Aman Khare commited on
Commit ·
7655d3c
1
Parent(s): 3856d60
final changes
Browse files- .gitignore +47 -0
- __pycache__/inference.cpython-314.pyc +0 -0
- environment/__pycache__/__init__.cpython-314.pyc +0 -0
- environment/__pycache__/env.cpython-314.pyc +0 -0
- environment/__pycache__/models.cpython-314.pyc +0 -0
- environment/__pycache__/reward.cpython-314.pyc +0 -0
- environment/env.py +44 -30
- environment/tasks/__pycache__/__init__.cpython-314.pyc +0 -0
- environment/tasks/__pycache__/task_easy.cpython-314.pyc +0 -0
- environment/tasks/__pycache__/task_hard.cpython-314.pyc +0 -0
- environment/tasks/__pycache__/task_medium.cpython-314.pyc +0 -0
- environment/tasks/task_easy.py +43 -15
- environment/tasks/task_hard.py +47 -15
- environment/tasks/task_medium.py +45 -15
- err.txt +0 -24
- inference.py +7 -6
- openenv.yaml +1 -1
- out.txt +0 -9
- server/__pycache__/__init__.cpython-314.pyc +0 -0
- server/__pycache__/app.cpython-314.pyc +0 -0
- server/__pycache__/routes.cpython-314.pyc +0 -0
- server/routes.py +31 -4
- test_inference.py +0 -26
- test_output.txt +0 -9
- test_reward.py +0 -75
.gitignore
ADDED
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@@ -0,0 +1,47 @@
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# --- Python ---
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__pycache__/
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+
*.py[cod]
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+
*$py.class
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*.so
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*.egg-info/
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dist/
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build/
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*.egg
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# --- Virtual environments ---
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.venv/
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venv/
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env/
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# --- IDE ---
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.vscode/
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.idea/
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*.swp
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*.swo
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*~
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# --- OS ---
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.DS_Store
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Thumbs.db
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desktop.ini
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+
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# --- Test artifacts ---
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out.txt
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err.txt
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test_output.txt
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test_full.py
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test_all_fixes.py
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test_inference.py
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test_reward.py
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test_presubmission.py
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# --- Non-submission folders ---
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next step/
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play/
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# --- Logs ---
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*.log
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# --- Secrets ---
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.env
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.env.*
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__pycache__/inference.cpython-314.pyc
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environment/__pycache__/__init__.cpython-314.pyc
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Binary file (443 Bytes)
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environment/__pycache__/env.cpython-314.pyc
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Binary file (15.3 kB)
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environment/__pycache__/models.cpython-314.pyc
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Binary file (5.51 kB)
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environment/__pycache__/reward.cpython-314.pyc
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Binary file (7.6 kB)
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environment/env.py
CHANGED
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@@ -240,9 +240,31 @@ def state(self) -> EnvironmentState:
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# --------------------------------------------------------------------- #
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def _handle_submit(self, action: Action, info: dict) -> Reward:
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-
"""Process a ``submit_note`` action.
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-
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-
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self._errors_so_far.append(error)
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return compute_reward(
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action,
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@@ -253,7 +275,7 @@ def _handle_submit(self, action: Action, info: dict) -> Reward:
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info={"error": error},
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)
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-
self._current_draft = _soap_to_text(
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self._done = True
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# Attempt to grade via the task-specific grader
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@@ -270,7 +292,7 @@ def _handle_submit(self, action: Action, info: dict) -> Reward:
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)
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try:
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raw_signals = grader(
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# Grader returns a signals dict; extract a single scalar score
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# as the mean of its values for use as grader_score.
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grader_score = (
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@@ -278,9 +300,9 @@ def _handle_submit(self, action: Action, info: dict) -> Reward:
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if raw_signals else 0.0
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)
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info["grader_signals"] = raw_signals
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except
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info["warning"] = "Grader
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grader_score = 0.
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return compute_reward(
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action,
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@@ -297,11 +319,9 @@ def _handle_clarify(self, action: Action, info: dict) -> Reward:
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if not question:
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error = "request_clarify requires a non-empty clarify_question."
