest (RF), Logistic Regression (LR), Support Vector Machine (SVM), XGBoost, and Decision Tree (DT) models. The latter showing the most promising results, with 95% accuracy, 100% recall, and a 0.92 F1-score.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Cummings JL, Morstorf T, Zhong K (2014) Cummings, Jeffrey L\_Alzheimer’s\_drug development candidates failures\_2014, pp 1–7
Cummings J, Lee G, Ritter A, Sabbagh M, Zhong K (2020) Alzheimer’s disease drug development pipeline: 2020. Alzheimer Dement Transl Res Clin Interv 6(1):e12050
Sarker A, Gonzalez G (2015) Portable automatic text classification for adverse drug reaction detection via multi-corpus training. J Biomed Inform 53:196–207. http://dx.doi.org/10.1016/j.jbi.2014.11.002
AAlAbdulsalam AK, Garvin JH, Redd A, Carter ME, Sweeny C, Meystre SM (2018) Automated extraction and classification of cancer stage mentions from unstructured text fields in a central cancer registry. In: AMIA Joint summits on translational science proceedings. AMIA Joint Summits on Translational Science, vol 2017, pp 16–25
Chen VW, Ruiz BA, Hsieh MC, Wu XC, Ries LA, Lewis DR (2014) Analysis of stage and clinical/prognostic factors for lung cancer from SEER registries: AJCC staging and collaborative stage data collection system. Cancer 120(S23):3781–3792
Clinicaltrials.gov (2020) Information on clinical trials and human research studies. https://clinicaltrials.gov. Accessed 29 Oct 2020
Cummings J, Lee G, Ritter A, Sabbagh M, Zhong K (2019) Alzheimer’s disease drug development pipeline: 2019. Alzheimer Dement Transl Res Clin Interv 5:272–293. https://doi.org/10.1016/j.trci.2019.05.008
Bozorgi M (2018) Application of machine learning in cancer research
Butt L, Zuccon G, Nguyen A, Bergheim A, Grayson N, Butt L (2013) Classification of cancer-related death certificates using machine learning what this study adds, pp 292–299
Mujtaba G, Shuib L, Raj RG, Rajandram R, Shaikh K (2018) Prediction of cause of death from forensic autopsy reports using text classification techniques: a comparative study. J Forensic Legal Med 57:41–50.https://doi.org/10.1016/j.jflm.2017.07.001
Bodenreider O (2004) The Unified Medical Language System (UMLS): integrating biomedical terminology. Nucleic Acids Res 32(DATABASE):267–270
Yao L, Mao C, Luo Y (2019) Clinical text classification with rule-based features and knowledge-guided convolutional neural networks. BMC Med Inform Decis Mak 19(3)
MacRae J, Love T, Baker MG, Dowell A, Carnachan M, Stubbe M, McBain L (2015) Identifying influenza-like illness presentation from unstructured general practice clinical narrative using a text classifier rule-based expert system versus a clinical expert. BMC Med Inform Decis Mak 15(1):1–11
Wang Y, Sohn S, Liu S, Shen F, Wang L, Atkinson EJ, Amin S, Liu H (2019) A clinical text classification paradigm using weak supervision and deep representation. BMC Med Inform Decis Mak 19(1):1
Cummings J, Lee G, Ritter A, Zhong K (2018) Alzheimer’s disease drug development pipeline: 2018. Alzheimer Dement Transl Res Clin Interv 4(2018):195–214. https://doi.org/10.1016/j.trci.2018.03.009
Chawla NV, Bowyer KW, Hall LO, Kegelmeyer WP (2002) SMOTE: synthetic minority over-sampling technique. J Artif Intell Res 16:321–357
Trstenjak B, Mikac S, Donko D (2014) KNN with TF-IDF based framework for text categorization. Proc Eng 69:1356–1364
Podgorelec V, Kokol P, Stiglic B, Rozman I (2002) Decision trees: an overview and their use in medicine. J Med Syst 26(5):445–463
Chen T, Guestrin C (2016) Xgboost: a scalable tree boosting system. In: Proceedings of the 22nd ACM sigkdd international conference on knowledge discovery and data mining, pp 785–794
Breiman L (2001) Random forests. Mach Learn 45(1):5–32
Hand DJ, Adams NM (2014) Data Mining. Wiley StatsRef: Statistics Reference Online, pp 1–7
Fonseca Cacho JR (2019) Improving OCR post processing with machine learning tools
Rehurek R, Sojka P (2010) Software framework for topic modelling with large corpora. In: Proceedings of the LREC 2010 workshop on new challenges for NLP frameworks. ELRA, Valletta, Malta, May 2010, pp 45–50
Pedregosa F, Varoquaux G, Gramfort A, Michel V, Thirion B, Grisel O, Blondel M, Prettenhofer P, Weiss R, Dubourg V, Vanderplas J, Passos A, Cournapeau D, Brucher M, Perrot M, Duchesnay E (2011) Scikit-learn: Machine Learning in {P}ython. J Mach Learn Res 12:2825–2830
McKinney W, Others (2010) Data structures for statistical computing in python. In: Proceedings of the 9th Python in science conference, vol 445. Austin, TX, pp 51–56
Baboota R, Kaur H (2019) Predictive analysis and modelling football results using machine learning approach for english premier league. Int J Forecast 35(2):741–755
Acknowledgements
This material is based upon work supported by the National Science Foundation under Grant No. 1625677.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2022 The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd.
About this paper
Cite this paper
Kambar, M.E.Z.N., Nahed, P., Cacho, J.R.F., Lee, G., Cummings, J., Taghva, K. (2022). Clinical Text Classification of Alzheimer’s Drugs’ Mechanism of Action. In: Yang, XS., Sherratt, S., Dey, N., Joshi, A. (eds) Proceedings of Sixth International Congress on Information and Communication Technology. Lecture Notes in Networks and Systems, vol 235. Springer, Singapore. https://doi.org/10.1007/978-981-16-2377-6_48
Download citation
DOI: https://doi.org/10.1007/978-981-16-2377-6_48
Published:
Publisher Name: Springer, Singapore
Print ISBN: 978-981-16-2376-9
Online ISBN: 978-981-16-2377-6
eBook Packages: Intelligent Technologies and RoboticsIntelligent Technologies and Robotics (R0)