Cell type identification via convolutional neural networks and self-organizing maps on single-cell RNA-seq data
Bibliographic record
Abstract
Recent studies on using single-cell RNA sequencing (scRNA-seq) technology have been widely applied in biological studies such as drug discovery. Prior to in-depth investigations of the functionality of single cells for pathological goals, identification of cell types is an essential step that can be sped up using computational methods. Recently, supervised learning methods have been developed to automatically identify cell types. Due to the lack of sufficient annotated datasets, these methods have not been commonly used in scRNA-seq studies. Classification methods can simply take advantage of feature selection techniques to improve cell type prediction while identifying the most informative genes among a high number of genes in high-dimensional scRNA-seq datasets. In this regard, we introduce a combination of two powerful techniques for representation learning and unsupervised feature selection to automatically achieve cell type identification in two steps. Average prediction accuracy of 98% obtained on six different cell types in a Human Pancreas scRNA-seq dataset. In addition, we found that 11 out of 13 selected genes are biologically related to two cell types in the Human Pancreas, which confirms the effectiveness of the proposed approach.
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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 | 0.000 | 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 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".