tmp_fix

.gitignore

@@ -6,8 +6,8 @@ __pycache__/
 *ipynb
 .vscode/
 
-eval-queue/
-eval-results/
-eval-queue-bk/
-eval-results-bk/
+#eval-queue/
+#eval-results/
+#eval-queue-bk/
+#eval-results-bk/
 logs/

.idea/deployment.xml

@@ -0,0 +1,112 @@
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+    "git-widget-placeholder": "main",
+    "last_opened_file_path": "C:/Users/chuan/OneDrive - University of Exeter/AIProjects/OmniGenomeLeaderboard/eval-queue",
+    "node.js.detected.package.eslint": "true",
+    "node.js.detected.package.tslint": "true",
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+    "node.js.selected.package.tslint": "(autodetect)",
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+    "vue.rearranger.settings.migration": "true"
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+}]]></component>
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+      <recent name="C:\Users\chuan\OneDrive - University of Exeter\AIProjects\OmniGenomeLeaderboard" />
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+      <module name="OmniGenomeLeaderboard" />
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+      <option name="INTERPRETER_OPTIONS" value="" />
+      <option name="PARENT_ENVS" value="true" />
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+      <EXTENSION ID="PythonCoverageRunConfigurationExtension" runner="coverage.py" />
+      <option name="SCRIPT_NAME" value="$PROJECT_DIR$/app.py" />
+      <option name="PARAMETERS" value="" />
+      <option name="SHOW_COMMAND_LINE" value="false" />
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+      <option name="MODULE_MODE" value="false" />
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+      <method v="2" />
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+  <component name="XDebuggerManager">
+    <breakpoint-manager>
+      <breakpoints>
+        <line-breakpoint enabled="true" suspend="THREAD" type="python-line">
+          <url>file://$PROJECT_DIR$/src/leaderboard/read_evals.py</url>
+          <line>169</line>
+          <option name="timeStamp" value="4" />
+        </line-breakpoint>
+        <line-breakpoint enabled="true" suspend="THREAD" type="python-line">
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+          <line>48</line>
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+    <SUITE FILE_PATH="coverage/OmniGenomeLeaderboard$app.coverage" NAME="app Coverage Results" MODIFIED="1726486285408" SOURCE_PROVIDER="com.intellij.coverage.DefaultCoverageFileProvider" RUNNER="coverage.py" COVERAGE_BY_TEST_ENABLED="false" COVERAGE_TRACING_ENABLED="false" WORKING_DIRECTORY="$PROJECT_DIR$" />
+  </component>
+</project>

app.py

@@ -35,7 +35,7 @@ def restart_space():
 
 
 ### Space initialisation
-"""
+
 try:
     print(EVAL_REQUESTS_PATH)
     snapshot_download(
@@ -60,7 +60,6 @@ try:
     )
 except Exception:
     restart_space()
-"""
 
 RGB_LEADERBOARD_DF = get_leaderboard_df(EVAL_RESULTS_PATH+"/RGB/", EVAL_REQUESTS_PATH+"/RGB/", RGB_COLS, RGB_BENCHMARK_COLS)
 PGB_LEADERBOARD_DF = get_leaderboard_df(EVAL_RESULTS_PATH+"/PGB/", EVAL_REQUESTS_PATH+"/PGB/", PGB_COLS, PGB_BENCHMARK_COLS)

bak/eval-queue/.gitattributes

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+*.pcm filter=lfs diff=lfs merge=lfs -text
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+*.png filter=lfs diff=lfs merge=lfs -text
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bak/eval-queue/GB/InstaDeepAI/nucleotide-transformer-v2-100m-multi-species_eval_request_False_bfloat16_Original.json

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bak/eval-queue/GB/LongSafari/hyenadna-large-1m-seqlen-hf_eval_request_False_bfloat16_Original.json

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bak/eval-queue/GB/README.md

@@ -0,0 +1,3 @@
+---
+license: mit
+---

bak/eval-queue/GB/kuleshov-group/caduceus-ps_seqlen-131k_d_model-256_n_layer-16_eval_request_False_bfloat16_Original.json

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bak/eval-queue/GB/multimolecule/splicebert_eval_request_False_bfloat16_Original.json

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bak/eval-queue/GB/multimolecule/utrbert-4mer_eval_request_False_bfloat16_Original.json

@@ -0,0 +1 @@
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bak/eval-queue/GB/yangheng/omnigenome-186M_eval_request_False_bfloat16_Original.json

@@ -0,0 +1 @@
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bak/eval-queue/GB/zhihan1996/DNABERT-2-117M_eval_request_False_bfloat16_Original.json

