| # Commands to run (Spec-RAG retrieval + sanity check + oracle) |
|
|
| Paths below use your env: `Spec-RAG`, `SpecBridge`, `De-SpecBridge`, `MassSpecGym_test.mgf`, and `out/retrieval/`. |
|
|
| --- |
|
|
| ## Improving retrieval performance (candidates_A / candidates_B) |
|
|
| - **`--ef-search 512`** (default): Higher FAISS HNSW `ef_search` at query time improves ANN recall. Increase to 1024 if you need better recall and can afford slower search. |
| - **`--formula-filter`**: When MGF has `FORMULA`/`formula`, restricts candidates to same-formula molecules (over-fetches from FAISS then reranks). Use this so Recall/Tanimoto improve when the library contains same-formula molecules. |
| - **`--chemberta-model`**: Must match the model used to build the library (`build_library.py --chemberta-model`). Default `Derify/ChemBERTa_augmented_pubchem_13m`. If your SpecBridge checkpoint was trained with a different ChemBERTa, set this and rebuild the library with that model. |
| - **Formula over-fetch**: `--formula-min-fetch`, `--formula-max-fetch`, `--formula-fetch-multiplier` control how many vectors are fetched when using `--formula-filter`; higher values can improve recall when formula buckets are large. |
| - **Rebuild FAISS with higher quality**: `python scripts/build_faiss.py --library-dir ... --ef-search 256` (default is now 256) before retrieving. |
|
|
| --- |
|
|
| ## 1) Build library (once) |
|
|
| ```bash |
| cd /cluster/tufts/liulab/yiwan01/Spec-RAG |
| |
| python scripts/build_library.py \ |
| --smiles-path /cluster/tufts/liulab/yiwan01/De-SpecBridge/data/pubchem_clean.smi \ |
| --out-dir /cluster/tufts/liulab/yiwan01/Spec-RAG/out/retrieval/library \ |
| --despecbridge-path /cluster/tufts/liulab/yiwan01/De-SpecBridge |
| ``` |
|
|
| --- |
|
|
| ## 2) Build FAISS indices |
|
|
| ```bash |
| python scripts/build_faiss.py \ |
| --library-dir /cluster/tufts/liulab/yiwan01/Spec-RAG/out/retrieval/library |
| ``` |
|
|
| --- |
|
|
| ## 3) Train mappers (only if using Variant A without --smited-mapper-ckpt) |
|
|
| ```bash |
| python scripts/train_mapper.py \ |
| --mgf-path /cluster/tufts/liulab/yiwan01/SpecBridge/data/MassSpecGym_train.mgf \ |
| --specbridge-ckpt /cluster/tufts/liulab/yiwan01/SpecBridge/runs/specbridge_align_chemberta_pub_v3g_msgym_mapper_spec/ckpt_001200.pt \ |
| --dreams-ckpt /cluster/tufts/liulab/yiwan01/SpecBridge/data/ssl_model.ckpt \ |
| --out-dir /cluster/tufts/liulab/yiwan01/Spec-RAG/out/retrieval/mappers \ |
| --despecbridge-path /cluster/tufts/liulab/yiwan01/De-SpecBridge |
| ``` |
|
|
| --- |
|
|
| ## 4) Retrieve (Variants A, B, C) |
|
|
| **Variant A (SMI-TED only; pretrained mapper):** |
|
|
| ```bash |
| python scripts/retrieve_generate.py \ |
| --mgf-path /cluster/tufts/liulab/yiwan01/SpecBridge/data/MassSpecGym_test.mgf \ |
