Getting Started

Installation

Install from source (uv):

uv venv
source .venv/bin/activate  # Windows: .venv\Scripts\activate
uv sync

Optional sequence alignment support

DTI sequence alignment diagnostics require EMBOSS stretcher.

sudo apt install emboss

Quick Start

Run one config:

python run.py --config configs/moleculenet/bbbp.yaml --out-root runs

Run a folder of configs:

python run.py --configs configs --out-root runs

Run with baseline benchmarking enabled:

python run.py --configs configs --out-root runs --benchmark

Outputs

Each run directory typically contains:

  • summary.json: high-level audit summary, including runtime metadata for new runs

  • records.csv: per-row standardized records

  • conflicts.jsonl: label conflicts among identical molecules

  • cliffs.jsonl: activity cliffs among similar molecules

  • sequence_alignments.jsonl: DTI sequence diagnostics (DTI only)

  • structure_alignments.jsonl: Foldseek-based structure diagnostics (DTI only)

  • performance.json: baseline model metrics and predictions (when --benchmark is enabled)

Runtime Reporting

Newly generated summary.json files include a runtime block with UTC start/end timestamps, total elapsed seconds/minutes, and stage-level timings. For older artifacts, generate an approximate runtime table with:

python experiments/report_runtimes.py --runs-root runs --out-dir experiments/plots

The report marks each row as exact recorded timing, sequential timestamp estimate, or artifact-write lower bound.