ivers 0.3.1

Python package for generating realistic training and testing splits for machine learning in cheminformatics and bioinformatics

Ivers

Ivers is a toolkit designed for creating realistic training and testing splits for machine learning models, particularly in cheminformatics and bioinformatics. It provides specialized methods, such as Leaky and AllForOne, to ensure models are trained on data that closely reflects real-world scenarios, improving their predictive performance.

Features

Temporal Leaky

This method allows controlled forward leakage in data, simulating how future models may learn from past observations. A compound can appear in both the training ($T$) and test ($X$) sets if its endpoints are measured at different times. Given a compound $c$, an endpoint $e$, and a measurement date $D_{c,e}$, the split is determined based on a global threshold date, $D_{\text{thresh}}$.

S(c, e) = 
\begin{cases} 
T & \text{if } D_{c,e} < D_{\text{thresh}} \\[6pt]
X & \text{if } D_{c,e} \geq D_{\text{thresh}}
\end{cases}

Temporal AllForFree

Ensures strict temporal independence, making it ideal for scenarios that require accurate long-term model projections without future data leakage. Each compound is assigned exclusively to either the training or test set based on its earliest recorded endpoint date, ${\min D_c}$.

S(c) = 
\begin{cases} 
T & \text{if } \min D_c < D_{\text{thresh}} \\[6pt]
X & \text{if } \min D_c \geq D_{\text{thresh}}
\end{cases}

Temporal Fold Split

Splits data chronologically, progressively increasing the training set size across multiple folds. This approach ensures a more robust evaluation of model performance over time.

Stratified Endpoint Split

Balances training and test sets based on endpoint distributions, ensuring that endpoints remain well-represented.

Balanced Scaffold CV

Enhances the representativeness of cross-validation splits by considering scaffold distributions, making it particularly useful for cheminformatics applications.

Installation

From Source:

git clone https://github.com/IversOhlsson/ivers.git
cd ivers
pip install -r requirements.txt

From Pip

pip install ivers

Usage Example

The library includes several functions tailored for different splitting strategies:

• stratify_endpoint, stratify_split_and_cv: Generate train/test and cross-validation splits while maintaining endpoint balance.
• leaky_endpoint_split, allforone_endpoint_split: Create single train/test splits while incorporating temporal dynamics.
• allforone_folds_endpoint_split, leaky_folds_endpoint_split: Generate progressive training splits that increase dataset size over time.
• balanced_scaffold_cv: Supports balanced scaffold-based cross-validation, improving data representativeness.

import pandas as pd
from ivers.temporal import (
    allforone_endpoint_split, 
    allforone_folds_endpoint_split, 
    leaky_endpoint_split, 
    leaky_folds_endpoint_split
)
from ivers.stratify import stratify_split_and_cv  
from ivers.scaffold import balanced_scaffold

# Sample DataFrame to demonstrate usage
# ----- Create a sample DataFrame -----
data = {
    'smiles':  [ 
        'C1CCCCC1', 'C1=CC=CC=C1', 'CCO', 'CCN',   'CCC', 
        'C1CCOC1', 'C1=CC=CN=C1', 'CCOC',  'CCNC',  'CCCC', 
        'C1CCNCC1', 'C1=CC=CC=N1', 'CCCO', 'CCCN',   'CCCCC', 
        'C1CCSCC1',  'C1=CC=COC1', 'CCCCO', 'CCCCN', 'CCCCCC', 
        'C1CCCN1', 'C1=CC=CC=C1O', 'CCOCC', 'CCNCC',  'CCCCCCC', 
        'C1CCCNC1', 'C1=CC=C(O)C=C1','CCCCCO', 'CCCCCN', 'CCCCCCCC' ],
    'value': [
        5.0, 7.2, 3.1, 4.8, 6.0,
        5.1, 7.3, 3.2, 4.9, 6.1,
        5.2, 7.4, 3.3, 5.0, 6.2,
        5.3, 7.5, 3.4, 5.1, 6.3,
        5.4, 7.6, 3.5, 5.2, 6.4,
        5.5, 7.7, 3.6, 5.3, 6.5
    ],
    'date_col1': ['2021-01-10', '2021-02-15', '2021-03-20', '2021-04-25', '2021-05-30'] * 6,
    'date_col2': ['2021-01-12', '2021-02-18', '2021-03-25', '2021-04-28', '2021-06-02'] * 6,
    'endpoint1': [100, 200, 150, 180, 170] * 6,
    'endpoint2': [110, 210, 160, 190, 180] * 6,
    'other_info': ['A', 'B', 'C', 'D', 'E'] * 6,
    'exclude_col': ['ignore'] * 30
}

df = pd.DataFrame(data)

# Mapping from endpoint names to their respective date columns
endpoint_date_columns = {
    'endpoint1': 'date_col1',
    'endpoint2': 'date_col2'
}

# Allforone: Simple train/test split
train_df, test_df = allforone_endpoint_split(
    df.copy(),
    split_size=0.5,
    smiles_column='smiles',
    endpoint_date_columns=endpoint_date_columns
)

# Leaky: Train/test split with data leakage
train_df_leaky, test_df_leaky = leaky_endpoint_split(
    df.copy(),
    split_size=0.5,
    smiles_column='smiles',
    endpoint_date_columns=endpoint_date_columns
)

# Allforone: Multiple folds with additional features for Chemprop
folds_splits = allforone_folds_endpoint_split(
    df.copy(),
    num_folds=2,
    smiles_column='smiles',
    endpoint_date_columns=endpoint_date_columns,
    chemprop=True,
    save_path='.',
    aggregation='first',
    feature_columns=feature_columns
)
# Leaky: Multiple folds with leaky data handling
folds_leaky = leaky_folds_endpoint_split(
    df.copy(),
    num_folds=2,
    smiles_column='smiles',
    endpoint_date_columns=endpoint_date_columns,
    chemprop=False,
    save_path='.',         # adjust this path as needed
    feature_columns=feature_columns
)

# ----- Stratified Split and CV -----
test_size = 0.4   
n_splits = 2      

aggregation_rules = {}

test_df_strat, cv_splits_strat, col_abbreviations = stratify_split_and_cv(
    df.copy(),
    endpoints=endpoints,
    smiles_column='smiles',
    exclude_columns=exclude_columns,
    aggregation_rules=aggregation_rules,
    test_size=test_size,
    n_splits=n_splits,
    random_state=1337,
    label_column=None,
    chemprop=False,
    save_path='.',
    feature_columns=feature_columns
)

# ----- Balanced Scaffold Cross-Validation -----
df_scaffold, scaffold_splits, scaffold_fold_counts = balanced_scaffold(
    df=df,
    endpoints=endpoints,
    smiles_column='smiles',
    n_splits=n_splits,
    random_state=1337,
    feature_columns=feature_columns,
    exclude_columns=exclude_columns,
    chemprop=False,
    save_path='.'
)

Integration with Chemprop

Ivers supports direct integration with Chemprop, allowing you to generate training and test splits that work seamlessly with its training scripts. Just set chemprop=True in any splitting function to output Chemprop-compatible files, making dataset preparation more straightforward.

Reference