Add continous value (plDDT and PPL) support for Curriculum Learning (#58

)

Co-authored-by: Tianlai Chen <[email protected]>
Co-authored-by: Tianlai Chen <[email protected]>
Co-authored-by: Tianlai Chen <[email protected]>

protein_lm/configs/train/toy_hf.yaml

@@ -9,8 +9,14 @@ dataset:
   sequence_column_name: "sequence"
   max_sequence_length: 10
   do_curriculum_learning: false
-  curriculum_learning_strategy: 'sequence_length'
-  curriculum_learning_column_name: 'sequence_length'
+  curriculum_learning_strategy:
+    - 'sequence_length'
+    - 'ppl'
+    - 'plddt'
+  curriculum_learning_column_name:
+    - 'sequence_length'
+    - 'ppl' 
+    - 'plddt' 
 
 # corresponds to HuggingFace's TrainingArguments
 training_arguments:

protein_lm/configs/train/toy_localcsv.yaml

@@ -9,8 +9,14 @@ dataset:
   sequence_column_name: "sequence"
   max_sequence_length: 10
   do_curriculum_learning: false
-  curriculum_learning_strategy: 'sequence_length'
-  curriculum_learning_column_name: 'sequence_length'
+  curriculum_learning_strategy:
+    - 'sequence_length'
+    - 'ppl'
+    - 'plddt'
+  curriculum_learning_column_name:
+    - 'sequence_length'
+    - 'ppl' 
+    - 'plddt' 
 
 # corresponds to HuggingFace's TrainingArguments
 training_arguments:

protein_lm/modeling/getters/dataset.py

@@ -49,17 +49,24 @@ def set_input_ids(
     return result
 
 def batch_set_curriculum_learning_column(
-    result = None,
-    input_column_name = 'sequence',
-    curriculum_learning_column_name = 'sequence_length',
-    strategy = 'sequence_length'
+    result=None,
+    input_column_name='sequence',
+    curriculum_learning_column_name='sequence_length',
+    strategy='sequence_length'
 ):
+    supported_strategies = ['sequence_length', 'ppl', 'plddt']
+
+    if strategy not in supported_strategies:
+        raise Exception(f'Invalid {strategy} provided. Supported strategy values include {", ".join(supported_strategies)}')
+
     if strategy == 'sequence_length':
-        #LengthGroupedSampler sorts in descending so we make it ascending by multplying with -1
+        # LengthGroupedSampler sorts in descending so we make it ascending by multiplying with -1
         result[curriculum_learning_column_name] = [-len(x) for x in result[input_column_name]]
-        return result
-    else:
-        raise Exception(f'invalid {strategy} provided. Supported strategy values include sequence_length')
+    elif strategy in ['ppl', 'plddt']:
+        result[curriculum_learning_column_name] = [-x for x in result[strategy]]
+
+    return result
+
 def set_labels(result):
     result["labels"] = result["input_ids"].copy()
     return result

protein_lm/tests/test_cl.py

@@ -92,7 +92,7 @@ def create_random_dataframe(sequence_column_name = 'sequence',curriculum_learnin
   random.seed(42)
   df = pd.DataFrame()
   def create_sequence(length):
-    seq = ''.join(random.choice(['A','T','G','C']) for _ in range(length))
+    seq = ''.join(random.choice('ACDEFGHIKLMNPQRSTVWY') for _ in range(length))
     return seq
 
   if curriculum_learning_strategy == 'sequence_length':

