Avoiding Machine Learning Becoming Pseudoscience in Biomedical Research

Meredita Susanty, Ira Puspasari, Nilam Fitriah, Dimitri Mahayana, Tati Erawati Latifah Rajab, Hasballah Zakaria, Agung Wahyu Setiawan, Rukman Hertadi

Abstract


The use of machine learning harbours the promise of more accurate, unbiased future predictions than human beings on their own can ever be capable of. However, because existing data sets are always utilized, these calculations are extrapolations of the past and serve to reproduce prejudices embedded in the data. In turn, machine learning prediction result raises ethical and moral dilemmas. As mirrors of society, algorithms show the status quo, reinforce errors, and are subject to targeted influences – for good and the bad. This phenomenon makes machine learning viewed as pseudoscience. Besides the limitations, injustices, and oracle-like nature of these technologies, there are also questions about the nature of the opportunities and possibilities they offer. This article aims to discuss whether machine learning in biomedical research falls into pseudoscience based on Popper and Kuhn's perspective and four theories of truth using three study cases. The discussion result explains several conditions that must be fulfilled so that machine learning in biomedical does not fall into pseudoscience

Keywords


deep learning; philosophy; pseudoscience; biomedical

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References


Alquraishi, M. (n.d.). End-to-end Differentiable Learning of Protein Structure. https://doi.org/10.1101/265231

AlQuraishi, M. (2018). End-to-end differentiable learning of protein structure. In bioRxiv (p. 265231). bioRxiv. https://doi.org/10.1101/265231

AlQuraishi, M. (2021). Machine learning in protein structure prediction. Current Opinion in Chemical Biology, 65, 1–8. https://doi.org/10.1016/j.cbpa.2021.04.005

Anusuya, M. A., & Katti, S. K. (2011). Front end analysis of speech recognition: A review. In International Journal of Speech Technology (Vol. 14, Issue 2). https://doi.org/10.1007/s10772-010-9088-7

Beritelli, F., Capizzi, G., Lo Sciuto, G., Napoli, C., & Scaglione, F. (2018). Automatic heart activity diagnosis based on Gram polynomials and probabilistic neural networks. Biomedical Engineering

Letters, 8(1), 85. https://doi.org/10.1007/S13534-017-0046-Z

Billah, M., & Waheed, S. (2018). Gastrointestinal polyp detection in endoscopic images using an improved feature extraction method. Biomedical Engineering Letters, 8(1), 69. https://doi.org/10.1007/S13534-017-0048-X

Bishop, C. M. (2006). Pattern Recognition and Machine Learning (Information Science and Statistics): .: : Amazon.com: Books. Springer. https://www.amazon.com/Pattern-Recognition-Learning-Information-Statistics/dp/0387310738

Bocquelet, F., Hueber, T., Girin, L., Chabardès, S., & Yvert, B. (2016). Key considerations in designing a speech brain-computer interface. Journal of Physiology-Paris, 110(4), 392–401. https://doi.org/10.1016/j.jphysparis.2017.07.002

Bolland, D. J., Koohy, H., Wood, A. L., Matheson, L. S., Krueger, F., Stubbington, M. J. T., Baizan-Edge, A., Chovanec, P., Stubbs, B. A., Tabbada, K., Andrews, S. R., Spivakov, M., & Corcoran, A. E. (2016). Two Mutually Exclusive Local Chromatin States Drive Efficient V(D)J Recombination. Cell Reports, 15(11), 2475–2487. https://doi.org/10.1016/J.CELREP.2016.05.020

Chang, E. F., Raygor, K. P., & Berger, M. S. (2015). Contemporary model of language organization: an overview for neurosurgeons. Journal of Neurosurgery, 122(2), 250–261. https://doi.org/10.3171/2014.10.JNS132647

Chen, E. H., Shofer, F. S., Dean, A. J., Hollander, J. E., Baxt, W. G., Robey, J. L., Sease, K. L., & Mills, A. M. (2008). Gender disparity in analgesic treatment of emergency department patients with acute abdominal pain. Academic Emergency Medicine : Official Journal of the Society for Academic Emergency Medicine, 15(5), 414–418. https://doi.org/10.1111/J.1553-2712.2008.00100.X

Cooney, C., Folli, R., & Coyle, D. (2019). Optimizing Layers Improves CNN Generalization and Transfer Learning for Imagined Speech Decoding from EEG. 2019 IEEE International Conference on Systems, Man and Cybernetics (SMC), 1311–1316. https://doi.org/10.1109/SMC.2019.8914246

Erickson, B. (2003). Heart sounds and murmurs across the lifespan (4th ed.). Mosby.

