Add aggregated performance table + example configs

evaluate.json

@@ -0,0 +1,78 @@
+{
+    "adam_lr": 0.001,
+    "adam_wd": 0.0,
+    "batch_size": 64,
+    "chroms": [
+        "chr8",
+        "chr20"
+    ],
+    "controls": null,
+    "device": "cuda",
+    "dtype": "bfloat16",
+    "early_stopping": 20,
+    "exclusion_lists": [
+        "https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"
+    ],
+    "expansion": 2,
+    "in_window": 2114,
+    "loci": [
+        "train_peaks.fold_0.bed",
+        "valid_peaks.fold_0.bed"
+    ],
+    "lw_lr": 0.001,
+    "lw_momentum": 0.9,
+    "lw_wd": 0.0,
+    "max_epochs": 20,
+    "max_jitter": 0,
+    "model": "cherimoya.fold_0.torch",
+    "muon_lr": 0.025,
+    "muon_wd": 0.03,
+    "n_filters": 128,
+    "n_layers": 9,
+    "n_warmup_epochs": 2,
+    "name": "cherimoya.fold_0",
+    "negative_ratio": 0.25,
+    "negatives": [
+        "train_nonpeaks.fold_0.bed",
+        "valid_nonpeaks.fold_0.bed"
+    ],
+    "num_workers": 1,
+    "out_window": 1000,
+    "performance_filename": "cherimoya.fold_0.performance.tsv",
+    "random_state": null,
+    "residual_scale": 0.15,
+    "reverse_complement": false,
+    "reverse_complement_average": false,
+    "sequences": "hg38.fa",
+    "signals": [
+        "ENCFF141BVL.bigWig"
+    ],
+    "skip": false,
+    "summits": false,
+    "training_chroms": [
+        "chr2",
+        "chr4",
+        "chr5",
+        "chr7",
+        "chr9",
+        "chr10",
+        "chr11",
+        "chr12",
+        "chr13",
+        "chr14",
+        "chr15",
+        "chr16",
+        "chr17",
+        "chr18",
+        "chr19",
+        "chr21",
+        "chr22",
+        "chrX",
+        "chrY"
+    ],
+    "validation_chroms": [
+        "chr8",
+        "chr20"
+    ],
+    "verbose": true
+}

fit.json

@@ -0,0 +1 @@
+{"n_filters": 128, "name": "cherimoya.fold_0", "batch_size": 64, "reverse_complement": true, "reverse_complement_average": false, "early_stopping": 20, "dtype": "bfloat16", "device": "cuda", "verbose": true, "training_chroms": ["chr2", "chr4", "chr5", "chr7", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr21", "chr22", "chrX", "chrY"], "validation_chroms": ["chr8", "chr20"], "sequences": "hg38.fa", "loci": ["train_peaks.fold_0.bed", "valid_peaks.fold_0.bed"], "exclusion_lists": ["https://www.encodeproject.org/files/ENCFF940NTE/@@download/ENCFF940NTE.bed.gz"], "negatives": ["train_nonpeaks.fold_0.bed", "valid_nonpeaks.fold_0.bed"], "signals": ["ENCFF141BVL.bigWig"], "controls": null, "random_state": null, "performance_filename": null, "num_workers": 1, "skip": false}