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self._errors_so_far.append(error)
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-
return
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-
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-
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step_count=self._step_count,
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errors_so_far=self._errors_so_far,
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done=False,
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info={"error": error},
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)
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@@ -315,12 +335,10 @@ def _handle_clarify(self, action: Action, info: dict) -> Reward:
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"No additional information available for that question."
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)
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#
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return
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step_count=self._step_count,
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errors_so_far=self._errors_so_far,
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done=False,
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info=info,
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)
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@@ -330,11 +348,9 @@ def _handle_revise(self, action: Action, info: dict) -> Reward:
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if action.section is None or action.revision_text is None:
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error = "revise_section requires both 'section' and 'revision_text'."
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self._errors_so_far.append(error)
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return
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-
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-
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step_count=self._step_count,
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errors_so_far=self._errors_so_far,
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done=False,
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info={"error": error},
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)
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info["revised_section"] = action.section
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#
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return
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step_count=self._step_count,
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errors_so_far=self._errors_so_far,
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done=False,
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info=info,
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)
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# --------------------------------------------------------------------- #
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def _handle_submit(self, action: Action, info: dict) -> Reward:
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"""Process a ``submit_note`` action.
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If ``action.soap_note`` is provided, it is used directly.
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Otherwise, if the agent has built up a draft via ``revise_section``,
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the draft is parsed into a SOAPNote automatically.
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"""
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soap = action.soap_note
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# Fall back to the current draft if no explicit note is provided
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if soap is None and self._current_draft:
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sections: dict[str, str] = {}
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for line in self._current_draft.split("\n"):
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for prefix in ("S: ", "O: ", "A: ", "P: "):
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if line.startswith(prefix):
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sections[prefix[0]] = line[len(prefix):]
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if all(k in sections for k in "SOAP"):
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soap = SOAPNote(
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subjective=sections["S"],
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objective=sections["O"],
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assessment=sections["A"],
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plan=sections["P"],
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)
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if soap is None:
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error = "submit_note requires a non-null soap_note (or a complete draft from revise_section)."
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self._errors_so_far.append(error)
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return compute_reward(
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action,
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info={"error": error},
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)
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self._current_draft = _soap_to_text(soap)
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self._done = True
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# Attempt to grade via the task-specific grader
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)
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try:
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raw_signals = grader(soap, self._task)
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# Grader returns a signals dict; extract a single scalar score
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# as the mean of its values for use as grader_score.
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grader_score = (
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if raw_signals else 0.0
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)
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info["grader_signals"] = raw_signals
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except Exception as exc:
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info["warning"] = f"Grader error: {exc}"
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grader_score = 0.0
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return compute_reward(
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action,
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if not question:
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error = "request_clarify requires a non-empty clarify_question."
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self._errors_so_far.append(error)
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return Reward(
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value=0.0,
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signals={"error": 1.0},
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done=False,
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info={"error": error},
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)
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"No additional information available for that question."
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)
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# Intermediate actions get zero reward — only submit_note earns score
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return Reward(
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value=0.0,
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signals={"intermediate_step": 1.0},
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done=False,
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info=info,
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)
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if action.section is None or action.revision_text is None:
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error = "revise_section requires both 'section' and 'revision_text'."
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self._errors_so_far.append(error)
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return Reward(
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value=0.0,
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signals={"error": 1.0},
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done=False,
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info={"error": error},
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)
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info["revised_section"] = action.section
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# Intermediate actions get zero reward — only submit_note earns score
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return Reward(
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value=0.0,
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signals={"intermediate_step": 1.0},
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done=False,
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info=info,
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)
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environment/tasks/__pycache__/__init__.cpython-314.pyc
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environment/tasks/__pycache__/task_easy.cpython-314.pyc
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environment/tasks/__pycache__/task_hard.cpython-314.pyc
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Binary file (2.4 kB)
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environment/tasks/__pycache__/task_medium.cpython-314.pyc
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environment/tasks/task_easy.py
CHANGED
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"""Easy task — routine check-up.
