D4CMPP2 1.0.0

PyTorch Geometric molecular property prediction models

D4CMPP2

D4CMPP2 is the next-generation implementation of the D4CMPP framework. It is based on the original D4CMPP project and was extensively redeveloped with OpenAI Codex through an AI-assisted, test-driven engineering workflow.

The package provides a unified PyTorch Geometric framework for molecular property prediction, supporting ordinary molecular graphs, compound–solvent pairs, and interpretable ISA models.

Key advantages of D4CMPP2 include:

• Unified model interface — Train general molecular, solvent-aware, and ISA-based models through a consistent Python API and command-line interface.
• Multiple graph neural network architectures — Use GCN, MPNN, DMPNN, AttentiveFP, GAT, graph-contribution, and ISA model families within the same workflow.
• Interpretable molecular predictions — Analyze fragment- and atom-level contributions with ISA models while preserving alignment between molecular structures and attribution scores.
• Reliable data handling — Detect invalid SMILES, missing columns, non-numeric targets, misaligned inputs, incompatible graph caches, and invalid dataset splits before they silently affect training.
• Efficient repeated experiments — Reuse fingerprinted graph caches and optionally skip previously completed data-quality and per-graph cache checks.
• Transfer learning and training resumption — Initialize compatible model parameters from existing models or resume complete optimizer and scheduler states from checkpoints.
• Reproducible experimentation — Control random seeds, deterministic execution, dataset splitting, and run metadata across CPU and CUDA environments.
• Multi-target and multi-input support — Train on multiple target properties, compound–solvent pairs, and additional numeric features without changing the overall workflow.
• Saved-model analysis — Reload trained models through Analyzer for single or batch prediction while retaining invalid and duplicate input rows.
• Experiment tracking and optimization — Record run manifests, compare completed experiments, and perform grid or Bayesian hyperparameter optimization.
• Backward compatibility — Preserve established D4CMPP APIs, model assets, configuration conventions, and legacy loading paths where practical.
• Deployment-oriented validation — Test source execution, packaged distributions, CLI entry points, model persistence, Analyzer workflows, and CPU-based end-to-end training.

Requirements and installation

Supported runtime:

• Python 3.10-3.12
• PyTorch >=2.2,<3
• PyTorch Geometric >=2.8,<3
• Linux and Windows
• CPU, or CUDA with a matching PyTorch build

Install the appropriate PyTorch build for the machine first, then install D4CMPP2:

python -m pip install D4CMPP2

Notebook extras are optional:

python -m pip install "D4CMPP2[notebook]"

DGL is not installed or loaded. DGL graph caches cannot be renamed or reused as PyG caches.

Supported models

Family	Network IDs
General	GCN, MPNN, DMPNN, AFP, GAT
With solvent	GCNwS, MPNNwS, DMPNNwS, AFPwS, GATwS
ISA	GC, ISAT, ISATPN

AGC, MegNet, MegNetwS, ALIGNN, and ALIGNNwS are not part of the PyG-only release.

Input data

A general model needs a compound SMILES column and one or more numeric target columns. A wS model additionally needs a solvent SMILES column:

compound,solvent,Solubility
CCO,O,-0.31
CCN,CO,-0.18

Useful optional columns and arguments:

• set: predefined train, val, and test labels.
• numeric_input_columns: additional finite numeric model inputs.
• molecule_columns: molecule columns in their model input order.
• explicit_h_columns: molecule columns that require explicit hydrogens.

Without a set column, the default split is a seeded 80/10/10 random split. Invalid SMILES, missing columns, non-numeric inputs, all-NaN targets, and misaligned arrays fail with the affected path, column, value, or row.

Quickstart

The package includes a small test.csv. Run a two-epoch CPU smoke training:

d4cmpp2 --data test --target Abs --network GCN --device cpu --epoch 2

Equivalent Python:

from D4CMPP2 import train

model_path = train(
    data="test",
    target=["Abs"],
    network="GCN",
    device="cpu",
    max_epoch=2,
    batch_size=4,
)
print(model_path)

Runnable examples for training, solvent and ISA models, saved-model modes, inference, uncertainty, optimization, callbacks, custom networks, and the CLI are indexed in examples/README.md.

For GPU training, use device="cuda:0" or --device cuda:0. D4CMPP2 validates the requested index and does not silently fall back to CPU.