Firuzbakht, F., Fallah, A., Rashidi, S., & Khoshnood, E. R. (2018). Abnormal Heart Sound Diagnosis Based on Phonocardiogram Signal Processing. 26th Iranian Conference on Electrical Engineering, ICEE 2018, 1450–1455. https://doi.org/10.1109/ICEE.2018.8472410

FS. (2021). Karl Popper on The Line Between Science and Pseudoscience. In Farnam Street Media Inc. https://fs.blog/2016/01/karl-popper-on-science-pseudoscience/

García-Salinas, J. S., Villaseñor-Pineda, L., Reyes-García, C. A., & Torres-García, A. A. (2019). Transfer learning in imagined speech EEG-based BCIs. Biomedical Signal Processing and Control, 50, 151–157. https://doi.org/10.1016/j.bspc.2019.01.006

Golkov, V., Skwark, M. J., Golkov, A., Dosovitskiy, A., Brox, T., Meiler, J., & Cremers, D. (n.d.). Protein contact prediction from amino acid co-evolution using convolutional networks for graph-valued images. Retrieved November 8, 2021, from http://hmmer.org

Ingraham, J., Riesselman, A., Sander, C., Marks, D., & School, H. M. (2018). Learning Protein Structure With A Differentiable Simulator.

Iqbal, S., Khan, M. U. G., Saba, T., & Rehman, A. (2018). Computer-assisted brain tumor type discrimination using magnetic resonance imaging features. Biomedical Engineering Letters, 8(1), 5. https://doi.org/10.1007/S13534-017-0050-3

Jon Christian. (2019). Statistician: Machine Learning Is Causing A “Crisis in Science.” https://futurism.com/neoscope/machine-learning-crisis-science

Jones, D. T., & Kandathil, S. M. (2018). High precision in protein contact prediction using fully convolutional neural networks and minimal sequence features. Bioinformatics, 34(19), 3308–3315. https://doi.org/10.1093/bioinformatics/bty341

Jones, D. T., Singh, T., Kosciolek, T., & Tetchner, S. (2015). MetaPSICOV: combining coevolution methods for accurate prediction of contacts and long range hydrogen bonding in proteins. Bioinformatics (Oxford, England), 31(7), 999–1006. https://doi.org/10.1093/BIOINFORMATICS/BTU791

Jones, G. E. (1981). Kuhn, Popper, and Theory Comparison. Dialectica, 35(4), 389–397. https://doi.org/10.1111/j.1746-8361.1981.tb00791.x

Jonic, S., & Vénien-Bryan, C. (2009). Protein structure determination by electron cryo-microscopy. Current Opinion in Pharmacology, 9(5), 636–642. https://doi.org/10.1016/J.COPH.2009.04.006

Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., Bridgland, A., Meyer, C., Kohl, S. A. A., Ballard, A. J., Cowie, A.,

Romera-Paredes, B., Nikolov, S., Jain, R., Adler, J., … Hassabis, D. (2021). Highly accurate protein structure prediction with AlphaFold. Nature. https://doi.org/10.1038/s41586-021-03819-2

Krishna, G., Tran, C., Yu, J., & Tewfik, A. H. (2019). Speech Recognition with No Speech or with Noisy Speech. ICASSP 2019 - 2019 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP), 1090–1094. https://doi.org/10.1109/ICASSP.2019.8683453

Larrazabal, A. J., Nieto, N., Peterson, V., Milone, D. H., & Ferrante, E. (2020). Gender imbalance in medical imaging datasets produces biased classifiers for computer-aided diagnosis. Proceedings of the National Academy of Sciences, 117(23).

