Polishing (#13)

* chore: isort/black

* doc: update README

* chore: name

Author: jannisborn

README.md

@@ -1,5 +1,7 @@
 # Regression Transformer
 [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
+[![Gradio demo](https://img.shields.io/website-up-down-green-red/https/hf.space/gradioiframe/GT4SD/regression_transformer/+.svg?label=demo%20status)](https://huggingface.co/spaces/GT4SD/regression_transformer)
 
 A multitask Transformer that reformulates regression as a conditional sequence modeling task.
 This yields a dichotomous language model that seamlessly integrates regression with property-driven conditional generation.
@@ -9,7 +11,7 @@ This yields a dichotomous language model that seamlessly integrates regression w
 This repo contains the development code.
 
 ## Demo with UI
-🤗 A gradio demo with a simple UI is available at: https://huggingface.co/spaces/jannisborn/regression_transformer
+🤗 A gradio demo with a simple UI is available on [HuggingFace spaces](https://huggingface.co/spaces/GT4SD/regression_transformer)
 ![Summary](assets/gradio_demo.png)
 
 
@@ -123,10 +125,10 @@ At this point the folder containing the vocabulary file can be used to load a to
 If you use the regression transformer, please cite:
 ```bib
 @article{born2022regression,
-  title={Regression Transformer: Concurrent Conditional Generation and Regression by Blending Numerical and Textual Tokens},
+  title={Regression Transformer enables concurrent sequence regression and generation for molecular language modeling},
   author={Born, Jannis and Manica, Matteo},
-  journal={arXiv preprint arXiv:2202.01338},
-  note={Spotlight talk at ICLR workshop on Machine Learning for Drug Discovery},
-  year={2022}
+  journal={Nature Machine Intelligence},
+  note={Article in press. arXiv preprint arXiv:2202.01338},
+  year={2023}
 }
 ```

terminator/__init__.py

@@ -1,2 +1,3 @@
 """Utiltities for transformer-based conditional molecule generation."""
 __version__ = "0.0.1"
+__name__ = "terminator"

terminator/collators.py

@@ -1,7 +1,8 @@
 from dataclasses import dataclass
 from typing import Dict, Iterable, List, Optional, Tuple, Union
-import transformers
+
 import torch
+import transformers
 from transformers import DataCollatorForPermutationLanguageModeling
 from transformers.tokenization_utils import PreTrainedTokenizer
 from transformers.tokenization_utils_base import BatchEncoding

terminator/datasets.py

@@ -8,7 +8,9 @@ def get_dataset(
     line_by_line: bool = True,
 ):
     if line_by_line:
-        return LineByLineTextDataset(tokenizer=tokenizer, file_path=filepath, block_size=block_size)
+        return LineByLineTextDataset(
+            tokenizer=tokenizer, file_path=filepath, block_size=block_size
+        )
     else:
         return TextDataset(
             tokenizer=tokenizer,

terminator/functional_groups.py

@@ -5,6 +5,8 @@
 #  which is included in the file license.txt, found at the root
 #  of the RDKit source tree.
 
+from collections import namedtuple
+
 #
 #
 # Richard hall 2017
@@ -13,7 +15,6 @@
 # refine output function
 # astex_ifg: identify functional groups a la Ertl, J. Cheminform (2017) 9:36
 from rdkit import Chem
-from collections import namedtuple
 
 
 def merge(mol, marked, aset):

terminator/nlp.py

@@ -5,7 +5,7 @@
 
 
 def parse_humicroedit(
-    dataset, expression_separator: str = '{', expression_end: str = '}'
+    dataset, expression_separator: str = "{", expression_end: str = "}"
 ) -> List[str]:
     """
     Parse the humicrocredit dataset in an appropriate format.

terminator/numerical_encodings.py

@@ -40,7 +40,7 @@ def get_float_encoding(
     else:
         digit = int(token[1])
         order = int(token.split("_")[-2])
-        val = digit * 10 ** order
+        val = digit * 10**order
 
     for i in range(0, embedding_size, 2):
         vals[i] = val / (i + 1)
@@ -72,7 +72,7 @@ def get_int_encoding(token: str, embedding_size: int) -> torch.Tensor:
     else:
         digit = int(token[1])
         order = int(token.split("_")[-2])
-        val = digit * 10 ** order
+        val = digit * 10**order
 
         if order < 0:
             raise ValueError(

terminator/tokenization.py

@@ -399,9 +399,9 @@ class XLNetRTTokenizer(XLNetTokenizer):
     def set_property_tokenizer(
         self,
         tokenizer: PropertyTokenizer,
-        expression_separator: str = '{',
-        expression_end: str = '}',
-        property_token: str = '[funny]',
+        expression_separator: str = "{",
+        expression_end: str = "}",
+        property_token: str = "[funny]",
     ):
         """
         Set the property tokenizer to be used by the main tokenizer.

terminator/trainer_utils.py

@@ -49,7 +49,7 @@ def get_trainer_dict(dictionary: Dict[str, Any]) -> Dict[str, Any]:
 
 
 def nested_new_like(arrays, num_samples, padding_index=-100):
-    """ Create the same nested structure as `arrays` with a first dimension always at `num_samples`."""
+    """Create the same nested structure as `arrays` with a first dimension always at `num_samples`."""
     if isinstance(arrays, (list, tuple)):
         return type(arrays)(nested_new_like(x, num_samples) for x in arrays)
     return np.full_like(arrays, padding_index, shape=(num_samples, *arrays.shape[1:]))