Solvent and ISA

from D4CMPP2 import train

solvent_model = train(
    data="solvent_data.csv",
    target=["Solubility"],
    network="GCNwS",
    molecule_columns=["compound", "solvent"],
    device="cpu",
)

isa_model = train(
    data="Aqsoldb",
    target=["Solubility"],
    network="ISATPN",
    sculptor_index=(6, 2, 0),
    device="cpu",
)

sculptor_index=(split, combine, absorb) controls ISA fragmentation. Existing fragment rules and saved functional_group.csv files are part of the model contract.

Training behavior

The most important defaults are:

Key	Default
batch_size	256
max_epoch	2000
optimizer	"Adam"
learning_rate	0.001
weight_decay	0.0005
device	"cuda:0"
scaler	"standard"
verbose	True

Configuration is resolved into an isolated working copy. Historical precedence is retained for numerical compatibility:

Mode	Lower to higher precedence
Scratch	defaults, API/CLI, registry
Full resume	saved config, explicit resume overrides
LOAD_PATH continue	saved config, current defaults/API
Transfer	source config, current defaults/API, registry
Optimization trial	resolved base, trial values

Unknown keys remain available to legacy configs and custom implementations. Resolved provenance is written to the run manifest without changing config.yaml.

Splitting and reproducibility

split_strategy accepts:

• "auto": use set when present, otherwise random 80/10/10.
• "random": always use row-level random splitting.
• "predefined": require the set column.
• "scaffold": keep RDKit Murcko-scaffold groups within one split.

Normal runs write split_report.json and split_assignments.csv.

model_path = train(
    data="Aqsoldb",
    target=["Solubility"],
    network="GCN",
    random_seed=42,
    split_random_seed=42,
    deterministic_algorithms=True,
    device="cpu",
)

random_seed controls Python, NumPy, torch/CUDA, shuffle, DataLoader workers, dropout, and partial-training selection. split_random_seed controls only the data split. Deterministic algorithms may reduce GPU performance or reject an unsupported operation.

Resume, continue, and transfer

The three saved-model modes are mutually exclusive:

• RESUME_PATH or --resume: exact full-state resume from checkpoints/latest.ckpt.
• LOAD_PATH or --load: load final.pth but reset optimizer, schedulers, epoch, and RNG.
• TRANSFER_PATH or --transfer: copy compatible same-name/same-shape parameters into a new model.

Full checkpoints preserve optimizer, both schedulers, epoch, best metric, early-stopping state, and RNG state. Transfer writes transfer_report.json with loaded and skipped parameters plus the source weight hash.

Outputs and caches

Training returns the model directory, normally below ./_Models/. Important artifacts include:

• config.yaml, network.py, final.pth, scaler.pkl
• network_identity.json, model_summary.txt
• checkpoints/latest.ckpt, checkpoints/best.ckpt
• runs/<run_id>/run_manifest.json
• result/prediction.csv, metrics, curves, and plots
• data-quality and split reports

Graph caches are atomic, fingerprinted PyG schema-v2 files. Identity includes ordered SMILES, feature dimensions, explicit-hydrogen settings, and ISA rules. The cache policies are:

• "v2": validate the current cache and fail clearly if it is incompatible.
• "regenerate": rebuild an invalid v2 cache from the source CSV.
• "legacy": explicitly load a compatible PyG v1 cache with a warning.

DGL caches are preserved but never loaded.

Data preparation reports when CSV validation and graph-cache loading start and finish, so a large cache no longer looks stalled before graph generation. Full per-graph tensor validation remains the default. After a cache has already been verified and the same data is trained repeatedly, it can be skipped explicitly:

train(
    data="data.csv",
    target=["target"],
    network="GCN",
    data_quality_report=False,
    validate_graph_cache=False,
)

data_quality_report=False skips the slower canonical-SMILES duplicate, split-overlap, and issue report after that dataset has already been reviewed. Required CSV columns, numeric values, split labels, row alignment, and nonempty targets are still checked. validate_graph_cache=False still checks the cache recipe, ordered SMILES, and graph count; it only skips tensor shape, dtype, finite-value, and edge-alignment checks inside each cached graph. Newly generated graphs are always validated before saving.

The CLI equivalents are --skip-data-quality-report and --skip-graph-cache-validation.

Prediction and analysis

from D4CMPP2 import Analyzer

analyzer = Analyzer(model_path, device="cpu", save_result=False)
print(analyzer.predict(["CCO", "CCN"]))

Analyzer reads the saved config and selects the general, solvent, or ISA implementation. It requires config.yaml, network.py, and final.pth; non-identity scaling also requires scaler.pkl, and ISA requires the saved functional_group.csv. Load pickle-based artifacts only from trusted model folders.