Ledford, H. (2019). Millions of black people affected by racial bias in health-care algorithms. Nature, 574(7780), 608–609. https://doi.org/10.1038/D41586-019-03228-6

Liu, Y., Palmedo, P., Ye, Q., Berger, B., & Peng, J. (2018). Enhancing Evolutionary Couplings with Deep Convolutional Neural Networks. Cell Systems, 6(1), 65-74.e3. https://doi.org/10.1016/j.cels.2017.11.014

Lyratzopoulos, G., Abel, G. A., McPhail, S., Neal, R. D., & Rubin, G. P. (2013). Gender inequalities in the promptness of diagnosis of bladder and renal cancer after symptomatic presentation: evidence from secondary analysis of an English primary care audit survey. BMJ

Open, 3(6), e002861. https://doi.org/10.1136/BMJOPEN-2013-002861

Madabhushi, A., & Lee, G. (2016). Image analysis and machine learning in digital pathology: Challenges and opportunities. Medical Image Analysis, 33, 170–175. https://doi.org/10.1016/J.MEDIA.2016.06.037

Mansour, R. F. (2018). Deep-learning-based automatic computer-aided diagnosis system for diabetic retinopathy. Biomedical Engineering Letters, 8(1), 41. https://doi.org/10.1007/S13534-017-0047-Y

Markwick, P. R. L., Malliavin, T., & Nilges, M. (2008). Structural Biology by NMR: Structure, Dynamics, and Interactions. PLOS Computational Biology, 4(9), e1000168. https://doi.org/10.1371/JOURNAL.PCBI.1000168

Maya Dusenbery. (2018, May 29). “Everybody was telling me there was nothing wrong” - BBC Future. https://www.bbc.com/future/article/20180523-how-gender-bias-affects-your-healthcare

Meghani, S. H., Byun, E., & Gallagher, R. M. (2012). Time to Take Stock: A Meta-Analysis and Systematic Review of Analgesic Treatment Disparities for Pain in the United States. Pain Medicine, 13(2), 150–174. https://doi.org/10.1111/J.1526-4637.2011.01310.X/2/PME_1310_F8IK.JPEG

Mitchell, T. M. (1997). Machine Learning (1st ed.). McGraw-Hill Education.

Nguyen, C. H., Karavas, G. K., & Artemiadis, P. (2018). Inferring imagined speech using EEG signals: a new approach using Riemannian manifold features. Journal of Neural Engineering, 15(1), 16002. https://doi.org/10.1088/1741-2552/aa8235

Ofer, D., Brandes, N., & Linial, M. (2021). The language of proteins: NLP, machine learning & protein sequences. In Computational and Structural Biotechnology Journal (Vol. 19, pp. 1750–1758). Elsevier B.V. https://doi.org/10.1016/j.csbj.2021.03.022

Onaral, B., & Cohen, A. (2006). Biomedical Signals. In J. D. Bronzino (Ed.), Medical Devices and Systems (3rd ed., pp. 1–22). CRC Press. https://doi.org/10.1201/9781420003864.sec1

Panch, T., Mattie, H., & Atun, R. (2019). Artificial intelligence and algorithmic bias: implications for health systems. Journal of Global Health, 9(2). https://doi.org/10.7189/JOGH.09.020318

Panch, T., Mattie, H., & Celi, L. A. (2019). The “inconvenient truth” about AI in healthcare. Npj Digital Medicine 2019 2:1, 2(1), 1–3. https://doi.org/10.1038/s41746-019-0155-4

Parhi, M., & Tewfik, A. H. (2021). Classifying imaginary vowels from frontal lobe EEG via deep learning. European Signal Processing Conference, 2021-January, 1195–1199. https://doi.org/10.23919/EUSIPCO47968.2020.9287599

Park, C., Took, C. C., & Seong, J. K. (2018). Machine learning in biomedical engineering. Biomedical Engineering Letters 2018 8:1, 8(1), 1–3. https://doi.org/10.1007/S13534-018-0058-3

Pelletier, R., Humphries, K. H., Shimony, A., Bacon, S. L., Lavoie, K. L., Rabi, D., Karp, I., Avgil Tsadok, M., & Pilote, L. (2014). Sex-related differences in access to care among patients with premature acute coronary syndrome. CMAJ, 186(7), 497–504. https://doi.org/10.1503/CMAJ.131450/-/DC1

Popper, K. R. (1963). Conjectures and Refutations. Routledge and Keagan Paul. https://eportfolios.macaulay.cuny.edu/liu10/files/2010/08/KPopper_Falsification.pdf

Potes, C., Parvaneh, S., Rahman, A., & Conroy, B. (2016). Ensemble of feature-based and deep learning-based classifiers for detection of abnormal heart sounds. Computing in Cardiology Conference, 621–

https://ieeexplore.ieee.org/document/7868819

Puspasari, I., Kusumawati, W. I., Oktarina, E. S., & Jusak, J. (2019). A New Heart Sound Signal Identification Approach Suitable for Smart Healthcare Systems. Proceedings of the 2019 2nd International Conference on Applied Engineering, ICAE 2019.

https://doi.org/10.1109/ICAE47758.2019.9221752

Ryan, M. J., & Frater, M. (2002). Communications and Information Systems. Argos Press.

