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Three readers streamed one patient through the model with their own copy of the same PackedLaneSampler loop. It now lives once in odyssey/inference/patient_stream.py (stream_patient, risk_within), and case_study and counterfactual use it. Behaviour is unchanged: the existing case-study and counterfactual tests pass unmodified. Also added, each with tests: - extract_patient_case reports risk at 8/24/72 h (event_risk_by_horizon); event_risk_24h is kept for the report that reads it. - ordered_sequence_rows: the exact row order build_patient_sequence tokenizes, so a position maps back to its raw row. - load_meds_subject: one subject from one shard, filter pushed into the scan. - code_metadata.load_code_descriptions, split out of steering so readers can name codes without importing steering. - occlude_codes: target-agnostic occlusion with a progress callback; occlusion_attribution is now a thin wrapper, plus event_occlusion_attribution for an event's risk. - concept_display_name moves from make_readout_table into concepts. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_012zuuVqnBfTsozfaj5F4y3r
A web app that replays one admission and shows, moment by moment, the model's risk of ICU admission, vasopressors, AKI, Sepsis-3 and death against an alert line, what it thinks is going on, what it expects next, what-if value edits, occlusion evidence, and a scorecard against the tuned GBM. Runbook: docs/clinician_demo.md. - Standard library HTTP only (the GPU host's environment is pinned); loopback bind, Host allowlist, custom API header, no CORS, no-store, same-origin CSP, static path containment. - Two data modes: credentialed (held-out MIMIC-IV) and open (MIMIC-IV Clinical Database Demo). Every chart says whether the model trained on that patient. - Honest by construction: the gallery shows misses and false alarms with their rates; lead time counts from the alert episode still on at the event; risk is hidden after onset; readmission, steering, label overrides and rollouts are never shown (a test enforces the imports). - Vanilla ES modules, no build step, no third-party JS. - 200+ CPU tests on synthetic data: every module, server security over a real socket, and spies proving the run's chunk_size reaches every model call. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_012zuuVqnBfTsozfaj5F4y3r
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Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## main #250 +/- ##
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+ Coverage 89.98% 90.08% +0.10%
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Files 69 71 +2
Lines 10771 10835 +64
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+ Hits 9692 9761 +69
+ Misses 1079 1074 -5
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- server: static files are served from a map built once at startup (static_files); a request is a dictionary lookup, so no filesystem path is ever built from request data. Clears the three CodeQL "uncontrolled data used in path expression" alerts. Symlinks out of the root and non-allowlisted extensions are still excluded, now at map-build time; tests cover both. - showcase: rename the `_thr` column and `thr` test argument, which the typos hook reads as "the". - pre-commit: no hook rewrites scripts/gemini/out/ (pre-commit.ci's end-of-file fixer had edited 12 verbatim GEMINI exports on this PR), and mypy/typos skip the two cohort producers committed verbatim as they ran. pyproject's mypy exclude never applied to them because pre-commit passes files by name; this is why main's code check has failed since 0de877f. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_012zuuVqnBfTsozfaj5F4y3r
This reverts commit 8348226, which added a trailing newline to 12 files under scripts/gemini/out/evals/. Those files are GEMINI's exported reports, kept byte-for-byte; the previous commit stops the hooks from touching them again. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_012zuuVqnBfTsozfaj5F4y3r
Front end only; the API and Python are unchanged.
- Light theme by default, dark via a footer toggle. One accent colour;
event colours only on lines and dots.
- Replay: patient one-liner, sticky "now" bar (play, scrub, clock time),
five risk tiles with a status word (Low / Watch / Alert on / Happened)
and "n× the average patient", then the chart, what happened in the
stay, what the model believes now, and the what-if / evidence tools.
- The chart fades everything after "now".
- Alert stories are composed client-side in clock time ("Began Day 1,
22:53. The alert had been on since Day 1, 01:16: 22 h of warning").
- The 29-row concept strip, alert-line statistics and next-token list
sit behind disclosures; model name and checkpoint move to the footer.
- Gallery cards carry one key line; the full admission list is a
collapsed per-patient list with a note on how many were in training.
- Scorecard cells show one number per model, intervals on hover.
- Fix: class display rules overrode the browser's [hidden] rule, so the
search box showed in open mode and "Alert on now" showed on every row.
- Runbook: static files can be copied over a running deployment.
Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01QebToqtFMVakRkx3PhF3ZX
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- check-docstring-first read the module-level attribute docstrings in the new target module and probe script as second module docstrings; they are comments now. - pre-commit.ci's autofix had rewritten 12 scripts/gemini/out/ JSONs (trailing newlines) on this branch, the same way it did on PR #250. This carries PR #250's hook config over: scripts/gemini/out/ is excluded from every hook, and mypy/typos skip the two cohort producers committed verbatim, which is also what has been failing main's code check. The 12 exports are byte-identical to main again. Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01StsjDmueuDqVNNuVoCEF1P
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Summary
A clinician-facing web app for the MIMIC-IV flagship model (
full_run_v10). It replays one admission and shows, moment by moment:Runbook:
docs/clinician_demo.md.Commits
odyssey/). The loop copied incase_studyandcounterfactualnow lives once inodyssey/inference/patient_stream.py. Also addsordered_sequence_rows,load_meds_subject,code_metadata.load_code_descriptions, a target-agnosticocclude_codes, and movesconcept_display_nameintoconcepts. Behaviour is unchanged: the existing tests pass unmodified.apps/clinician_demo/), with its tests (tests/apps/) and the runbook.pyproject.tomlonly addsappsto coverage.Design notes
Hostallowlist, a requiredX-Odyssey-Demoheader, no CORS,Cache-Control: no-store, same-origin CSP, static files from an allowlisted directory with path containment.credentialedserves held-out MIMIC-IV and is for PhysioNet-credentialed viewers only.openserves the MIMIC-IV Clinical Database Demo. 90 of those 100 patients were in the model's training split, and every chart says so.Test plan
odyssey scripts apps.chunk_sizereaches every model call. The trace equalsscore_record_atat every bundle end.CI fixes (commits 3 and 4)
ab3368b):thris renamed tothreshold, since the typos hook read it as "the".scripts/gemini/out/.pyproject.tomlexcludes them from mypy, but pre-commit passes files by name, which bypasses that exclude. This is also whymain's code check has failed since0de877f. Merging this fixesmaintoo.35b5e9a). The bot added a trailing newline to 12 verbatim GEMINI exports on this branch. They are byte-identical tomainagain.Caveats
~/odyssey_demo, not frommain. After merge it can move to the normalgit resetpath.🤖 Generated with Claude Code
https://claude.ai/code/session_012zuuVqnBfTsozfaj5F4y3r