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Grader
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"""
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from __future__ import annotations
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# ---------------------------------------------------------------------------
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-
# Grader
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# ---------------------------------------------------------------------------
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def grade_easy(soap_note: SOAPNote, task: dict[str, Any]) -> dict[str, float]:
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"""Score a submitted SOAP note against the easy-task rubric.
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-
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soap_note:
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The agent's submitted clinical note.
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task:
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The task definition dict (``EASY_TASK``).
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Returns
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-------
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dict mapping signal names
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Raises
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------
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NotImplementedError
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Grader has not been implemented yet.
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"""
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"""Easy task — routine check-up.
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Grader uses keyword-based clinical rubric scoring to evaluate the SOAP note
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against expected findings from a simple cold / blood pressure check visit.
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"""
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from __future__ import annotations
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# ---------------------------------------------------------------------------
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+
# Grader
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# ---------------------------------------------------------------------------
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def grade_easy(soap_note: SOAPNote, task: dict[str, Any]) -> dict[str, float]:
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| 40 |
"""Score a submitted SOAP note against the easy-task rubric.
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Checks for mention of key clinical findings from the transcript:
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chief complaints, vitals, viral URI assessment, and supportive plan.
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Returns
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-------
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dict mapping signal names to float scores in [0, 1].
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"""
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text_s = soap_note.subjective.lower()
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text_o = soap_note.objective.lower()
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text_a = soap_note.assessment.lower()
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text_p = soap_note.plan.lower()
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# 1. Subjective — chief complaints
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s_score = 0.0
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if "sore throat" in text_s or "runny nose" in text_s or "congestion" in text_s:
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s_score += 0.5
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if "5 days" in text_s or "five days" in text_s or "headache" in text_s:
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s_score += 0.5
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# 2. Objective — vitals
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o_score = 0.0
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if "118/76" in text_o or "118 over 76" in text_o or "blood pressure" in text_o:
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o_score += 0.5
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if "72" in text_o or "heart rate" in text_o or "lungs clear" in text_o:
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o_score += 0.5
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+
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# 3. Assessment — viral URI
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a_score = 0.0
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if "viral" in text_a or "uri" in text_a or "upper respiratory" in text_a:
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a_score += 1.0
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# 4. Plan — supportive care
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p_score = 0.0
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if "fluids" in text_p or "rest" in text_p or "hydrat" in text_p:
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p_score += 0.5
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if "dayquil" in text_p or "follow" in text_p or "return" in text_p:
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p_score += 0.5
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return {
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| 81 |
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"subjective_accuracy": min(s_score, 1.0),
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"objective_accuracy": min(o_score, 1.0),
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"assessment_accuracy": min(a_score, 1.0),
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"plan_accuracy": min(p_score, 1.0),
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}
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environment/tasks/task_hard.py
CHANGED
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"""Hard task — complex ER visit.
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Grader
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"""
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from __future__ import annotations
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# ---------------------------------------------------------------------------
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| 64 |
-
# Grader
|
| 65 |
# ---------------------------------------------------------------------------
|
| 66 |
|
| 67 |
def grade_hard(soap_note: SOAPNote, task: dict[str, Any]) -> dict[str, float]:
|
| 68 |
"""Score a submitted SOAP note against the hard-task rubric.
|
| 69 |
|
| 70 |
-
|
| 71 |
-
-
|
| 72 |
-
|
| 73 |
-
The agent's submitted clinical note.
|
| 74 |
-
task:
|
| 75 |
-
The task definition dict (``HARD_TASK``).
|
| 76 |
|
| 77 |
Returns
|
| 78 |
-------
|
| 79 |
-
dict mapping signal names
|
| 80 |
-
|
| 81 |
-
Raises
|
| 82 |
-
------
|
| 83 |
-
NotImplementedError
|
| 84 |
-
Grader has not been implemented yet.
|
| 85 |
"""
|
| 86 |
-
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
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|
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|
|
|
|
|
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|
|
|
|
|
|
|
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|
|
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|
|
|
|
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|
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|
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|
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|
|
|
|
|
|
|
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|
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|
|
|
|
|
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|
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|
|
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|
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|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
| 1 |
"""Hard task — complex ER visit.