Use row-preserving inference when duplicates or invalid inputs matter:

result = analyzer.predict_rows(
    compound=["CCO", "CCO", "not-a-smiles"],
)
print(result.to_dataframe())

Every row retains its original index, inputs, prediction, status, and error. Solvent and numeric-input models require every saved input column with equal length:

result = analyzer.predict_rows(
    compound=["CCO", "CCN"],
    solvent=["O", "CO"],
    temperature=[298.0, 310.0],
)

CSV inference preserves source rows and commits the output atomically:

output_path = analyzer.predict_csv(
    "molecules.csv",
    "molecules_prediction.csv",
    uncertainty_samples=30,
    uncertainty_seed=42,
)

predict_uncertainty() uses MC dropout and Analyzer.predict_ensemble() uses compatible independently trained models. Their standard deviations are model dispersion estimates, not calibrated prediction intervals.

ISA analyzers also provide analyze_rows() and plot_analysis(). Fragment indices are validated against atom alignment before scores or features are returned.

Experiment comparison and optimization

from D4CMPP2 import compare_experiments

leaderboard = compare_experiments(
    ["./_Models"],
    output_path="leaderboard.csv",
    metric="val_rmse",
)

Ranking is calculated separately per target. Legacy, failed, and interrupted runs remain visible without borrowing another run's metrics.

For new hyperparameter searches, use the model-aware API:

import D4CMPP2

result = D4CMPP2.optimize(
    data="Aqsoldb.csv",
    target=["Solubility"],
    network="GCN",
    HP=["hidden_dim", "dropout"],
    optimize_strategy="bayesian",
    n_trials=20,
    device="cpu",
)
print(result.best_params, result.best_model_path)

HP=None uses the model's default optimization space. A key list uses declared model ranges; a dictionary supplies categorical values or numeric ranges. Supported strategies are "bayesian" and "grid". Atomic JSON/CSV summaries and trial directories allow compatible searches to resume.

The legacy grid_search() API remains available with its historical None return value and continue-on-trial-error behavior.

Callbacks and custom networks

Observation-only training callbacks are runtime objects and are not saved:

from D4CMPP2 import train
from D4CMPP2.src.TrainManager.callbacks import EventHistory

history = EventHistory()
model_path = train(
    data="test",
    target=["Abs"],
    network="GCN",
    device="cpu",
    callbacks=[history],
)

Callbacks receive immutable run/epoch/validation/checkpoint/error events. A callback failure stops training and preserves the original failure contract.

Custom models subclass D4CMPP2.MolecularNetwork, declare model_name, input_contract, hyperparameters, and optionally compute_loss(), then call:

D4CMPP2.register_network(CustomGCN, data_contract="molecule")

Available data contracts are "molecule", "solvent", and "isa". Define the class at module scope in an importable file. Training copies that source to the model directory as network.py; reload and transfer prefer the saved snapshot. See examples/custom_network.py for a complete implementation.

CLI

python -m D4CMPP2 --help
d4cmpp2 --help

Target columns are comma-separated. --quiet hides routine information and progress but not warnings or errors. --cuda 0 remains a deprecated alias for --device cuda:0.

Migration and compatibility

• Public train, grid_search, Analyzer, Segmentator, and Data names remain available.
• New runs fit the target scaler on training rows by default. Old configs without the policy retain historical full-data scaling with a warning.
• The loader prefers the saved model folder's network.py, config, weights, scaler, and ISA rules over obsolete absolute paths.
• The historical ISATPM saved name is supported through the ISATPN compatibility adapter.
• Keep DGL-era models and caches with their original environment for archival reproduction. Automatic conversion is not provided.
• Package version and saved-model/config contract version are separate.

Public API or saved-asset compatibility breaks require a major release. Deprecations should include a warning and a migration path.

Troubleshooting

• torch_geometric import failure: install torch and PyG builds compatible with the same Python and CPU/CUDA runtime.
• CUDA unavailable or index out of range: select an existing cuda:N or use device="cpu" explicitly.
• Missing target/SMILES column: compare the reported available columns with the configured target and molecule columns.
• Invalid SMILES: fix or remove the reported rows; related arrays share one alignment mask.
• Cache shape or recipe mismatch: use the source CSV with graph_cache_policy="regenerate" after reviewing the diagnostic.
• Model path missing or ambiguous: pass the exact saved-model directory.
• Old model fails to load: preserve the complete folder and original environment; report config, package versions, and the error without sharing private data.

Repository maintenance

Implementation contracts, compatibility constraints, validation commands, and change notes live in the nearest AGENTS.md file within each source area. Read the workspace and nearest folder instructions before modifying code.