| --library-dir /cluster/tufts/liulab/yiwan01/Spec-RAG/out/retrieval/library \ |
| --specbridge-ckpt /cluster/tufts/liulab/yiwan01/SpecBridge/runs/specbridge_align_chemberta_pub_v3g_msgym_mapper_spec/ckpt_001200.pt \ |
| --dreams-ckpt /cluster/tufts/liulab/yiwan01/SpecBridge/data/ssl_model.ckpt \ |
| --smited-mapper-ckpt /cluster/tufts/liulab/yiwan01/De-SpecBridge/runs/smited_mapper_final/mapper_best.pt \ |
| --despecbridge-path /cluster/tufts/liulab/yiwan01/De-SpecBridge \ |
| --variant A \ |
| --K 100 \ |
| --ef-search 512 \ |
| --formula-filter \ |
| --out-jsonl /cluster/tufts/liulab/yiwan01/Spec-RAG/out/retrieval/candidates_A.jsonl |
| ``` |
|
|
| **Variant B (ChemBERTa retrieval; no mapper-dir needed):** |
|
|
| ```bash |
| python scripts/retrieve_generate.py \ |
| --mgf-path /cluster/tufts/liulab/yiwan01/SpecBridge/data/MassSpecGym_test.mgf \ |
| --library-dir /cluster/tufts/liulab/yiwan01/Spec-RAG/out/retrieval/library \ |
| --specbridge-ckpt /cluster/tufts/liulab/yiwan01/SpecBridge/runs/specbridge_align_chemberta_pub_v3g_msgym_mapper_spec/ckpt_001200.pt \ |
| --dreams-ckpt /cluster/tufts/liulab/yiwan01/SpecBridge/data/ssl_model.ckpt \ |
| --variant B \ |
| --K 100 \ |
| --ef-search 512 \ |
| --formula-filter \ |
| --chemberta-model Derify/ChemBERTa_augmented_pubchem_13m \ |
| --out-jsonl /cluster/tufts/liulab/yiwan01/Spec-RAG/out/retrieval/candidates_B.jsonl |
| ``` |
|
|
| **Variant B formula-keyed candidate-pool mode (direct exact rerank inside the provided candidate pool; no dependency on library overlap, and no FAISS needed unless a query falls back):** |
|
|
| ```bash |
| python scripts/retrieve_generate.py \ |
| --mgf-path /cluster/tufts/liulab/yiwan01/SpecBridge/data/MassSpecGym_test.mgf \ |
| --library-dir /cluster/tufts/liulab/yiwan01/Spec-RAG/out/retrieval/library \ |
| --specbridge-ckpt /cluster/tufts/liulab/yiwan01/SpecBridge/runs/specbridge_align_chemberta_pub_v3g_msgym_mapper_spec/ckpt_001200.pt \ |
| --dreams-ckpt /cluster/tufts/liulab/yiwan01/SpecBridge/data/ssl_model.ckpt \ |
| --variant B \ |
| --K 100 \ |
| --formula-filter \ |
| --candidate-json /cluster/tufts/liulab/yiwan01/SpecBridge/data/MassSpecGym_retrieval_candidates_formula.json \ |
| --candidate-key-field formula \ |
| --out-jsonl /cluster/tufts/liulab/yiwan01/Spec-RAG/out/retrieval/candidates_B_benchmark.jsonl |
| ``` |
|
|
| `--candidate-key-field smiles_gt` is still supported, but it is oracle-only benchmarking because it selects the candidate pool using the ground-truth molecule. |
|
|
| **Variant C:** |
|
|
| ```bash |
| python scripts/retrieve_generate.py \ |
| --mgf-path /cluster/tufts/liulab/yiwan01/SpecBridge/data/MassSpecGym_test.mgf \ |
| --library-dir /cluster/tufts/liulab/yiwan01/Spec-RAG/out/retrieval/library \ |
