Deep Learning Models for Predicting Phenotypic Traits and Diseases from Omics Data
Why this work is in the frame
A frame that forgets how it found something cannot be audited. These are the routes that admitted this work.
Bibliographic record
Abstract
Computational analysis of high-throughput omics data, such as gene expressions, copy number alterations and DNA methylation (DNAm), has become popular in disease studies in recent decades because such analyses can be very helpful to predict whether a patient has certain disease or its subtypes. However, due to the high-dimensional nature of the data sets with hundreds of thousands of variables and very small number of samples, traditional machine learning approaches, such as support vector machines (SVMs) and random forests, have limitations to analyze these data efficiently. In this chapter, we reviewed the progress in applying deep learning algorithms to solve some biological questions. The focus is on potential software tools and public data sources for the tasks. Particularly, we show some case studies using deep neural network (DNN) models for classifying molecular subtypes of breast cancer and DNN-based regression models to account for interindividual variation in triglyceride concentrations measured at different visits of peripheral blood samples using DNAm profiles. We show that integration of multi-omics profiles into DNN-based learning methods could improve the prediction of the molecular subtypes of breast cancer. We also demonstrate the superiority of our proposed DNN models over the SVM model for predicting triglyceride concentrations.
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Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.000 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from it