|
| 2 |
|
| 3 |
+
Grader uses keyword-based clinical rubric scoring to evaluate the SOAP note
|
| 4 |
+
against expected findings from a complex ER visit with overlapping chest pain,
|
| 5 |
+
SOB, and a possible PE complicated by a contrast dye allergy.
|
| 6 |
"""
|
| 7 |
|
| 8 |
from __future__ import annotations
|
|
|
|
| 63 |
|
| 64 |
|
| 65 |
# ---------------------------------------------------------------------------
|
| 66 |
+
# Grader
|
| 67 |
# ---------------------------------------------------------------------------
|
| 68 |
|
| 69 |
def grade_hard(soap_note: SOAPNote, task: dict[str, Any]) -> dict[str, float]:
|
| 70 |
"""Score a submitted SOAP note against the hard-task rubric.
|
| 71 |
|
| 72 |
+
Checks for chest pain / SOB and the nitroglycerin contradiction (subjective),
|
| 73 |
+
D-dimer and contrast allergy (objective), ACS vs PE differential (assessment),
|
| 74 |
+
and V/Q scan + ICU admission (plan).
|
|
|
|
|
|
|
|
|
|
| 75 |
|
| 76 |
Returns
|
| 77 |
-------
|
| 78 |
+
dict mapping signal names to float scores in [0, 1].
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 79 |
"""
|
| 80 |
+
text_s = soap_note.subjective.lower()
|
| 81 |
+
text_o = soap_note.objective.lower()
|
| 82 |
+
text_a = soap_note.assessment.lower()
|
| 83 |
+
text_p = soap_note.plan.lower()
|
| 84 |
+
|
| 85 |
+
# 1. Subjective — catching the contradiction and presenting complaints
|
| 86 |
+
s_score = 0.0
|
| 87 |
+
if "chest pain" in text_s or "shortness of breath" in text_s or "sob" in text_s:
|
| 88 |
+
s_score += 0.5
|
| 89 |
+
if "nitroglycerin" in text_s or "contradict" in text_s or "denied" in text_s:
|
| 90 |
+
s_score += 0.5
|
| 91 |
+
|
| 92 |
+
# 2. Objective — elevated D-dimer and allergy awareness
|
| 93 |
+
o_score = 0.0
|
| 94 |
+
if "d-dimer" in text_o or "1840" in text_o or "d dimer" in text_o:
|
| 95 |
+
o_score += 0.5
|
| 96 |
+
if "allergy" in text_o or "contrast" in text_o or "troponin" in text_o:
|
| 97 |
+
o_score += 0.5
|
| 98 |
+
|
| 99 |
+
# 3. Assessment — the dual differential (ACS vs PE)
|
| 100 |
+
a_score = 0.0
|
| 101 |
+
if "acs" in text_a or "acute coronary" in text_a or "coronary" in text_a or "ischemia" in text_a:
|
| 102 |
+
a_score += 0.5
|
| 103 |
+
if "pe" in text_a or "pulmonary embolism" in text_a or "embolism" in text_a:
|
| 104 |
+
a_score += 0.5
|
| 105 |
+
|
| 106 |
+
# 4. Plan — adapting to the allergy (V/Q scan) and admission
|
| 107 |
+
p_score = 0.0
|
| 108 |
+
if "v/q" in text_p or "ventilation" in text_p or "perfusion" in text_p:
|
| 109 |
+
p_score += 0.5
|
| 110 |
+
if "icu" in text_p or "admit" in text_p or "cardiac" in text_p:
|
| 111 |
+
p_score += 0.5
|
| 112 |
+
|
| 113 |
+
return {
|
| 114 |
+
"subjective_accuracy": min(s_score, 1.0),
|
| 115 |
+
"objective_accuracy": min(o_score, 1.0),
|
| 116 |
+
"assessment_accuracy": min(a_score, 1.0),
|
| 117 |
+
"plan_accuracy": min(p_score, 1.0),
|
| 118 |
+
}
|
environment/tasks/task_medium.py
CHANGED
|
@@ -1,6 +1,7 @@
|
|
| 1 |
"""Medium task — chronic disease follow-up.
