Massspecgym

MassSpecGym Reference

NeurIPS 2024 Spotlight benchmark for molecular discovery from MS/MS spectra. Three challenges: de novo generation, molecule retrieval, spectrum simulation.

• GitHub: https://github.com/pluskal-lab/MassSpecGym
• Paper: arXiv:2410.23326
• HuggingFace: roman-bushuiev/MassSpecGym
• PyPI: massspecgym (v1.3.1, requires Python ≥3.11)

Installation

pip install massspecgym
# or with extras:
pip install massspecgym[notebooks,dev]

Dataset Schema

231,104 spectra total (train: 194,119 / val: 19,429 / test: 17,556). HuggingFace dataset with a single main subset.

When loaded via load_massspecgym(), identifier becomes the DataFrame index (not a column). The 13 columns are:

| Column | Type (loaded) | Type (raw HF) | Description | |--------|--------------|----------------|-------------| | mzs | np.ndarray (float64) | str | m/z values per peak | | intensities | np.ndarray (float64) | str | Intensity values per peak | | smiles | str | str | SMILES string (5–255 chars) | | inchikey | str | str | InChI Key (14 chars) | | formula | str | str | Molecular formula | | precursor_formula | str | str | Precursor formula | | parent_mass | float64 | float64 | Parent mass (59–998) | | precursor_mz | float64 | float64 | Precursor m/z (60–999) | | adduct | str | str | [M+H]+ or [M+Na]+ | | instrument_type | str | str | Orbitrap or QTOF | | collision_energy | float64 | float64 | 0–358, nullable | | fold | str | str | train, val, or test | | simulation_challenge | bool | bool | Part of simulation challenge |

Important: In the raw HuggingFace Parquet files, mzs and intensities are comma-separated strings. load_massspecgym() parses them to numpy arrays automatically.

Data Loading

Quick load (pandas DataFrame)

from massspecgym.utils import load_massspecgym

df = load_massspecgym()              # full dataset, identifier as index
df = load_massspecgym(fold="train")  # single fold

Returns DataFrame with mzs/intensities already parsed to numpy arrays.

Direct HuggingFace load (no massspecgym dependency)

from datasets import load_dataset
ds = load_dataset("roman-bushuiev/MassSpecGym")
# ds["val"] is a Dataset; use .to_pandas() to get DataFrame
# NOTE: mzs/intensities remain as strings — parse manually

Direct Parquet load

import pandas as pd
df = pd.read_parquet("hf://datasets/roman-bushuiev/MassSpecGym/main/val/*.parquet")

Utility functions

from massspecgym.utils import (
    load_massspecgym,         # full dataset → DataFrame
    load_massspecgym_mols,    # molecules only → Series of SMILES
    load_train_mols,          # training fold molecules
    load_val_mols,            # validation fold molecules
    load_unlabeled_mols,      # ~3.9M unlabeled molecules (disjoint from test)
    parse_spec_array,         # comma-separated string → np.ndarray
    pad_spectrum,             # pad to fixed peak count
    compute_mass,             # SMILES → exact mass via RDKit
)

Splits

Fold assignments are in the fold column: train, val, test. Unique molecules: 25,046 in train, 31,602 total. The MassSpecDataModule reads these from the dataset metadata or a custom TSV with identifier and fold columns.

Transforms

Spectrum transforms (SpecTransform subclasses)

from massspecgym.data.transforms import SpecTokenizer, SpecBinner, SpecToMzsInts

# Top-k peaks as (m/z, intensity) matrix, zero-padded
SpecTokenizer(n_peaks=60, prec_mz_intensity=1.1)
# Output: tensor of shape (n_peaks+1, 2) if prec_mz_intensity set, else (n_peaks, 2)

# Binned histogram representation
SpecBinner(max_mz=1005, bin_width=1, to_rel_intensities=True)
# Output: tensor of shape (max_mz / bin_width,)

# Sparse representation (no padding)
SpecToMzsInts(n_peaks=None, mz_from=10.0, mz_to=1000.0, mz_bin_res=0.01)
# Output: dict with separate mz and intensity tensors

