add makotu method

Author: rcannood

src/methods/neurips2022_makotu/config.vsh.yaml

@@ -0,0 +1,45 @@
+__merge__: ../../api/comp_method.yaml
+name: neurips2022_makotu
+
+label: "Makotu"
+summary: "3rd place solution from NeurIPS 2022 multimodal competition by Makotu"
+description: |
+  This is the 3rd place solution from the NeurIPS 2022 multimodal single-cell
+  integration competition by Makotu. The method features:
+  
+  - Advanced preprocessing with Okapi BM25 transformation instead of TF-IDF
+  - LSI (Latent Semantic Indexing) dimensionality reduction using muon
+  - Rich feature engineering including binary features and Word2Vec embeddings
+  - Leiden clustering features for capturing cell neighborhood information
+  - Ensemble of MLPs and CatBoost models with weighted averaging
+  - Multi-branch neural architecture with skip connections
+  
+  For CITEseq: Uses correlation loss and cluster-based features
+  For Multiome: Uses Okapi BM25 preprocessing and LSI dimensionality reduction
+
+links:
+  repository: https://github.com/makotu1208/open-problems-multimodal-3rd-solution
+  documentation: https://www.kaggle.com/competitions/open-problems-multimodal/writeups/makotu-3rd-place-solution
+
+resources:
+  - type: python_script
+    path: script.py
+
+engines:
+  - type: docker
+    image: openproblems/base_pytorch_nvidia:1
+    setup:
+      - type: python
+        pypi:
+          - muon
+          - gensim
+          - catboost
+          - scanpy
+          - scikit-learn>=1.0.0
+          - leidenalg
+
+runners:
+  - type: executable
+  - type: nextflow
+    directives:
+      label: [highmem, veryhightime, midcpu, highsharedmem]