|
| 2 |
|
| 3 |
-
Grader
|
|
|
|
| 4 |
"""
|
| 5 |
|
| 6 |
from __future__ import annotations
|
|
@@ -43,26 +44,55 @@
|
|
| 43 |
|
| 44 |
|
| 45 |
# ---------------------------------------------------------------------------
|
| 46 |
-
# Grader
|
| 47 |
# ---------------------------------------------------------------------------
|
| 48 |
|
| 49 |
def grade_medium(soap_note: SOAPNote, task: dict[str, Any]) -> dict[str, float]:
|
| 50 |
"""Score a submitted SOAP note against the medium-task rubric.
|
| 51 |
|
| 52 |
-
|
| 53 |
-
|
| 54 |
-
soap_note:
|
| 55 |
-
The agent's submitted clinical note.
|
| 56 |
-
task:
|
| 57 |
-
The task definition dict (``MEDIUM_TASK``).
|
| 58 |
|
| 59 |
Returns
|
| 60 |
-------
|
| 61 |
-
dict mapping signal names
|
| 62 |
-
|
| 63 |
-
Raises
|
| 64 |
-
------
|
| 65 |
-
NotImplementedError
|
| 66 |
-
Grader has not been implemented yet.
|
| 67 |
"""
|
| 68 |
-
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
"""Medium task — chronic disease follow-up.
|
| 2 |
|
| 3 |
+
Grader uses keyword-based clinical rubric scoring to evaluate the SOAP note
|
| 4 |
+
against expected findings from a Type 2 Diabetes / Hypertension follow-up.
|
| 5 |
"""
|
| 6 |
|
| 7 |
from __future__ import annotations
|
|
|
|
| 44 |
|
| 45 |
|
| 46 |
# ---------------------------------------------------------------------------
|
| 47 |
+
# Grader
|
| 48 |
# ---------------------------------------------------------------------------
|
| 49 |
|
| 50 |
def grade_medium(soap_note: SOAPNote, task: dict[str, Any]) -> dict[str, float]:
|
| 51 |
"""Score a submitted SOAP note against the medium-task rubric.
|
| 52 |
|
| 53 |
+
Checks for mention of dietary habits, HbA1c lab values, core diagnoses,
|
| 54 |
+
and medication adjustments (glipizide, lisinopril uptitration).
|
|
|
|
|
|
|
|
|
|
|
|
|
| 55 |
|
| 56 |
Returns
|
| 57 |
-------
|
| 58 |
+
dict mapping signal names to float scores in [0, 1].
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 59 |
"""
|
| 60 |
+
text_s = soap_note.subjective.lower()
|
| 61 |
+
text_o = soap_note.objective.lower()
|
| 62 |
+
text_a = soap_note.assessment.lower()
|
| 63 |
+
text_p = soap_note.plan.lower()
|
| 64 |
+
|
| 65 |
+
# 1. Subjective — dietary habits / statin gap
|
| 66 |
+
s_score = 0.0
|
| 67 |
+
if "restaurant" in text_s or "diet" in text_s or "eating" in text_s:
|
| 68 |
+
s_score += 0.5
|
| 69 |
+
if "statin" in text_s or "gap" in text_s or "missed" in text_s:
|
| 70 |
+
s_score += 0.5
|
| 71 |
+
|
| 72 |
+
# 2. Objective — HbA1c values
|
| 73 |
+
o_score = 0.0
|
| 74 |
+
if "7.8" in text_o or "7.2" in text_o or "a1c" in text_o or "hba1c" in text_o:
|
| 75 |
+
o_score += 0.5
|
| 76 |
+
if "156" in text_o or "fasting glucose" in text_o or "glucose" in text_o:
|
| 77 |
+
o_score += 0.5
|
| 78 |
+
|
| 79 |
+
# 3. Assessment — core diagnoses
|
| 80 |
+
a_score = 0.0
|
| 81 |
+
if "diabetes" in text_a or "t2dm" in text_a or "dm" in text_a:
|
| 82 |
+
a_score += 0.5
|
| 83 |
+
if "hypertension" in text_a or "htn" in text_a or "blood pressure" in text_a:
|
| 84 |
+
a_score += 0.5
|
| 85 |
+
|
| 86 |
+
# 4. Plan — medication changes
|
| 87 |
+
