iSOM-GSN: an integrative approach for transforming multi-omic data into gene similarity networks via self-organizing maps
Bibliographic record
Abstract
MOTIVATION: One of the main challenges in applying graph convolutional neural networks (CNNs) on gene-interaction data is the lack of understanding of the vector space to which they belong, and also the inherent difficulties involved in representing those interactions on a significantly lower dimension, viz Euclidean spaces. The challenge becomes more prevalent when dealing with various types of heterogeneous data. We introduce a systematic, generalized method, called iSOM-GSN, used to transform 'multi-omic' data with higher dimensions onto a 2D grid. Afterwards, we apply a CNN to predict disease states of various types. Based on the idea of Kohonen's self-organizing map, we generate a 2D grid for each sample for a given set of genes that represent a gene similarity network. RESULTS: We have tested the model to predict breast and prostate cancer using gene expression, DNA methylation and copy number alteration. Prediction accuracies in the 94-98% range were obtained for tumor stages of breast cancer and calculated Gleason scores of prostate cancer with just 14 input genes for both cases. The scheme not only outputs nearly perfect classification accuracy, but also provides an enhanced scheme for representation learning, visualization, dimensionality reduction and interpretation of multi-omic data. AVAILABILITY AND IMPLEMENTATION: The source code and sample data are available via a Github project at https://github.com/NaziaFatima/iSOM_GSN. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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How this classification was reachedexpand
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 | 0.001 | 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 itClassification
machine, unvalidatedMachine predicted; a candidate call from one teacher head, not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".