Update Match Modalities results

CHANGELOG.md

@@ -2,10 +2,14 @@
 
 ## MAJOR CHANGES
 
+* Update Matching Modalities task to OpenProblems v2 results (PR #328).
+
 * Migrated the result scaling from R to JavaScript to allow dynamically updating the results (PR #332).
 
 ## MINOR CHANGES
 
+* Update Mathing Modalities task name to Match Modalities (PR #328).
+
 * Improve Equations visualisation (PR #329).
 
 ## BUG FIXES

results/match_modalities/data/dataset_info.json

@@ -0,0 +1,26 @@
+[
+  {
+    "task_id": "match_modalities",
+    "dataset_id": "openproblems_v1_multimodal/scicar_mouse_kidney",
+    "dataset_name": "sci-CAR Mouse Kidney",
+    "dataset_summary": "sci-CAR profiles of 11k mouse kidney cells",
+    "data_reference": "cao2018joint",
+    "data_url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE117089"
+  },
+  {
+    "task_id": "match_modalities",
+    "dataset_id": "openproblems_v1_multimodal/citeseq_cbmc",
+    "dataset_name": "CITE-Seq CBMC",
+    "dataset_summary": "CITE-seq profiles of 8k Cord Blood Mononuclear Cells",
+    "data_reference": "stoeckius2017simultaneous",
+    "data_url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE100866"
+  },
+  {
+    "task_id": "match_modalities",
+    "dataset_id": "openproblems_v1_multimodal/scicar_cell_lines",
+    "dataset_name": "sci-CAR Cell Lines",
+    "dataset_summary": "sci-CAR profiles of 5k cell line cells (HEK293T, NIH/3T3, A549) across three treatment conditions (DEX 0h, 1h and 3h)",
+    "data_reference": "cao2018joint",
+    "data_url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE117089"
+  }
+]

results/match_modalities/data/method_info.json

@@ -0,0 +1,74 @@
+[
+  {
+    "task_id": "match_modalities",
+    "method_id": "random_features",
+    "method_name": "Random Features",
+    "method_summary": "Randomly permutated features",
+    "is_baseline": true,
+    "paper_reference": null,
+    "code_url": null,
+    "implementation_url": "https://github.com/openproblems-bio/openproblems-v2/tree/cf678cdaee2b5f1cc3bbae256de382ea3cc96acb/src/tasks/match_modalities/control_methods/random_features/config.vsh.yaml",
+    "code_version": null,
+    "commit_sha": "cf678cdaee2b5f1cc3bbae256de382ea3cc96acb"
+  },
+  {
+    "task_id": "match_modalities",
+    "method_id": "true_features",
+    "method_name": "True Features",
+    "method_summary": "A 1 to 1 mapping of features between modalities",
+    "is_baseline": true,
+    "paper_reference": null,
+    "code_url": null,
+    "implementation_url": "https://github.com/openproblems-bio/openproblems-v2/tree/cf678cdaee2b5f1cc3bbae256de382ea3cc96acb/src/tasks/match_modalities/control_methods/true_features/config.vsh.yaml",
+    "code_version": null,
+    "commit_sha": "cf678cdaee2b5f1cc3bbae256de382ea3cc96acb"
+  },
+  {
+    "task_id": "match_modalities",
+    "method_id": "scot",
+    "method_name": "Single Cell Optimal Transport",
+    "method_summary": "Run Single Cell Optimal Transport",
+    "is_baseline": false,
+    "paper_reference": "Demetci2020scot",
+    "code_url": "https://github.com/rsinghlab/SCOT",
+    "implementation_url": "https://github.com/openproblems-bio/openproblems-v2/tree/cf678cdaee2b5f1cc3bbae256de382ea3cc96acb/src/tasks/match_modalities/methods/scot/config.vsh.yaml",
+    "code_version": null,
+    "commit_sha": "cf678cdaee2b5f1cc3bbae256de382ea3cc96acb"
+  },
+  {
+    "task_id": "match_modalities",
+    "method_id": "harmonic_alignment",
+    "method_name": "Harmonic Alignment",
+    "method_summary": "Harmonic Alignment",
+    "is_baseline": false,
+    "paper_reference": "stanley2020harmonic",
+    "code_url": "https://github.com/KrishnaswamyLab/harmonic-alignment",
+    "implementation_url": "https://github.com/openproblems-bio/openproblems-v2/tree/cf678cdaee2b5f1cc3bbae256de382ea3cc96acb/src/tasks/match_modalities/methods/harmonic_alignment/config.vsh.yaml",
+    "code_version": null,
+    "commit_sha": "cf678cdaee2b5f1cc3bbae256de382ea3cc96acb"
+  },
+  {
+    "task_id": "match_modalities",
+    "method_id": "fastmnn",
+    "method_name": "fastMNN",
+    "method_summary": "A simpler version of the original mnnCorrect algorithm.",
+    "is_baseline": false,
+    "paper_reference": "haghverdi2018batch",
+    "code_url": "https://github.com/LTLA/batchelor",
+    "implementation_url": "https://github.com/openproblems-bio/openproblems-v2/tree/cf678cdaee2b5f1cc3bbae256de382ea3cc96acb/src/tasks/match_modalities/methods/fastmnn/config.vsh.yaml",
+    "code_version": null,
+    "commit_sha": "cf678cdaee2b5f1cc3bbae256de382ea3cc96acb"
+  },
+  {
+    "task_id": "match_modalities",
+    "method_id": "procrustes",
+    "method_name": "Procrustes",
+    "method_summary": "\"Procrustes superimposition embeds cellular data from each modality into a common space.\"\n",
+    "is_baseline": false,
+    "paper_reference": "gower1975generalized",
+    "code_url": "https://github.com/scipy/scipy",
+    "implementation_url": "https://github.com/openproblems-bio/openproblems-v2/tree/cf678cdaee2b5f1cc3bbae256de382ea3cc96acb/src/tasks/match_modalities/methods/procrustes/config.vsh.yaml",
+    "code_version": null,
+    "commit_sha": "cf678cdaee2b5f1cc3bbae256de382ea3cc96acb"
+  }
+]