Add BPNet model ENCSR209MEV (ENCSR026RAK)

.gitattributes

@@ -33,3 +33,8 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
 *.zip filter=lfs diff=lfs merge=lfs -text
 *.zst filter=lfs diff=lfs merge=lfs -text
 *tfevents* filter=lfs diff=lfs merge=lfs -text
+fold_0/saved_model/variables/variables.data-00000-of-00001 filter=lfs diff=lfs merge=lfs -text
+fold_1/saved_model/variables/variables.data-00000-of-00001 filter=lfs diff=lfs merge=lfs -text
+fold_2/saved_model/variables/variables.data-00000-of-00001 filter=lfs diff=lfs merge=lfs -text
+fold_3/saved_model/variables/variables.data-00000-of-00001 filter=lfs diff=lfs merge=lfs -text
+fold_4/saved_model/variables/variables.data-00000-of-00001 filter=lfs diff=lfs merge=lfs -text

README.md

@@ -0,0 +1,137 @@
+---
+license: cc-by-4.0
+library_name: bpnet
+tags:
+  - bpnet
+  - dna
+  - genomics
+  - transcription-factor-binding
+  - chip-seq
+  - encode
+  - encode-bpnet-atlas
+  - hg38
+  - qc-unvalidated
+  - MXD1
+---
+
+# ENCODE BPNet Atlas
+
+As part of the ENCODE 4 Project, we trained BPNet models on 2,339 ENCODE
+transcription factor ChIP-seq experiments spanning 788 targets across
+175 biosamples. Here, we provide all models for open-source use.
+
+For more information about the models, see:
+
+- Main ENCODE 4 Paper
+- A unified lexicon of predictive DNA sequence motifs from ENCODE transcription
+  factor binding and chromatin accessibility assays (Deshpande et al., Zenodo 2025)
+- Base-resolution models of transcription-factor binding reveal soft motif syntax
+  (Avsec et al., Nat Genet 2021)
+
+## BPNet model: MXD1 ChIP-seq in K562 (ENCSR026RAK)
+
+- Model: BPNet
+- Assay: TF ChIP-seq
+- Target: MXD1
+- Experiment: [ENCSR026RAK](https://www.encodeproject.org/experiments/ENCSR026RAK/)
+- Model annotation: [ENCSR209MEV](https://www.encodeproject.org/annotations/ENCSR209MEV/)
+- Biosample: K562 (Full name: Homo sapiens K562 genetically modified (insertion) using CRISPR targeting H. sapiens MXD1)
+- Cell slim(s): leukocyte, hematopoietic cell, cancer cell
+- Organ slim(s): bodily fluid, blood
+- Developmental slim(s): mesoderm
+- System slim(s): immune system
+- Assembly: hg38
+
+## QC
+
+- Status: unvalidated
+- Notes: Found potential direct motif (counts, profile); No known direct/potential direct motif;
+
+## Directory structure
+
+5-fold cross-validation. Each `fold_*/` contains the trained BPNet model in two formats:
+
+- `fold_0/model.h5` — BPNet model in .h5 (Keras) format
+- `fold_0/saved_model/` — BPNet model in TensorFlow SavedModel format (a directory; load directly)
+- `config.json` — training / architecture parameters
+
+## Instructions
+
+BPNet takes a one-hot DNA sequence plus control (bias) inputs and predicts
+stranded profile logits and total logcounts. The control inputs come from the
+matched WCE/Input DNA control and **can be passed as zeros**.
+
+### 1. Loading the SavedModel and making predictions
+
+```python
+import numpy as np
+import tensorflow as tf
+from scipy.special import logsumexp
+
+model = tf.saved_model.load("fold_0/saved_model")
+# sequence: (N, 2114, 4) one-hot [A,C,G,T]
+# profile_bias_input: (N, 1000, 2) per-base profile bias from WCE/Input control, or zeros
+# counts_bias_input:  (N, 2) log2 total counts from WCE/Input control, or zeros
+predictions = model.signatures["serving_default"](**{
+    "sequence": sequence.astype("float32"),
+    "profile_bias_input_0": profile_bias_input.astype("float32"),
+    "counts_bias_input_0": counts_bias_input.astype("float32")})
+# predictions["profile_predictions"]:   (N, 1000, 2) logits (strands NOT independent)
+# predictions["logcounts_predictions"]: (N, 1) total logcount
+
+output_len = 1000
+def vectorized_prediction_to_profile(predictions):
+    logits_arr = predictions["profile_predictions"]
+    counts_arr = predictions["logcounts_predictions"]
+    pred_profile_logits = np.reshape(logits_arr, [-1, 1, output_len * 2])
+    probVals_array = np.exp(pred_profile_logits - logsumexp(
+        pred_profile_logits, axis=2).reshape([len(logits_arr), 1, 1]))
+    profile_predictions = np.multiply(
+        np.exp(counts_arr).reshape([len(counts_arr), 1, 1]), probVals_array)
+    plus  = np.reshape(profile_predictions, [len(counts_arr), output_len, 2])[:, :, 0]
+    minus = np.reshape(profile_predictions, [len(counts_arr), output_len, 2])[:, :, 1]
+    return plus, minus, counts_arr
+
+plus, minus, logcounts = vectorized_prediction_to_profile(predictions)
+```
+
+### 2. Loading the .h5 (Keras) and making predictions
+
+```python
+import numpy as np
+import tensorflow as tf
+import tensorflow.keras.backend as kb
+from tensorflow.keras.models import load_model
+from tensorflow.keras.utils import CustomObjectScope
+from bpnet.model.custommodel import CustomModel
+
+def get_model(model_path):
+    with CustomObjectScope({"kb": kb, "tf": tf, "CustomModel": CustomModel}):
+        return load_model(model_path)
+
+model = get_model("fold_0/model.h5")
+N = sequence.shape[0]
+predictions = model.predict([
+    sequence,                     # (N, 2114, 4)
+    np.zeros((N, 1000, 2)),       # profile_bias_input (or real WCE/Input control values)
+    np.zeros((N, 2))])            # counts_bias_input  (or real control log2 counts)
+# predictions[0]: (N, 1000, 2) logits;  predictions[1]: (N, 1) logcounts
+# convert with the same vectorized_prediction_to_profile() (predictions[0], predictions[1])
+```
+
+## Docker image to load and use the models
+
+`kundajelab/bpnet-atlas` (placeholder — image forthcoming).
+
+## Code
+
+- Code: https://github.com/kundajelab/bpnet/
+- Toolbox & downstream analysis: https://github.com/kundajelab/bpnet/wiki
+
+## License & citation
+
+External data users may freely download, analyze and publish results based on any
+ENCODE data without restrictions.
+
+Released under the ENCODE data-use policy. Please cite the ENCODE Project
+Consortium and the model software: BPNet (Avsec et al., Nat Genet 2021).