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bak/eval-queue/GUE/InstaDeepAI/nucleotide-transformer-v2-100m-multi-species_eval_request_False_bfloat16_Original.json

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bak/eval-queue/GUE/LongSafari/hyenadna-large-1m-seqlen-hf_eval_request_False_bfloat16_Original.json

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bak/eval-queue/GUE/README.md

@@ -0,0 +1,3 @@
+---
+license: mit
+---

bak/eval-queue/GUE/kuleshov-group/caduceus-ps_seqlen-131k_d_model-256_n_layer-16_eval_request_False_bfloat16_Original.json

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bak/eval-queue/GUE/multimolecule/splicebert_eval_request_False_bfloat16_Original.json

@@ -0,0 +1 @@
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bak/eval-queue/GUE/multimolecule/utrbert-4mer_eval_request_False_bfloat16_Original.json

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bak/eval-queue/GUE/yangheng/omnigenome-186M_eval_request_False_bfloat16_Original.json

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bak/eval-queue/GUE/zhihan1996/DNABERT-2-117M_eval_request_False_bfloat16_Original.json

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bak/eval-queue/GleghornLab/cdsBERT_eval_request_False_bfloat16_Original.json

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bak/eval-queue/InstaDeepAI/agro-nucleotide-transformer-1b_eval_request_False_bfloat16_Original.json

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bak/eval-queue/LongSafari/hyenadna-large-1m-seqlen-hf_eval_request_False_bfloat16_Original.json

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bak/eval-queue/PGB/GleghornLab/cdsBERT_eval_request_False_bfloat16_Original.json

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+{"model": "GleghornLab/cdsBERT", "base_model": "", "revision": "main", "private": false, "precision": "bfloat16", "weight_type": "Original", "status": "FINISHED", "submitted_time": "2023-11-21T18:10:08Z", "model_type": "\ud83d\udfe2 : pretrained", "likes": 0, "params": 420, "license": "custom"}

bak/eval-queue/PGB/InstaDeepAI/agro-nucleotide-transformer-1b_eval_request_False_bfloat16_Original.json

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+{"model": "InstaDeepAI/agro-nucleotide-transformer-1b", "base_model": "", "revision": "main", "private": false, "precision": "bfloat16", "weight_type": "Original", "status": "FINISHED", "submitted_time": "2023-11-21T18:10:08Z", "model_type": "\ud83d\udfe2 : pretrained", "likes": 0, "params": 985, "license": "custom"}

bak/eval-queue/PGB/InstaDeepAI/nucleotide-transformer-v2-100m-multi-species_eval_request_False_bfloat16_Original.json

@@ -0,0 +1 @@
+{"model": "InstaDeepAI/nucleotide-transformer-v2-100m-multi-species", "base_model": "", "revision": "main", "private": false, "precision": "bfloat16", "weight_type": "Original", "status": "FINISHED", "submitted_time": "2023-11-21T18:10:08Z", "model_type": "\ud83d\udfe2 : pretrained", "likes": 0, "params": 96, "license": "custom"}

bak/eval-queue/PGB/LongSafari/hyenadna-large-1m-seqlen-hf_eval_request_False_bfloat16_Original.json

@@ -0,0 +1 @@
+{"model": "LongSafari/hyenadna-large-1m-seqlen-hf", "base_model": "", "revision": "main", "private": false, "precision": "bfloat16", "weight_type": "Original", "status": "FINISHED", "submitted_time": "2023-11-21T18:10:08Z", "model_type": "\ud83d\udfe2 : pretrained", "likes": 0, "params": 47, "license": "custom"}

bak/eval-queue/PGB/README.md

@@ -0,0 +1,3 @@
+---
+license: mit
+---

bak/eval-queue/PGB/kuleshov-group/caduceus-ps_seqlen-131k_d_model-256_n_layer-16_eval_request_False_bfloat16_Original.json

@@ -0,0 +1 @@
+{"model": "kuleshov-group/caduceus-ps_seqlen-131k_d_model-256_n_layer-16", "base_model": "", "revision": "main", "private": false, "precision": "bfloat16", "weight_type": "Original", "status": "FINISHED", "submitted_time": "2023-11-21T18:10:08Z", "model_type": "\ud83d\udfe2 : pretrained", "likes": 0, "params": 7.73, "license": "custom"}

bak/eval-queue/PGB/multimolecule/rnabert_eval_request_False_bfloat16_Original.json