| --specbridge-ckpt /cluster/tufts/liulab/yiwan01/SpecBridge/runs/specbridge_align_chemberta_pub_v3g_msgym_mapper_spec/ckpt_001200.pt \ |
| --dreams-ckpt /cluster/tufts/liulab/yiwan01/SpecBridge/data/ssl_model.ckpt \ |
| --variant C \ |
| --K 100 \ |
| --out-jsonl /cluster/tufts/liulab/yiwan01/Spec-RAG/out/retrieval/candidates_C.jsonl |
| ``` |
|
|
| --- |
|
|
| ## 5) Evaluate spectrum-based retrieval (Recall + Tanimoto) |
|
|
| ```bash |
| python scripts/evaluate_massspecgym.py \ |
| --pred-jsonl /cluster/tufts/liulab/yiwan01/Spec-RAG/out/retrieval/candidates_A.jsonl \ |
| --report /cluster/tufts/liulab/yiwan01/Spec-RAG/out/retrieval/metrics_A.json \ |
| --tanimoto |
| |
| python scripts/evaluate_massspecgym.py \ |
| --pred-jsonl /cluster/tufts/liulab/yiwan01/Spec-RAG/out/retrieval/candidates_B.jsonl \ |
| --report /cluster/tufts/liulab/yiwan01/Spec-RAG/out/retrieval/metrics_B.json \ |
| --tanimoto |
| |
| python scripts/evaluate_massspecgym.py \ |
| --pred-jsonl /cluster/tufts/liulab/yiwan01/Spec-RAG/out/retrieval/candidates_C.jsonl \ |
| --report /cluster/tufts/liulab/yiwan01/Spec-RAG/out/retrieval/metrics_C.json \ |
| --tanimoto |
| ``` |
|
|
| --- |
|
|
| ## 6) Self-retrieval sanity check (Priority 2) — true mol embeddings |
|
|
| Index = test molecules only; query = same true molecule embeddings. **Expected Recall@1 ≈ 1.0** for both. |
|
|
| - If either fails → that embedding/index pipeline is broken. |
| - If ChemBERTa passes and SMI-TED fails → SMI-TED embedding issue. |
| - If both pass → issue is likely library coverage / eval mismatch. |
|
|
| ```bash |
| python scripts/self_retrieval_sanity_check.py \ |
| --pred-jsonl /cluster/tufts/liulab/yiwan01/Spec-RAG/out/retrieval/candidates_B.jsonl \ |
| --despecbridge-path /cluster/tufts/liulab/yiwan01/De-SpecBridge \ |
| --report /cluster/tufts/liulab/yiwan01/Spec-RAG/out/retrieval/self_retrieval_report.json |
| ``` |
|
|
| (You can use any of `candidates_A.jsonl`, `candidates_B.jsonl`, or `candidates_C.jsonl`; they share the same `smiles_gt` per row.) |
|
|
| --- |
|
|
| ## 6b) Mapped-embedding self-retrieval sanity check |
|
|
| Index = **spectrum→mapper** embeddings of test set (same MGF); query = same mapped embeddings. **Expected Recall@1 ≈ 1.0.** |
|
|
| - Tests spectrum→ChemBERTa-mapped (SpecBridge) and spectrum→SMI-TED-mapped (DreamsToSmiTed or M_smi). |
| - If either fails → spectrum→mapped-embedding pipeline is broken. |
| |
| ```bash |
| # With De-SpecBridge SMI-TED mapper (recommended) |
| python scripts/self_retrieval_mapped_sanity_check.py \ |
| --mgf-path /cluster/tufts/liulab/yiwan01/SpecBridge/data/MassSpecGym_test.mgf \ |
| --specbridge-ckpt /cluster/tufts/liulab/yiwan01/SpecBridge/runs/specbridge_align_chemberta_pub_v3g_msgym_mapper_spec/ckpt_001200.pt \ |
| --dreams-ckpt /cluster/tufts/liulab/yiwan01/SpecBridge/data/ssl_model.ckpt \ |