Molecule transforms (MolTransform subclasses)

from massspecgym.data.transforms import (
    MolFingerprinter,    # SMILES → Morgan fingerprint vector
    MolToInChIKey,       # SMILES → InChIKey string
    MolToFormulaVector,  # SMILES → 118-dim element count vector
    MolToPyG,            # SMILES → PyTorch Geometric Data graph
    MolToFingerprints,   # SMILES → concatenated multi-type fingerprints
)

MolFingerprinter(type="morgan", fp_size=2048, radius=2)  # output: (fp_size,) int32
MolToInChIKey(twod=True)  # output: str (14-char InChIKey)
MolToFormulaVector()  # output: (118,) element count vector
MolToPyG(pyg_node_feats=[...], pyg_edge_feats=[...])
MolToFingerprints(fp_types=["morgan", "maccs", "rdkit"])

Dataset Classes

Base: MassSpecDataset

from massspecgym.data import MassSpecDataset

dataset = MassSpecDataset(
    spec_transform=SpecTokenizer(n_peaks=60),
    mol_transform=MolFingerprinter(),
    pth=None,                  # downloads from HF if None
    return_mol_freq=False,     # include molecular frequency in output
    return_identifier=False,   # include identifier string in output
    identifiers_subset=None,   # filter to specific IDs
    dtype=torch.float32,
)

__getitem__ returns dict. Base keys always present: spec, mol, precursor_mz, adduct. With defaults, that's all 4 keys. Set return_mol_freq=True to add mol_freq (tensor), return_identifier=True to add identifier (str).

RetrievalDataset

from massspecgym.data import RetrievalDataset

dataset = RetrievalDataset(
    spec_transform=SpecTokenizer(n_peaks=60),
    mol_transform=MolFingerprinter(fp_size=4096),
    mol_label_transform=MolToInChIKey(),  # default
    candidates_pth=None,                   # downloads candidate JSON if None
)

Per-item keys (from __getitem__): base keys plus smiles (str), candidates_smiles (list[str]), candidates_mol (tensor [N_cands, fp_size]), labels (list[bool]), identifier, mol_freq.

Per-batch keys (after collate_fn): candidates are flattened across the batch:

• candidates_mol: (total_cands, fp_size) — all candidates concatenated
• candidates_smiles: flat list of all candidate SMILES
• labels: (total_cands,) bool tensor
• batch_ptr: (batch_size,) int64 tensor — number of candidates per sample
• smiles: list of query SMILES
• Plus standard: spec, mol, precursor_mz, adduct, mol_freq, identifier

Candidate lists are variable-length per sample. Use batch_ptr to reconstruct per-sample groups (e.g., torch.split(scores, batch_ptr.tolist())).

DataModule

from massspecgym.data import MassSpecDataModule

dm = MassSpecDataModule(
    dataset=dataset,
    batch_size=32,
    num_workers=0,
    persistent_workers=True,
    split_pth=None,  # optional custom split TSV
)

Splits into train/val/test subsets based on the fold column. Training loader shuffles; val/test do not.

Model Base Classes

Built on PyTorch Lightning.

MassSpecGymModel (abstract base)

from massspecgym.models.base import MassSpecGymModel, Stage

# Stage enum: TRAIN, VAL, TEST, NONE
# stage.to_pref() → "train_", "val_", "test_", or ""

class MassSpecGymModel(pl.LightningModule, ABC):
    def __init__(self, lr=1e-4, weight_decay=0.0, ...):
        ...

    @abstractmethod
    def step(self, batch: dict, stage: Stage) -> dict:
        # Must return dict with at least "loss" key
        ...

    def configure_optimizers(self):
        # Default: Adam(lr, weight_decay)
        ...

RetrievalMassSpecGymModel

from massspecgym.models.retrieval.base import RetrievalMassSpecGymModel

class MyRetrieval(RetrievalMassSpecGymModel):
    def __init__(self, at_ks=(1, 5, 20), myopic_mces_kwargs=None, **kwargs):
        super().__init__(at_ks=at_ks, **kwargs)

    def step(self, batch: dict, stage: Stage) -> dict:
        # batch keys: spec, mol, candidates_mol, labels, batch_ptr, smiles, ...
        # Must return: dict(loss=..., scores=...)
        # scores: flat tensor aligned with concatenated candidates_mol
        ...

