Update README.md

README.md

@@ -1,203 +1,258 @@
----
-dataset_info:
-- config_name: BindingDB_filtered
-  features:
-  - name: Index 
-    dtype: string
-  - name: Drug_ID
-    dtype: string
-  - name: Drug
-    dtype: string
-  - name: Target_ID
-    dtype: string
-  - name: Target
-    dtype: string
-  - name: Y
-    dtype: float32
-  splits:
-  - name: train
-    num_examples: 24700
-- config_name: CATS
-  features:
-  - name: Index 
-    dtype: string
-  - name: Drug
-    dtype: string
-  - name: IC50
-    dtype: float32
-  - name: Target
-    dtype: string
-  - name: Y
-    dtype: float32
-  splits:
-  - name: train
-    num_examples: 393
-- config_name: HIF2A
-  features:
-  - name: Index 
-    dtype: string
-  - name: Y
-    dtype: float32
-  - name: Drug
-    dtype: string
-  - name: Target
-    dtype: string
-  splits:
-  - name: train
-    num_examples: 37
-- config_name: HSP90
-  features:
-  - name: Index
-    dtype: string
-  - name: Drug
-    dtype: string
-  - name: IC50 (nM)
-    dtype: float32
-  - name: Target
-    dtype: string
-  - name: Y
-    dtype: float32
-  splits:
-  - name: train
-    num_examples: 147
-- config_name: LeakyPDB
-  features:
-  - name: Index 
-    dtype: string
-  - name: header
-    dtype: string
-  - name: smiles
-    dtype: string
-  - name: category
-    dtype: string
-  - name: seq
-    dtype: string
-  - name: resolution
-    dtype: float32
-  - name: date
-    dtype: string
-  - name: type
-    dtype: string
-  - name: new_split
-    dtype: string
-  - name: CL1
-    dtype: bool
-  - name: CL2
-    dtype: bool
-  - name: CL3
-    dtype: bool
-  - name: remove_for_balancing_val
-    dtype: bool
-  - name: kd/ki
-    dtype: string
-  - name: value
-    dtype: float32
-  - name: covalent
-    dtype: bool
-  splits:
-  - name: train
-    num_examples: 19443
-- config_name: MCL1
-  features:
-  - name: Index 
-    dtype: string
-  - name: Y
-    dtype: float32
-  - name: Drug
-    dtype: string
-  - name: Target
-    dtype: string
-  splits:
-  - name: train
-    num_examples: 25
-- config_name: Mpro
-  features:
-  - name: Index 
-    dtype: string
-  - name: Drug
-    dtype: string
-  - name: Y
-    dtype: float32
-  - name: Target
-    dtype: string
-  splits:
-  - name: train
-    num_examples: 2062
-- config_name: SYK
-  features:
-  - name: Index 
-    dtype: string
-  - name: Y
-    dtype: float32
-  - name: Drug
-    dtype: string
-  - name: Target
-    dtype: string
-  splits:
-  - name: train
-    num_examples: 44
-configs:
-- config_name: BindingDB_filtered
-  data_files:
-  - split: train
-    path: BindingDB_filtered/train/data-*
-- config_name: CATS
-  data_files:
-  - split: train
-    path: CATS/train/data-*
-- config_name: HIF2A
-  data_files:
-  - split: train
-    path: HIF2A/train/data-*
-- config_name: HSP90
-  data_files:
-  - split: train
-    path: HSP90/train/data-*
-- config_name: LeakyPDB
-  data_files:
-  - split: train
-    path: LeakyPDB/train/data-*
-- config_name: MCL1
-  data_files:
-  - split: train
-    path: MCL1/train/data-*
-- config_name: Mpro
-  data_files:
-  - split: train
-    path: Mpro/train/data-*
-- config_name: SYK
-  data_files:
-  - split: train
-    path: SYK/train/data-*
-license: cc-by-4.0
-pretty_name: BALM-Benchmark
-tags:
-  - chemistry
-  - biology
-size_categories:
-  - 10K<n<100K
----
-
-# Dataset Card for BALM-Benchmark
-
-<!-- Provide a quick summary of the dataset. -->
-
-## Dataset Details
-
-### Dataset Description
-
-## Citation
-
-<!-- If there is a paper or blog post introducing the dataset, the APA and Bibtex information for that should go in this section. -->
-
-**BibTeX:**
-
-```
-
-```
-
-## Dataset Card Contact
-
-- Rohan Gorantla (rohan.[email protected])
-- Aryo Pradipta Gema ([email protected])
-- Antonia Mey ()
+---
+dataset_info:
+- config_name: BindingDB_filtered
+  features:
+  - name: Index 
+    dtype: string
+  - name: Drug_ID
+    dtype: string
+  - name: Drug
+    dtype: string
+  - name: Target_ID
+    dtype: string
+  - name: Target
+    dtype: string
+  - name: Y
+    dtype: float32
+  splits:
+  - name: train
+    num_examples: 24700
+- config_name: CATS
+  features:
+  - name: Index 
+    dtype: string
+  - name: Drug
+    dtype: string
+  - name: IC50
+    dtype: float32
+  - name: Target
+    dtype: string
+  - name: Y
+    dtype: float32
+  splits:
+  - name: train
+    num_examples: 393
+- config_name: HIF2A
+  features:
+  - name: Index 
+    dtype: string
+  - name: Y
+    dtype: float32
+  - name: Drug
+    dtype: string
+  - name: Target
+    dtype: string
+  splits:
+  - name: train
+    num_examples: 37
+- config_name: HSP90
+  features:
+  - name: Index
+    dtype: string
+  - name: Drug
+    dtype: string