protein_lm/tests/test_cl_continuous.py

@@ -0,0 +1,209 @@
+import os
+import pytest
+import torch
+import torch.nn as nn
+import yaml
+from transformers import Trainer
+from protein_lm.modeling.getters.data_collator import get_data_collator
+from protein_lm.modeling.getters.model import get_model
+from protein_lm.modeling.getters.tokenizer import get_tokenizer
+from protein_lm.modeling.getters.training_args import get_training_args
+from datasets import Dataset, load_dataset
+from datasets.dataset_dict import DatasetDict
+from pydantic import BaseModel
+from protein_lm.modeling.getters.dataset import DatasetConfig,get_csv_dataset,set_input_ids,set_labels,batch_set_curriculum_learning_column
+##data collator imports
+from dataclasses import dataclass
+from typing import Dict, Literal,Any, Callable, Dict, List, NewType, Optional, Tuple, Union
+from transformers.tokenization_utils_base import BatchEncoding, PreTrainedTokenizerBase
+import pandas as pd
+import random
+
+CONFIG_PATH = "protein_lm/configs/train/toy_localcsv.yaml"
+strategies = ['ppl']
+strategy2col = {'ppl': 'ppl'} #mapping of strategy to the computed column name storing the values of respective strategy
+total = 0 #number of batches/steps
+unsorted = 0 #number of unsorted batches/steps
+InputDataClass = NewType("InputDataClass", Any)
+
+global max_value_of_previous_batch
+max_value_of_previous_batch = None
+global batch_comparison_values
+batch_comparison_values = []
+
+def cl_data_collator(features: List[InputDataClass]) -> Dict[str, torch.Tensor]:
+    global total
+    global unsorted
+    global max_value_of_previous_batch
+    global batch_comparison_values
+    """
+    Very simple data collator that simply collates batches of dict-like objects and performs special handling for
+    potential keys named:
+
+        - ``label``: handles a single value (int or float) per object
+        - ``label_ids``: handles a list of values per object
+
+    Does not do any additional preprocessing: property names of the input object will be used as corresponding inputs
+    to the model. See glue and ner for example of how it's useful.
+    """
+
+    # In this function we'll make the assumption that all `features` in the batch
+    # have the same attributes.
+    # So we will look at the first element as a proxy for what attributes exist
+    # on the whole batch.
+    if not isinstance(features[0], (dict, BatchEncoding)):
+        features = [vars(f) for f in features]
+
+    first = features[0]
+    batch = {}
+
+    # Special handling for labels.
+    # Ensure that tensor is created with the correct type
+    # (it should be automatically the case, but let's make sure of it.)
+    if "label" in first and first["label"] is not None:
+        label = first["label"].item() if isinstance(first["label"], torch.Tensor) else first["label"]
+        dtype = torch.long if isinstance(label, int) else torch.float
+        batch["labels"] = torch.tensor([f["label"] for f in features], dtype=dtype)
+    elif "label_ids" in first and first["label_ids"] is not None:
+        if isinstance(first["label_ids"], torch.Tensor):
+            batch["labels"] = torch.stack([f["label_ids"] for f in features])
+        else:
+            dtype = torch.long if type(first["label_ids"][0]) is int else torch.float
+            batch["labels"] = torch.tensor([f["label_ids"] for f in features], dtype=dtype)
+
+    # Handling of all other possible keys.
+    # Again, we will use the first element to figure out which key/values are not None for this model.
+    for k, v in first.items():
+
+        if k not in ("label", "label_ids") and v is not None and not isinstance(v, str):
+            if isinstance(v, torch.Tensor):
+                batch[k] = torch.stack([f[k] for f in features])
+            else:
+                if k == 'ppl':
+                    batch[k] = [-f[k] for f in features]
+                else:
+                    batch[k] = torch.tensor([f[k] for f in features])
+    lens = batch['ppl']
+    print('######lens(cl_data_collator)#########')
+    print(lens)
+    total = total + 1
+    try:
+        assert lens == sorted(lens)
+    except:
+        unsorted = unsorted + 1
+        print('not sorted')
+
+    # Compare between currect batch and previous one
+    # Append min of current batch and placeholder
+    batch_comparison_values.append([lens[0], None])
+
+    if max_value_of_previous_batch is not None:
+        # Append max of the previous batch
+        batch_comparison_values[-1][1] = max_value_of_previous_batch
+
+    max_value_of_previous_batch = lens[-1]
+
+    return {'input_ids':batch['input_ids'],'labels': batch['labels']}
+
+
+def create_random_dataframe(sequence_column_name = 'sequence',
+                            curriculum_learning_column_name = 'ppl',
+                            curriculum_learning_strategy = 'ppl',
+                            max_sequence_length = 30,
+                            max_perplexity = 100.0,