| --smited-mapper-ckpt /cluster/tufts/liulab/yiwan01/De-SpecBridge/runs/smited_mapper_final/mapper_best.pt \ |
| --despecbridge-path /cluster/tufts/liulab/yiwan01/De-SpecBridge \ |
| --report /cluster/tufts/liulab/yiwan01/Spec-RAG/out/retrieval/self_retrieval_mapped_report.json |
| ``` |
| |
| If you use Spec-RAG mappers instead of the pretrained SMI-TED mapper: |
| |
| ```bash |
| python scripts/self_retrieval_mapped_sanity_check.py \ |
| --mgf-path /cluster/tufts/liulab/yiwan01/SpecBridge/data/MassSpecGym_test.mgf \ |
| --specbridge-ckpt /cluster/tufts/liulab/yiwan01/SpecBridge/runs/specbridge_align_chemberta_pub_v3g_msgym_mapper_spec/ckpt_001200.pt \ |
| --dreams-ckpt /cluster/tufts/liulab/yiwan01/SpecBridge/data/ssl_model.ckpt \ |
| --mapper-dir /cluster/tufts/liulab/yiwan01/Spec-RAG/out/retrieval/mappers \ |
| --report /cluster/tufts/liulab/yiwan01/Spec-RAG/out/retrieval/self_retrieval_mapped_report.json |
| ``` |
| |
| --- |
| |
| ## 6c) True-index + Mapped-query sanity check |
| |
| **Index** = true molecule embeddings (ChemBERTa/SMI-TED of test SMILES). **Query** = mapped embeddings (spectrum → mapper). So we build a tiny index from the test set’s true mol embeddings, then query with the spectrum→mapper embeddings. This tests how well the mapper aligns spectrum to molecule space (Recall@1/10/50). |
| |
| ```bash |
| python scripts/sanity_check_true_index_mapped_query.py \ |
| --mgf-path /cluster/tufts/liulab/yiwan01/SpecBridge/data/MassSpecGym_test.mgf \ |
| --specbridge-ckpt /cluster/tufts/liulab/yiwan01/SpecBridge/runs/specbridge_align_chemberta_pub_v3g_msgym_mapper_spec/ckpt_001200.pt \ |
| --dreams-ckpt /cluster/tufts/liulab/yiwan01/SpecBridge/data/ssl_model.ckpt \ |
| --smited-mapper-ckpt /cluster/tufts/liulab/yiwan01/De-SpecBridge/runs/smited_mapper_final/mapper_best.pt \ |
| --despecbridge-path /cluster/tufts/liulab/yiwan01/De-SpecBridge \ |
| --report /cluster/tufts/liulab/yiwan01/Spec-RAG/out/retrieval/true_index_mapped_query_report.json |
| ``` |
| |
| --- |
| |
| ## 7) Oracle retrieval (true mol embedding vs library) |
| |
| ```bash |
| python scripts/evaluate_oracle_retrieval.py \ |
| --pred-jsonl /cluster/tufts/liulab/yiwan01/Spec-RAG/out/retrieval/candidates_B.jsonl \ |
| --library-dir /cluster/tufts/liulab/yiwan01/Spec-RAG/out/retrieval/library \ |
| --despecbridge-path /cluster/tufts/liulab/yiwan01/De-SpecBridge \ |
| --K 100 \ |
| --report /cluster/tufts/liulab/yiwan01/Spec-RAG/out/retrieval/metrics_oracle.json |
| ``` |
| |
| --- |
| |
| ## Minimal “all commands” copy-paste (after library + FAISS exist) |
| |
| ```bash |
| cd /cluster/tufts/liulab/yiwan01/Spec-RAG |
|
|
| # Self-retrieval sanity check — true mol embeddings (expect Recall@1 ≈ 1.0) |
| python scripts/self_retrieval_sanity_check.py \ |
| --pred-jsonl /cluster/tufts/liulab/yiwan01/Spec-RAG/out/retrieval/candidates_B.jsonl \ |