+  - name: IC50 (nM)
+    dtype: float32
+  - name: Target
+    dtype: string
+  - name: Y
+    dtype: float32
+  splits:
+  - name: train
+    num_examples: 147
+- config_name: LeakyPDB
+  features:
+  - name: Index 
+    dtype: string
+  - name: header
+    dtype: string
+  - name: smiles
+    dtype: string
+  - name: category
+    dtype: string
+  - name: seq
+    dtype: string
+  - name: resolution
+    dtype: float32
+  - name: date
+    dtype: string
+  - name: type
+    dtype: string
+  - name: new_split
+    dtype: string
+  - name: CL1
+    dtype: bool
+  - name: CL2
+    dtype: bool
+  - name: CL3
+    dtype: bool
+  - name: remove_for_balancing_val
+    dtype: bool
+  - name: kd/ki
+    dtype: string
+  - name: value
+    dtype: float32
+  - name: covalent
+    dtype: bool
+  splits:
+  - name: train
+    num_examples: 19443
+- config_name: MCL1
+  features:
+  - name: Index 
+    dtype: string
+  - name: Y
+    dtype: float32
+  - name: Drug
+    dtype: string
+  - name: Target
+    dtype: string
+  splits:
+  - name: train
+    num_examples: 25
+- config_name: Mpro
+  features:
+  - name: Index 
+    dtype: string
+  - name: Drug
+    dtype: string
+  - name: Y
+    dtype: float32
+  - name: Target
+    dtype: string
+  splits:
+  - name: train
+    num_examples: 2062
+- config_name: SYK
+  features:
+  - name: Index 
+    dtype: string
+  - name: Y
+    dtype: float32
+  - name: Drug
+    dtype: string
+  - name: Target
+    dtype: string
+  splits:
+  - name: train
+    num_examples: 44
+configs:
+- config_name: BindingDB_filtered
+  data_files:
+  - split: train
+    path: BindingDB_filtered/train/data-*
+- config_name: CATS
+  data_files:
+  - split: train
+    path: CATS/train/data-*
+- config_name: HIF2A
+  data_files:
+  - split: train
+    path: HIF2A/train/data-*
+- config_name: HSP90
+  data_files:
+  - split: train
+    path: HSP90/train/data-*
+- config_name: LeakyPDB
+  data_files:
+  - split: train
+    path: LeakyPDB/train/data-*
+- config_name: MCL1
+  data_files:
+  - split: train
+    path: MCL1/train/data-*
+- config_name: Mpro
+  data_files:
+  - split: train
+    path: Mpro/train/data-*
+- config_name: SYK
+  data_files:
+  - split: train
+    path: SYK/train/data-*
+license: cc-by-4.0
+pretty_name: BALM-Benchmark
+tags:
+  - chemistry
+  - biology
+size_categories:
+  - 10K<n<100K
+---
+
+# Dataset Card for BALM-Benchmark
+
+<!-- Provide a quick summary of the dataset. -->
+
+BALM-Benchmark is a comprehensive benchmark suite that combines multiple seminal binding affinity prediction datasets in one place.
+...
+
+## Dataset Details
+
+### Dataset Description
+
+<!-- Provide a longer summary of what this dataset is. -->
+
+Each dataset contains:
+- **Column A**
+- **Column B**
+- **Column C**
+- **...**
+
+- **Dataset Repository:** https://huggingface.co/datasets/BALM/BALM-benchmark
+- **Code Repository:** https://github.com/meyresearch/BALM
+- **Paper:** TBA
+- **Language(s) (NLP):** English
+- **License:** CC-BY-4.0
+
+
+### Dataset Sources 
+
+- **BindingDB_filtered**:
+- **CATS**: 
+- **HIF2A**:
+- **HSP90**:
+- **LeakyPDB**:
+- **MCL1**:
+- **Mpro**:
+- **SYK**:
+
+## Uses
+
+BALM-Benchmark was initially created as a part of the BALM project (https://github.com/meyresearch/BALM) which fine-tunes Protein and Ligand Language Models by optimizing the distance between protein and ligand embeddings in a shared space using the cosine similarity metric that directly represents experimental binding affinity.
+Nevertheless, BALM-Benchmark can be used by itself, just like any other HuggingFace dataset:
+
+```python
+from datasets import load_dataset
+
+# For instance, you want to load SYK data. Change the second argument into SYK
+syk_data = load_dataset("BALM/BALM-benchmark", "SYK", split="train")
+```
+
+As mentioned in the [Dataset Sources](#dataset-sources), the available datasets are:
+
+- `BindingDB_filtered`
+- `CATS`
+- `HIF2A`
+- `HSP90`
+- `LeakyPDB`
+- `MCL1`
+- `Mpro`
+- `SYK`
+
+Notice that all datasets only have one split (`train`). This is intentional such that the users can define their own splits, and can experiment with more random seeds for robustness.
+We highly recommend checking out different strategies for splitting the data (e.g., BindingDB) in [our BALM code repository](https://github.com/meyresearch/BALM/blob/refactor/balm/datasets/bindingdb_filtered.py#L157-L169).
+
+## Citation
+
+<!-- If there is a paper or blog post introducing the dataset, the APA and Bibtex information for that should go in this section. -->
+
+**BibTeX:**
+
+```
+In preparation
+```
+
+## Dataset Card Contact
+
+- Rohan Gorantla ([email protected])
+- Aryo Pradipta Gema ([email protected])
+- Antonia Mey ([email protected])