@@ -0,0 +1 @@
+{"model": "multimolecule/rnabert", "base_model": "", "revision": "main", "private": false, "precision": "bfloat16", "weight_type": "Original", "status": "FINISHED", "submitted_time": "2023-11-21T18:10:08Z", "model_type": "\ud83d\udfe2 : pretrained", "likes": 0, "params": 0.48, "license": "custom"}

bak/eval-queue/PGB/multimolecule/rnafm_eval_request_False_bfloat16_Original.json

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+{"model": "multimolecule/rnafm", "base_model": "", "revision": "main", "private": false, "precision": "bfloat16", "weight_type": "Original", "status": "FINISHED", "submitted_time": "2023-11-21T18:10:08Z", "model_type": "\ud83d\udfe2 : pretrained", "likes": 0, "params": 99.52, "license": "custom"}

bak/eval-queue/PGB/multimolecule/rnamsm_eval_request_False_bfloat16_Original.json

@@ -0,0 +1 @@
+{"model": "multimolecule/rnamsm", "base_model": "", "revision": "main", "private": false, "precision": "bfloat16", "weight_type": "Original", "status": "FINISHED", "submitted_time": "2023-11-21T18:10:08Z", "model_type": "\ud83d\udfe2 : pretrained", "likes": 0, "params": 96.5, "license": "custom"}

bak/eval-queue/PGB/multimolecule/splicebert_eval_request_False_bfloat16_Original.json

@@ -0,0 +1 @@
+{"model": "multimolecule/splicebert", "base_model": "", "revision": "main", "private": false, "precision": "bfloat16", "weight_type": "Original", "status": "FINISHED", "submitted_time": "2023-11-21T18:10:08Z", "model_type": "\ud83d\udfe2 : pretrained", "likes": 0, "params": 19.7, "license": "custom"}

bak/eval-queue/PGB/multimolecule/utrbert-4mer_eval_request_False_bfloat16_Original.json

@@ -0,0 +1 @@
+{"model": "multimolecule/utrbert-4mer", "base_model": "", "revision": "main", "private": false, "precision": "bfloat16", "weight_type": "Original", "status": "FINISHED", "submitted_time": "2023-11-21T18:10:08Z", "model_type": "\ud83d\udfe2 : pretrained", "likes": 0, "params": 86, "license": "custom"}

bak/eval-queue/PGB/yangheng/omnigenome-186M_eval_request_False_bfloat16_Original.json

@@ -0,0 +1 @@
+{"model": "yangheng/omnigenome-186M", "base_model": "", "revision": "main", "private": false, "precision": "bfloat16", "weight_type": "Original", "status": "FINISHED", "submitted_time": "2023-11-21T18:10:08Z", "model_type": "\ud83d\udfe2 : pretrained", "likes": 0, "params": 186, "license": "custom"}

bak/eval-queue/PGB/zhihan1996/DNABERT-2-117M_eval_request_False_bfloat16_Original.json

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+{"model": "zhihan1996/DNABERT-2-117M", "base_model": "", "revision": "main", "private": false, "precision": "bfloat16", "weight_type": "Original", "status": "FINISHED", "submitted_time": "2023-11-21T18:10:08Z", "model_type": "\ud83d\udfe2 : pretrained", "likes": 0, "params": 117, "license": "custom"}

bak/eval-queue/README.md

@@ -0,0 +1,3 @@
+---
+license: mit
+---

bak/eval-queue/RGB/GleghornLab/cdsBERT_eval_request_False_bfloat16_Original.json

@@ -0,0 +1 @@
+{"model": "GleghornLab/cdsBERT", "base_model": "", "revision": "main", "private": false, "precision": "bfloat16", "weight_type": "Original", "status": "FINISHED", "submitted_time": "2023-11-21T18:10:08Z", "model_type": "\ud83d\udfe2 : pretrained", "likes": 0, "params": 420, "license": "custom"}

bak/eval-queue/RGB/InstaDeepAI/agro-nucleotide-transformer-1b_eval_request_False_bfloat16_Original.json

@@ -0,0 +1 @@
+{"model": "InstaDeepAI/agro-nucleotide-transformer-1b", "base_model": "", "revision": "main", "private": false, "precision": "bfloat16", "weight_type": "Original", "status": "FINISHED", "submitted_time": "2023-11-21T18:10:08Z", "model_type": "\ud83d\udfe2 : pretrained", "likes": 0, "params": 985, "license": "custom"}

bak/eval-queue/RGB/InstaDeepAI/nucleotide-transformer-v2-100m-multi-species_eval_request_False_bfloat16_Original.json

