{"submission_id":"3acf301e-81ef-4be7-a57a-cf92b5fc6863","submission_revision_id":"7d9dc6a4-557b-43c9-aa53-c5eee723eb0a","revision_version":3,"submission_status":"under_review","submitted_at":"2026-09-30T23:38:25.268799Z","submitter_name":"Ashfaq Iftakher","submitter_email":"iftakher@mit.edu","task":{"status":"submitted","version":3,"extra_fields":{},"submitted_at":"2026-09-30T23:38:25.268799+00:00","industry_domain":"Chemistry ","task_short_name":"process_chemistry_route_audit_01","operating_system":"MacOS","task_description":"Objective: Audit whether three patent publications (WO2016066673A1, WO2016000476A1 and WO2015074464A1) support the proposed synthesis routes to stereochemically specified Ibrutinib.\n\nYou receive a neutral index of patent and original-PDF URLs, 18 candidate molecular structures in SDF and SVG formats, 12 untrusted claims, route-boundary definitions, and an output schema. Retrieve and inspect the indexed patent text and chemical drawings; no patent PDFs are supplied.\n\nTask: Assign the 18 source compound labels to structures, preserving connectivity and specified stereochemistry. Classify eight identity comparisons, reconstruct the operations in 13 experimental records, and adjudicate each claim as supported, contradicted or not established, with source evidence. Assess what each of the three proposed routes demonstrates within its declared starting boundary, identify missing evidence, and calculate the yield products. Resolve translation or OCR discrepancies using the original publication.\n\nScope: Work within the indexed source boundary and follow input/TASK.md. Do not infer unreported transformations, precursor supply or manufacturing readiness. This task requires no laboratory work or legal patent assessment.\n\nOutput: Deliver output/audit.json conforming to the supplied schema and output/audit_report.md containing 400–900 words that explain the consequential corrections and evidence needed to close remaining gaps. Internet access and PDF/image viewing are required.","software_licensing":"Free/Open Source","evaluation_criteria":null,"verification_method":"Evaluate the agent’s two deliverables, audit.json and audit_report.md, using the supplied frozen evaluator. Keep the reference answers, evaluator and self-test evidence inaccessible to the agent during its attempt.\n\n1. Set up and verify the evaluator\n\nExtract 02_reference_and_evaluation.zip and open a terminal. Using Python 3.12, run:\n\npython3.12 -m venv .venv\n.venv/bin/python -m pip install -r requirements.txt\n.venv/bin/python verify.py\n\nThe verification should report package_hashes_valid: true, reference_score: 1.0 and empty_score: 0.0. A failed verification is an evaluator/setup problem and must be resolved before scoring the agent.\n\n2. Grade the agent’s unchanged outputs\n\nPlace audit.json and audit_report.md in one output directory. Replace /absolute/path/to/agent/output below with that directory, then run:\n\n.venv/bin/python main.py grade /absolute/path/to/agent/output > ../score.json\n\nmain.py is the entry point; its grade subcommand calls grader.py and loads the packaged schema and private reference automatically.\n\nThe resulting score.json contains a top-level score between 0 and 1. Multiply this value by 100 for the percentage. The criteria field contains section and item scores, and errors lists failed checks. \n\n3. Apply the scoring rules\n\nThe total score is the weighted sum of six sections. Within each section, average the scores of the required items:\n\n• Source-to-structure assignments — 25%. Check all 18 assignments against the reference using molecular connectivity, specified stereochemistry, candidate-card identity, molecular formula and CIP labels. Each assignment must satisfy all its checks to receive credit.\n\n• Identity comparisons — 15%. Check the relationship assigned to each of the eight compound pairs.\n\n• Observed operations — 25%. Check all 13 experimental records. Each item awards 65% for correct substrate/product connections, 20% for the reported numerical yield or null, and 15% for the required evidence IDs.\n\n• Claims — 15%. Check all 12 verdicts. A correct verdict earns 65% of that item’s credit; satisfying its citation policy earns the remaining 35%. An incorrect verdict receives zero for the entire item. \n\n• Route assessments — 10%. For each of the three routes, award 25% for target-preparation status, 25% for boundary completeness, 20% for the missing-requirements set, 15% for the full-boundary yield or null, and 15% for citations.