config.json

@@ -0,0 +1,45 @@
+{
+    "input_len": 2114,
+    "output_profile_len": 1000,
+    "motif_module_params": {
+        "filters": [64],
+        "kernel_sizes": [21],
+        "padding": "valid"
+    },
+    "syntax_module_params": {
+        "num_dilation_layers": 8,
+        "filters": 64,
+        "kernel_size": 3,
+        "padding": "valid",
+        "pre_activation_residual_unit": true
+    },
+    "profile_head_params": {
+        "filters": 1,
+        "kernel_size":  75,
+        "padding": "valid"
+    },
+    "counts_head_params": {
+        "filters": 1,
+        "kernel_size":  75,
+        "padding": "valid",
+        "units": [1],
+        "activations":["linear"],
+		"dropouts":[0]
+		
+    },
+    "profile_bias_module_params": {
+        "kernel_sizes": [1]
+    },
+    "counts_bias_module_params": {
+    },
+    "use_attribution_prior": false,
+    "attribution_prior_params": {
+        "frequency_limit": 150,
+        "limit_softness": 0.2,
+        "grad_smooth_sigma": 3,
+        "profile_grad_loss_weight": 200,
+        "counts_grad_loss_weight": 100        
+    },
+    "loss_weights": [1, 99.03010471204189],
+    "counts_loss": "MSE"
+}

fold_0/model.h5

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:5c1e81164320c3782c81b1a6ee35ffc95567d787d84f34623d532f2bd7212b05
+size 561784

fold_0/saved_model/saved_model.pb

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:db20af3f93ce893f5a866eb26e029fe7e59770ff6c955b6754fe930429da89d3
+size 750201

fold_0/saved_model/variables/variables.data-00000-of-00001

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:25f7e6b2c451dbed82c69fab39ef1f25f2e4ff3acdd61563eea4c3344aef7b06
+size 1393322

fold_1/model.h5

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:037a9b2b5c5ca650e8aca56892f53581b8bbc8c982567b8fd05892cb481cbf99
+size 561784

fold_1/saved_model/saved_model.pb

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:b6ad140fbeec75d4ef4ac5968a67ac4c4577eb02a60ba2118a2959e182099d28
+size 750201

fold_1/saved_model/variables/variables.data-00000-of-00001

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:fa3f45368eb383462335aba9df94b6254437c1ca850e9baa78c2e69bde30f19e
+size 1393322

fold_2/model.h5

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:f0727acac883160dc3138a5779bb0fc04dc7fead76a9a9b12e28aebb9a0faf39
+size 561784

fold_2/saved_model/saved_model.pb

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:63235c6724ca6be0d0b4bd879fe82478d997173bd02933efb3212d6a3bd9750a
+size 750201

fold_2/saved_model/variables/variables.data-00000-of-00001

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:f457d4a31968c2d0a815ec07bbb2f288dd468e705a7012ab88e0b766cbfe8cea
+size 1393322

fold_3/model.h5

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:e5dec0d9d590d32caeb5a6262b23717e26bbc19c17a58c0c7ad1b9ebffb229d2
+size 561784

fold_3/saved_model/saved_model.pb

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:fec89fd5543a9e678c653e9bd0c51617cb683e72d4a76282fe7e69fac9db74eb
+size 750201

fold_3/saved_model/variables/variables.data-00000-of-00001

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:ea3a741e0699bcfcfcb816d8bd10ae8ec56ac39aad7532232a237740e9e30b7a
+size 1393322

fold_4/model.h5

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:da23c9df311e9907e2b0242f6d9b8816d19d5401082b28d9d354045fe1e5c021
+size 561784

fold_4/saved_model/saved_model.pb

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:f7a5cb88642c39c6c322bf242c078b5e771a4311ee112e9d3c0cc356fa76fa9a
+size 750201

fold_4/saved_model/variables/variables.data-00000-of-00001

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:40a896422c463d488b3f82b8bbfede9d4ad708ad0ad51610a9d46f03587589e3
+size 1393322