+                            n = 5000):
+  assert max_sequence_length > 2
+  random.seed(42)
+  df = pd.DataFrame()
+  def create_sequence(length):
+    seq = ''.join(random.choice('ACDEFGHIKLMNPQRSTVWY') for _ in range(length))
+    return seq
+
+  if curriculum_learning_strategy == 'ppl':
+    df[sequence_column_name] = [create_sequence(random.randint(2, max_sequence_length)) for i in range(n)]
+    df[curriculum_learning_column_name] = [random.uniform(1.0, max_perplexity) for _ in range(n)]
+    return df
+
+@pytest.mark.parametrize("strategy",strategies)
+def test_curriculum_learning(strategy):
+
+    with open(CONFIG_PATH, "r") as cf:
+        print('loading file.....')
+        config_dict = yaml.safe_load(cf)
+
+        config_dict['dataset']['max_sequence_length'] = 40
+        config_dict['dataset']['do_curriculum_learning'] = True
+        config_dict['dataset']['curriculum_learning_column_name'] = strategy2col[strategy]
+        config_dict['dataset']['curriculum_learning_strategy'] = strategy
+        config_dict['dataset']['val_size'] = 100
+        config_dict['dataset']['test_size'] = 100
+        config_dict['dataset']['subsample_size'] = 500
+        config_dict["training_arguments"]['group_by_length'] = True
+        config_dict["training_arguments"]['length_column_name'] = config_dict['dataset']['curriculum_learning_column_name']
+        config_dict["training_arguments"]['remove_unused_columns'] = False # this is necessary to keep curriculum_learning_column_name
+        config_dict["training_arguments"]['per_device_train_batch_size'] = 20
+        config_dict["training_arguments"]['max_steps'] = -1
+        config_dict["training_arguments"]['num_train_epochs'] = 2
+
+        print(config_dict)
+
+    tokenizer = get_tokenizer(config_dict=config_dict["tokenizer"])
+    dataset = DatasetDict()
+    val_df = create_random_dataframe(sequence_column_name = config_dict['dataset']['sequence_column_name'],curriculum_learning_column_name = config_dict['dataset']['curriculum_learning_column_name'],max_sequence_length = config_dict['dataset']['max_sequence_length'], n = config_dict['dataset']['val_size'] )
+    test_df = create_random_dataframe(sequence_column_name = config_dict['dataset']['sequence_column_name'],curriculum_learning_column_name = config_dict['dataset']["curriculum_learning_column_name"],max_sequence_length = config_dict['dataset']['max_sequence_length'], n = config_dict['dataset']['test_size'] )
+    train_df = create_random_dataframe(sequence_column_name = config_dict['dataset']['sequence_column_name'],curriculum_learning_column_name = config_dict['dataset']["curriculum_learning_column_name"],max_sequence_length = config_dict['dataset']['max_sequence_length'], n = config_dict['dataset']['subsample_size'] )
+
+    dataset['train'] = Dataset.from_pandas(train_df)
+    dataset['val'] = Dataset.from_pandas(val_df)
+    dataset['test'] = Dataset.from_pandas(test_df)
+    dataset = dataset.map(
+        lambda e: set_input_ids(
+            result=e,
+            tokenizer=tokenizer,
+            sequence_column_name=config_dict['dataset']['sequence_column_name'],
+            max_sequence_length=config_dict['dataset']['max_sequence_length'],
+        ),
+        batched=True,
+    )
+    dataset = dataset.map(set_labels, batched=True)
+    dataset = dataset.map(lambda e: batch_set_curriculum_learning_column(
+        result = e,
+        input_column_name = config_dict['dataset']['sequence_column_name'],
+        curriculum_learning_column_name = config_dict['dataset']['curriculum_learning_column_name'],
+        strategy = config_dict['dataset']['curriculum_learning_strategy']
+
+    ),batched=True)
+    dataset = dataset.select_columns(['input_ids', 'labels', strategy2col[strategy]])
+    model = get_model(
+        config_dict=config_dict["model"],
+    )
+
+    training_args = get_training_args(
+        config_dict=config_dict["training_arguments"],
+    )
+
+    trainer = Trainer(
+        model=model,
+        args=training_args,
+        train_dataset=dataset["train"],
+        eval_dataset=dataset.get("val", None),
+        data_collator=cl_data_collator,
+    )
+
+    trainer.train()
+
+    threshold = 10
+    num = 0
+    # Iterate over the list
+    print(batch_comparison_values)
+    for i in batch_comparison_values:
+        print(i)
+        current_min_val, previous_max_val = i
+        if previous_max_val is not None:
+            if current_min_val < previous_max_val and previous_max_val - current_min_val <= threshold:
+                num += 1
+    assert num == 0
+    percentage_unsorted = int((unsorted / total) * 100) #computing the number of times the list in collator was not sorted
+    #there are sometimes cases where the list is off by a few entries aa the LengthGroupedSampler has a bit of randomness
+    print(f'percentage_unsorted:{percentage_unsorted}')
+    assert percentage_unsorted < 10 # just a rough heuristic