| --despecbridge-path /cluster/tufts/liulab/yiwan01/De-SpecBridge \ |
| --report /cluster/tufts/liulab/yiwan01/Spec-RAG/out/retrieval/self_retrieval_report.json |
|
|
| # Mapped-embedding self-retrieval (spectrum→mapper; expect Recall@1 ≈ 1.0) |
| python scripts/self_retrieval_mapped_sanity_check.py \ |
| --mgf-path /cluster/tufts/liulab/yiwan01/SpecBridge/data/MassSpecGym_test.mgf \ |
| --specbridge-ckpt /cluster/tufts/liulab/yiwan01/SpecBridge/runs/specbridge_align_chemberta_pub_v3g_msgym_mapper_spec/ckpt_001200.pt \ |
| --dreams-ckpt /cluster/tufts/liulab/yiwan01/SpecBridge/data/ssl_model.ckpt \ |
| --smited-mapper-ckpt /cluster/tufts/liulab/yiwan01/De-SpecBridge/runs/smited_mapper_final/mapper_best.pt \ |
| --despecbridge-path /cluster/tufts/liulab/yiwan01/De-SpecBridge \ |
| --report /cluster/tufts/liulab/yiwan01/Spec-RAG/out/retrieval/self_retrieval_mapped_report.json |
|
|
| # True-index + Mapped-query (index = true mol emb, query = spectrum→mapper) |
| python scripts/sanity_check_true_index_mapped_query.py \ |
| --mgf-path /cluster/tufts/liulab/yiwan01/SpecBridge/data/MassSpecGym_test.mgf \ |
| --specbridge-ckpt /cluster/tufts/liulab/yiwan01/SpecBridge/runs/specbridge_align_chemberta_pub_v3g_msgym_mapper_spec/ckpt_001200.pt \ |
| --dreams-ckpt /cluster/tufts/liulab/yiwan01/SpecBridge/data/ssl_model.ckpt \ |
| --smited-mapper-ckpt /cluster/tufts/liulab/yiwan01/De-SpecBridge/runs/smited_mapper_final/mapper_best.pt \ |
| --despecbridge-path /cluster/tufts/liulab/yiwan01/De-SpecBridge \ |
| --report /cluster/tufts/liulab/yiwan01/Spec-RAG/out/retrieval/true_index_mapped_query_report.json |
|
|
| # Oracle retrieval (true mol embedding vs library) |
| python scripts/evaluate_oracle_retrieval.py \ |
| --pred-jsonl /cluster/tufts/liulab/yiwan01/Spec-RAG/out/retrieval/candidates_B.jsonl \ |
| --library-dir /cluster/tufts/liulab/yiwan01/Spec-RAG/out/retrieval/library \ |
| --despecbridge-path /cluster/tufts/liulab/yiwan01/De-SpecBridge \ |
| --K 100 \ |
| --report /cluster/tufts/liulab/yiwan01/Spec-RAG/out/retrieval/metrics_oracle.json |
|
|
| # Spectrum-based eval (if you have candidates_*.jsonl) |
| python scripts/evaluate_massspecgym.py --pred-jsonl /cluster/tufts/liulab/yiwan01/Spec-RAG/out/retrieval/candidates_A.jsonl --report /cluster/tufts/liulab/yiwan01/Spec-RAG/out/retrieval/metrics_A.json --tanimoto |
| python scripts/evaluate_massspecgym.py --pred-jsonl /cluster/tufts/liulab/yiwan01/Spec-RAG/out/retrieval/candidates_B.jsonl --report /cluster/tufts/liulab/yiwan01/Spec-RAG/out/retrieval/metrics_B.json --tanimoto |
| python scripts/evaluate_massspecgym.py --pred-jsonl /cluster/tufts/liulab/yiwan01/Spec-RAG/out/retrieval/candidates_C.jsonl --report /cluster/tufts/liulab/yiwan01/Spec-RAG/out/retrieval/metrics_C.json --tanimoto |
| ``` |
| |