Evaluation methods (called automatically):

• evaluate_retrieval_step() — computes HitRate@K (Recall@K) using torchmetrics.functional.retrieval
• evaluate_mces_at_1() — MCES distance between top-ranked and ground-truth molecule
• test_step() — sorts candidates by score, optionally saves to DataFrame

DeNovoMassSpecGymModel

For structure generation from spectra.

SimulationMassSpecGymModel

For spectrum prediction from molecular structures.

Evaluation Metrics

| Metric | Description | Direction | |--------|-------------|-----------| | Recall@K (HitRate@K) | Ground truth in top-K ranked | higher = better | | MRR | Mean Reciprocal Rank | higher = better | | MCES@1 | Max Common Edge Subgraph distance at rank 1 | lower = better |

MCES is computed via MyopicMCES — graph edit distance based on maximum common edge subgraph.

Retrieval Candidate Libraries

MassSpecGym provides two candidate libraries per spectrum for retrieval:

1. Weight-based: candidates by molecular weight from precursor m/z
2. Formula-based: candidates by matching chemical formula

Candidate mappings are JSON files: {query_smiles: [candidate_smiles_1, ...]}. Downloaded automatically by RetrievalDataset.

Special Tokens

from massspecgym.definitions import PAD_TOKEN, SOS_TOKEN, EOS_TOKEN, UNK_TOKEN
# "", "", "", ""

Common Patterns

Bypassing massspecgym for custom pipelines (like GLMR)

The massspecgym package is PyTorch-Lightning-heavy. For custom training loops:

# Option A: use load_massspecgym() for data, skip their DataModule/Model classes
from massspecgym.utils import load_massspecgym
df = load_massspecgym(fold="train")
# df has parsed mzs (np.ndarray), intensities (np.ndarray), smiles (str), etc.
# Build your own Dataset/DataLoader around this DataFrame

# Option B: skip massspecgym entirely, load from HF
from datasets import load_dataset
ds = load_dataset("roman-bushuiev/MassSpecGym")
df = ds["val"].to_pandas()
# Parse mzs/intensities yourself:
import numpy as np
df["mzs"] = df["mzs"].apply(lambda s: np.fromstring(s, sep=","))
df["intensities"] = df["intensities"].apply(lambda s: np.fromstring(s, sep=","))

Retrieval evaluation without their framework

# Compute Recall@K manually
def recall_at_k(ranks, k):
    return (ranks <= k).float().mean().item() * 100

# Compute MRR manually
def mrr(ranks):
    return (1.0 / ranks).mean().item() * 100

# MCES requires rdkit + myopic-mces package
from myopic_mces import MCES
mces_dist = MCES(mol1, mol2)  # lower = more similar

Loading candidate libraries directly

Candidate JSONs map each query SMILES to its candidate list. They're auto-downloaded by RetrievalDataset, but you can also download them manually from the HuggingFace repo's data files.

Key Gotchas

1. Python ≥3.11 required for massspecgym package. If using Python 3.10, load data via HuggingFace datasets directly instead.
2. mzs/intensities are strings in the raw HuggingFace dataset — must parse to arrays.
3. Variable-length candidates — each query has a different number of candidates. Handle with padding or batch_ptr.
4. Fold column — use fold column for splits, not random splitting. The test fold is held out.
5. InChIKey for matching — ground-truth matching uses InChIKey comparison, not SMILES string equality.
6. SpecTokenizer prepends precursor — if prec_mz_intensity is set, an extra row (precursor_mz, prec_mz_intensity) is prepended, making output shape (n_peaks+1, 2).
7. MolFingerprinter returns int32 but the dataset casts tensors to float32 by default (dtype param). So mol in batch is float32 even though raw fingerprints are int32.
8. RetrievalDataset always returns mol_freq/identifier regardless of the return_mol_freq/return_identifier flags (those only apply to base MassSpecDataset).

Source & license

This open-source skill is cataloged on AgentStack and links to its original source — we do not rehost the code.

• Author: mcox3406
• Source: mcox3406/claude-comp-chem-skills
• License: MIT

Install and usage instructions live in the source repository linked above.