@@ -0,0 +1 @@
+{"model": "InstaDeepAI/nucleotide-transformer-v2-100m-multi-species", "base_model": "", "revision": "main", "private": false, "precision": "bfloat16", "weight_type": "Original", "status": "FINISHED", "submitted_time": "2023-11-21T18:10:08Z", "model_type": "\ud83d\udfe2 : pretrained", "likes": 0, "params": 100, "license": "custom"}

bak/eval-queue/RGB/LongSafari/hyenadna-large-1m-seqlen-hf_eval_request_False_bfloat16_Original.json

@@ -0,0 +1 @@
+{"model": "LongSafari/hyenadna-large-1m-seqlen-hf", "base_model": "", "revision": "main", "private": false, "precision": "bfloat16", "weight_type": "Original", "status": "FINISHED", "submitted_time": "2023-11-21T18:10:08Z", "model_type": "\ud83d\udfe2 : pretrained", "likes": 0, "params": 47, "license": "custom"}

bak/eval-queue/RGB/README.md

@@ -0,0 +1,3 @@
+---
+license: mit
+---

bak/eval-queue/RGB/multimolecule/splicebert_eval_request_False_bfloat16_Original.json

@@ -0,0 +1 @@
+{"model": "multimolecule/splicebert", "base_model": "", "revision": "main", "private": false, "precision": "bfloat16", "weight_type": "Original", "status": "FINISHED", "submitted_time": "2023-11-21T18:10:08Z", "model_type": "\ud83d\udfe2 : pretrained", "likes": 0, "params": 19.7, "license": "custom"}

bak/eval-queue/RGB/multimolecule/utrbert-4mer_eval_request_False_bfloat16_Original.json

@@ -0,0 +1 @@
+{"model": "multimolecule/utrbert-4mer", "base_model": "", "revision": "main", "private": false, "precision": "bfloat16", "weight_type": "Original", "status": "FINISHED", "submitted_time": "2023-11-21T18:10:08Z", "model_type": "\ud83d\udfe2 : pretrained", "likes": 0, "params": 86, "license": "custom"}

bak/eval-queue/RGB/yangheng/omnigenome-186M_eval_request_False_bfloat16_Original.json

@@ -0,0 +1 @@
+{"model": "yangheng/omnigenome-186M", "base_model": "", "revision": "main", "private": false, "precision": "bfloat16", "weight_type": "Original", "status": "FINISHED", "submitted_time": "2023-11-21T18:10:08Z", "model_type": "\ud83d\udfe2 : pretrained", "likes": 0, "params": 186, "license": "custom"}

bak/eval-queue/RGB/yangheng/omnigenome-52M_eval_request_False_bfloat16_Original.json

@@ -0,0 +1 @@
+{"model": "yangheng/omnigenome-52M", "base_model": "", "revision": "main", "private": false, "precision": "bfloat16", "weight_type": "Original", "status": "FINISHED", "submitted_time": "2023-11-21T18:10:08Z", "model_type": "\ud83d\udfe2 : pretrained", "likes": 0, "params": 52, "license": "custom"}

bak/eval-queue/RGB/zhihan1996/DNABERT-2-117M_eval_request_False_bfloat16_Original.json

@@ -0,0 +1 @@
+{"model": "zhihan1996/DNABERT-2-117M", "base_model": "", "revision": "main", "private": false, "precision": "bfloat16", "weight_type": "Original", "status": "FINISHED", "submitted_time": "2023-11-21T18:10:08Z", "model_type": "\ud83d\udfe2 : pretrained", "likes": 0, "params": 117, "license": "custom"}

bak/eval-queue/multimolecule/splicebert_eval_request_False_bfloat16_Original.json

@@ -0,0 +1 @@
+{"model": "multimolecule/splicebert", "base_model": "", "revision": "main", "private": false, "precision": "bfloat16", "weight_type": "Original", "status": "FINISHED", "submitted_time": "2023-11-21T18:10:08Z", "model_type": "\ud83d\udfe2 : pretrained", "likes": 0, "params": 19.7, "license": "custom"}

bak/eval-queue/multimolecule/utrbert-4mer_eval_request_False_bfloat16_Original.json

@@ -0,0 +1 @@
+{"model": "multimolecule/utrbert-4mer", "base_model": "", "revision": "main", "private": false, "precision": "bfloat16", "weight_type": "Original", "status": "FINISHED", "submitted_time": "2023-11-21T18:10:08Z", "model_type": "\ud83d\udfe2 : pretrained", "likes": 0, "params": 86, "license": "custom"}