Create README.md

README.md

@@ -0,0 +1,41 @@
+# Model Card: algaGPT
+
+## Overview
+
+**Name:** algaGPT
+**Type:** Causal language model for protein sequence classification
+**Base:** nanoGPT (Andrej Karpathy)
+**Task:** Binary classification of microalgal vs. contaminant protein sequences
+**Mode:** TI-inclusive (full-length sequences)
+
+## Training
+
+- **Data:** ~58.6M protein sequences (1:1 algal:contaminant ratio)
+- **Algal sources:** 166 microalgal genomes across 10 phyla
+- **Contaminant sources:** Bacterial, archaeal, and fungal sequences from NCBI nr
+
+## Performance
+
+| Metric | Score |
+|--------|-------|
+| Recall | >99% |
+| Speed vs BLASTP+ | > 10,701x faster |
+
+## Usage
+
+Input a protein sequence; model generates a classification tag (algal/bacterial) via next-token prediction.
+
+## Limitations
+
+- Under-representation of some algal lineages (dinoflagellates, rhodophytes, Chromerida)
+- Up to ~10% false positive rate for species with complex endosymbiotic histories
+- Does not classify eukaryotic protist contaminants
+
+## Citation
+
+Nelson DR, Jaiswal AK, Ismail NS, Mystikou A, Salehi-Ashtiani K. Pan-microalgal dark proteome mapping via interpretable deep learning and synthetic chimeras. *Patterns*. 2024;6(11).
+
+## Contact
+
+Kourosh Salehi-Ashtiani
+ksa3@nyu.edu