\n\n• Nominal yield calculations — 10%. For each of the three calculations, award 35% for the ordered operation IDs, 40% for the numerical product, and 25% for correctly identifying its measurement status.\n\nMolecular comparisons use RDKit and accept equivalent SMILES traversals and atom numbering while preserving specified stereochemistry. Nominal yield products must be within 0.001 percentage points of the reference. No image-pixel comparison is used.\n\n\n4. Handle invalid outputs and interpretation limits\n\nMissing or schema-invalid audit.json receives zero. The report must contain 400–900 whitespace-separated words and meet the documented file-size limit. A missing or nonconforming report caps the total score at 0.95. Scientific reasoning in claim explanations and the report is not semantically graded.","software_and_version":"Python 3.12.14; RDKit 2025.9.3; NumPy 2.3.5; jsonschema 4.26.0; PyMuPDF 1.26.7; Pillow 12.3.0; internet access and PDF/image viewing. CPU only.","specific_requirements":null,"expected_completion_time":null},"files":[{"file_id":"7680b93c-7bd9-417c-ba00-cb6a0baf5470","filename":"01_input_materials.zip","category":"input_materials","content_type":"application/zip","size_bytes":63794},{"file_id":"42cb4cf8-4a95-4917-acc7-9c5a964bc592","filename":"02_reference_and_evaluation.zip","category":"reference_output","content_type":"application/zip","size_bytes":112101}],"deep_review":{"overall_verdict":"Accept","review_text":"**Overall Verdict:** Accept — The submission is complete, professionally scoped, technically coherent, and end-to-end reachable, with only optional independent scientific qualification remaining.\n\n**Completeness Check:**\n\n- Instruction: Complete — The source boundary, 18 assignments, eight comparisons, 13 operations, 12 claims, three route assessments, yield calculations, citation rules, and output requirements are explicit.\n- Inputs: Complete — The package contains the indexed public sources, route definitions, claims, JSON schema, 18-record SDF library, and 18 matching SVG structure cards.\n- Toolchain: Complete — Exact open-source Python dependencies are pinned; the CPU-only workflow requires no paid chemistry software or specialized hardware.\n- Reference output: Complete — The private solution covers every required row and includes a conforming 428-word report. Source hashes and a contributor cross-check are recorded; independent chemistry review is transparently not claimed.\n- Rubric: Complete — Section weights sum to one, partial-credit rules and tolerances are explicit, and static inspection confirms the evaluator implements them.\n\n**File and Task Reachability:**\n\nThe attachment set is `reachable`, and the end-to-end task is `reachable`. Both `01_input_materials.zip` and `02_reference_and_evaluation.zip` were inspected. Their downloaded sizes match the manifest; both are readable, unencrypted ZIP archives with 29 and 50 entries respectively, no traversal paths, unsafe links, device entries, or excessive expansion. Internal manifests verify all packaged file hashes. JSON documents parse, the SDF contains 18 uniquely titled V2000 records, and all SVGs are 650×360 RDKit drawings without scripts, external resources, entities, or event handlers. The SVGs could not be raster-previewed with available reviewer tooling, so their inspection was limited to XML/path content, SDF structure data, and the supplied topology-validation evidence. No manifest attachment remains unreviewed.\n\nThe external patent bodies are intentionally not packaged and were not independently retrieved under this review’s evidence restrictions. The evaluation package records fresh successful access to all three HTML and PDF sources, including page counts, hashes, representative figures, and targeted text checks. A solver can retrieve those public sources, inspect scanned drawings, use the supplied molecular files and pinned tools, produce the two specified outputs, and be scored by the isolated private evaluator. License keys, accounts, tokens, and other credentials are not required from the contributor. Confidential, proprietary, or internal material may be evaluated as submitted evidence without requiring additional disclosure.\n\n**Special Screening:**\n\nNone\n\n**Recommended Changes:**\n\nThe submission already provides strong boundary definitions, answer isolation, reproducible manifests, granular scoring, and explicit evaluator limitations. No changes are required. Independent chemist signoff and a full production Linux-VM qualification would be useful optional confidence measures, but their absence does not block this revision.","reviewed_at":"2026-09-30T23:47:26.525297Z"},"claim":null}