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Using autoencoders as a weight initialization method on deep neural networks for disease detection.
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- Author(s): Ferreira MF;Ferreira MF;Ferreira MF; Camacho R; Camacho R; Camacho R; Teixeira LF; Teixeira LF; Teixeira LF
- Source:
BMC medical informatics and decision making [BMC Med Inform Decis Mak] 2020 Aug 20; Vol. 20 (Suppl 5), pp. 141. Date of Electronic Publication: 2020 Aug 20.- Publication Type:
Journal Article; Research Support, Non-U.S. Gov't- Language:
English - Source:
- Additional Information
- Source: Publisher: BioMed Central Country of Publication: England NLM ID: 101088682 Publication Model: Electronic Cited Medium: Internet ISSN: 1472-6947 (Electronic) Linking ISSN: 14726947 NLM ISO Abbreviation: BMC Med Inform Decis Mak Subsets: MEDLINE
- Publication Information: Original Publication: London : BioMed Central, [2001-
- Subject Terms:
- Abstract: Background: As of today, cancer is still one of the most prevalent and high-mortality diseases, summing more than 9 million deaths in 2018. This has motivated researchers to study the application of machine learning-based solutions for cancer detection to accelerate its diagnosis and help its prevention. Among several approaches, one is to automatically classify tumor samples through their gene expression analysis.
Methods: In this work, we aim to distinguish five different types of cancer through RNA-Seq datasets: thyroid, skin, stomach, breast, and lung. To do so, we have adopted a previously described methodology, with which we compare the performance of 3 different autoencoders (AEs) used as a deep neural network weight initialization technique. Our experiments consist in assessing two different approaches when training the classification model - fixing the weights after pre-training the AEs, or allowing fine-tuning of the entire network - and two different strategies for embedding the AEs into the classification network, namely by only importing the encoding layers, or by inserting the complete AE. We then study how varying the number of layers in the first strategy, the AEs latent vector dimension, and the imputation technique in the data preprocessing step impacts the network's overall classification performance. Finally, with the goal of assessing how well does this pipeline generalize, we apply the same methodology to two additional datasets that include features extracted from images of malaria thin blood smears, and breast masses cell nuclei. We also discard the possibility of overfitting by using held-out test sets in the images datasets.
Results: The methodology attained good overall results for both RNA-Seq and image extracted data. We outperformed the established baseline for all the considered datasets, achieving an average F1 score of 99.03, 89.95, and 98.84 and an MCC of 0.99, 0.84, and 0.98, for the RNA-Seq (when detecting thyroid cancer), the Malaria, and the Wisconsin Breast Cancer data, respectively.
Conclusions: We observed that the approach of fine-tuning the weights of the top layers imported from the AE reached higher results, for all the presented experiences, and all the considered datasets. We outperformed all the previous reported results when comparing to the established baselines. - References: Bioinformatics. 2020 Mar 1;36(5):1360-1366. (PMID: 31603465)
Nat Commun. 2019 Jan 23;10(1):390. (PMID: 30674886)
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Sensors (Basel). 2017 Sep 21;17(10):. (PMID: 28934170)
Comput Methods Programs Biomed. 2018 Nov;166:99-105. (PMID: 30415723)
Comput Struct Biotechnol J. 2014 Nov 15;13:8-17. (PMID: 25750696)
Oncogenesis. 2019 Aug 16;8(9):44. (PMID: 31420533)
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BMC Genomics. 2017 Nov 17;18(Suppl 9):845. (PMID: 29219072)
Sci Rep. 2019 Nov 21;9(1):17256. (PMID: 31754222) - Contributed Indexing: Keywords: Autoencoders; Cancer; Classification; Deep learning; Gene expression analysis
- Publication Date: Date Created: 20200822 Date Completed: 20210210 Latest Revision: 20210210
- Publication Date: 20240105
- Accession Number: PMC7439655
- Accession Number: 10.1186/s12911-020-01150-w
- Accession Number: 32819347
- Source:
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