Saha, P., & Fels, S. (2019). Hierarchical Deep Feature Learning for Decoding Imagined Speech from EEG. Proceedings of the AAAI Conference on Artificial Intelligence, 33, 10019–10020. https://doi.org/10.1609/aaai.v33i01.330110019

Schultz, T., Wand, M., Hueber, T., Krusienski, D. J., Herff, C., & Brumberg, J. S. (2017). Biosignal-Based Spoken Communication: A Survey. IEEE/ACM Transactions on Audio Speech and Language Processing, 25(12), 2257–2271. https://doi.org/10.1109/TASLP.2017.2752365

Senior, A. W., Evans, R., Jumper, J., Kirkpatrick, J., Sifre, L., Green, T.,

Qin, C., Žídek, A., Nelson, A. W. R., Bridgland, A., Penedones, H.,

Petersen, S., Simonyan, K., Crossan, S., Kohli, P., Jones, D. T., Silver,

D., Kavukcuoglu, K., & Hassabis, D. (2019). Protein structure prediction using multiple deep neural networks in the 13th Critical Assessment of Protein Structure Prediction (CASP13). Proteins: Structure, Function and Bioinformatics, 87(12), 1141–1148. https://doi.org/10.1002/prot.25834

Senior, A. W., Evans, R., Jumper, J., Kirkpatrick, J., Sifre, L., Green, T., Qin, C., Žídek, A., Nelson, A. W. R., Bridgland, A., Penedones, H.,

Petersen, S., Simonyan, K., Crossan, S., Kohli, P., Jones, D. T., Silver,

D., Kavukcuoglu, K., & Hassabis, D. (2020). Improved protein structure prediction using potentials from deep learning. Nature, 577(7792), 706–710. https://doi.org/10.1038/s41586-019-1923-7

Slabinski, L., Jaroszewski, L., Rodrigues, A. P. C., Rychlewski, L., Wilson, I. A., Lesley, S. A., & Godzik, A. (2007). The challenge of protein structure determination--lessons from structural genomics. Protein Science : A Publication of the Protein Society, 16(11), 2472–2482. https://doi.org/10.1110/PS.073037907

Thomas S . Kuhn. (1990). The Road since Structure. Proceedings of the Biennial Meeting of the Philosophy of Science Association, 2, 3–13.

Wang, S., Sun, S., Li, Z., Zhang, R., & Xu, J. (2017). Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model. PLOS Computational Biology, 13(1), e1005324. https://doi.org/10.1371/journal.pcbi.1005324

Wei, R., Zhang, X., Wang, J., & Dang, X. (2017). The research of sleep staging based on single-lead electrocardiogram and deep neural network. Biomedical Engineering Letters, 8(1), 87–93. https://doi.org/10.1007/S13534-017-0044-1

Xu, J. (2018). Distance-based Protein Folding Powered by Deep Learning. Proceedings of the National Academy of Sciences of the United States of America, 116(34), 16856–16865. http://arxiv.org/abs/1811.03481

Xu, J., McPartlon, M., & Li, J. (2020). Improved protein structure prediction by deep learning irrespective of co-evolution information. In bioRxiv. bioRxiv. https://doi.org/10.1101/2020.10.12.336859

Yang, J., Anishchenko, I., Park, H., Peng, Z., Ovchinnikov, S., & Baker, D. (2020). Improved protein structure prediction using predicted interresidue orientations. Proceedings of the National Academy of Sciences of the United States of America, 117(3), 1496–1503. https://doi.org/10.1073/PNAS.1914677117/-/DCSUPPLEMENTAL

Zemla, A. (2003). LGA: A method for finding 3D similarities in protein structures. Nucleic Acids Research, 31(13), 3370–3374. https://doi.org/10.1093/nar/gkg571




DOI: https://doi.org/10.31294/inf.v10i1.12787

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