p_score = 0.0
|
| 88 |
+
if "glipizide" in text_p and ("5" in text_p or "add" in text_p):
|
| 89 |
+
p_score += 0.5
|
| 90 |
+
if "lisinopril" in text_p and ("40" in text_p or "increase" in text_p or "uptitrat" in text_p):
|
| 91 |
+
p_score += 0.5
|
| 92 |
+
|
| 93 |
+
return {
|
| 94 |
+
"subjective_accuracy": min(s_score, 1.0),
|
| 95 |
+
"objective_accuracy": min(o_score, 1.0),
|
| 96 |
+
"assessment_accuracy": min(a_score, 1.0),
|
| 97 |
+
"plan_accuracy": min(p_score, 1.0),
|
| 98 |
+
}
|
err.txt
DELETED
|
@@ -1,24 +0,0 @@
|
|
| 1 |
-
{"event": "START", "timestamp": 1775576189.364181, "task_id": "easy_routine_checkup"}
|
| 2 |
-
[DEBUG] Model request failed: Error code: 401 - {'error': 'Invalid username or password.'}
|
| 3 |
-
{"event": "STEP", "timestamp": 1775576190.2672057, "step": 1, "action_type": "submit_note", "reward": 0.7}
|
| 4 |
-
{"event": "END", "timestamp": 1775576190.2674263, "task_id": "easy_routine_checkup", "final_score": 0.7}
|
| 5 |
-
{"event": "START", "timestamp": 1775576190.269494, "task_id": "medium_chronic_disease_followup"}
|
| 6 |
-
[DEBUG] Model request failed: Error code: 401 - {'error': 'Invalid username or password.'}
|
| 7 |
-
{"event": "STEP", "timestamp": 1775576190.6036963, "step": 1, "action_type": "submit_note", "reward": 0.7}
|
| 8 |
-
{"event": "END", "timestamp": 1775576190.6037915, "task_id": "medium_chronic_disease_followup", "final_score": 0.7}
|
| 9 |
-
{"event": "START", "timestamp": 1775576190.604777, "task_id": "hard_complex_er_visit"}
|
| 10 |
-
[DEBUG] Model request failed: Error code: 401 - {'error': 'Invalid username or password.'}
|
| 11 |
-
{"event": "STEP", "timestamp": 1775576190.9611442, "step": 1, "action_type": "submit_note", "reward": 0.7}
|
| 12 |
-
{"event": "END", "timestamp": 1775576190.961212, "task_id": "hard_complex_er_visit", "final_score": 0.7}
|
| 13 |
-
|
| 14 |
-
============================================================
|
| 15 |
-
SUMMARY
|
| 16 |
-
============================================================
|
| 17 |
-
Task Score Steps
|
| 18 |
-
------------------------------- ------- -----
|
| 19 |
-
easy_routine_checkup 0.7000 1
|
| 20 |
-
medium_chronic_disease_followup 0.7000 1
|
| 21 |
-
hard_complex_er_visit 0.7000 1
|
| 22 |
-
------------------------------- ------- -----
|
| 23 |
-
AVERAGE 0.7000
|
| 24 |
-
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
inference.py
CHANGED
|
@@ -212,17 +212,18 @@ def run_task(client: OpenAI, env: ClinicalNoteScribeEnv, task_id: str) -> dict[s
|
|
| 212 |
action = Action(**action_dict)
|
| 213 |
action_str = f"submit_note(sections=S,O,A,P)"
|
| 214 |
except Exception as exc:
|
| 215 |
-
# On model / parse failure, submit
|
|
|
|
| 216 |
action = Action(
|
| 217 |
action_type="submit_note",
|
| 218 |
soap_note=SOAPNote(
|
| 219 |
-
subjective="
|
| 220 |
-
objective="
|
| 221 |
-
assessment="
|
| 222 |
-
plan="
|
| 223 |
),
|
| 224 |
)
|
| 225 |
-
action_str =
|
| 226 |
last_error = str(exc)
|
| 227 |
|
| 228 |
# ---- step ----
|
|
|
|
| 212 |
action = Action(**action_dict)
|
| 213 |
action_str = f"submit_note(sections=S,O,A,P)"
|
| 214 |
except Exception as exc:
|
| 215 |
+
# On model / parse failure, submit an empty note so all sub-signals
|
| 216 |
+
# grade to 0.0 (format_valid=0 because fields are empty, grader=0).
|
| 217 |
action = Action(
|
| 218 |
action_type="submit_note",
|
| 219 |
soap_note=SOAPNote(
|
| 220 |
+
subjective="",
|
| 221 |
+
objective="",
|
| 222 |
+
assessment="",
|
| 223 |
+
plan="",
|
| 224 |
),
|
| 225 |
)
|
| 226 |
+
action_str = "submit_note(fallback)"
|
| 227 |
last_error = str(exc)
|
| 228 |
|
| 229 |
# ---- step ----
|
openenv.yaml
CHANGED
|
@@ -206,6 +206,6 @@ graders:
|
|
| 206 |
inference:
|
| 207 |
script: inference.py
|
| 208 |
env_vars:
|
| 209 |
-
-
|
| 210 |
- API_BASE_URL
|
| 211 |
- MODEL_NAME
|
|
|
|
| 206 |
inference:
|
| 207 |
script: inference.py
|
| 208 |
env_vars:
|
| 209 |
+
- HF_TOKEN
|
| 210 |
- API_BASE_URL
|
| 211 |
- MODEL_NAME
|
out.txt
DELETED
|
@@ -1,9 +0,0 @@
|
|
| 1 |
-
[START] task=easy_routine_checkup env=clinical-note-scribe model=gpt-4o-mini
|
| 2 |
-
[STEP] step=1 action=submit_note(fallback) reward=0.70 done=true error=Error code: 401 - {'error': 'Invalid username or password.'}
|
| 3 |
-
[END] success=true steps=1 score=0.70 rewards=0.70
|
| 4 |
-
[START] task=medium_chronic_disease_followup env=clinical-note-scribe model=gpt-4o-mini
|
| 5 |
-
[STEP] step=1 action=submit_note(fallback) reward=0.70 done=true error=Error code: 401 - {'error': 'Invalid username or password.'}
|
| 6 |
-
[END] success=true steps=1 score=0.70 rewards=0.70
|
| 7 |
-
[START] task=hard_complex_er_visit env=clinical-note-scribe model=gpt-4o-mini
|
| 8 |
-
[STEP] step=1 action=submit_note(fallback) reward=0.70 done=true error=Error code: 401 - {'error': 'Invalid username or password.'}
|
| 9 |
-
[END] success=true steps=1 score=0.70 rewards=0.70
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
server/__pycache__/__init__.cpython-314.pyc
DELETED
|
Binary file (221 Bytes)
|
|
|
server/__pycache__/app.cpython-314.pyc
DELETED
|
Binary file (1.26 kB)
|
|
|
server/__pycache__/routes.cpython-314.pyc
DELETED
|
Binary file (6.37 kB)
|
|
|
server/routes.py
CHANGED
|
@@ -110,12 +110,39 @@ async def reset(body: ResetRequest) -> Observation:
|
|
| 110 |
response_model=StepResponse,
|
| 111 |
summary="Submit an action and advance the environment by one step",
|
| 112 |
)
|
| 113 |
-
async def step(
|
| 114 |
-
"""Execute
|
| 115 |
|
| 116 |
-
|
| 117 |
-
|
|
|
|
| 118 |
"""
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 119 |
_log("STEP", endpoint="/step", action_type=action.action_type)
|
| 120 |
try:
|
| 121 |
obs, reward, done, info = _env.step(action)
|
|
|
|
| 110 |
response_model=StepResponse,
|
| 111 |
summary="Submit an action and advance the environment by one step",
|
| 112 |
)
|
| 113 |
+
async def step(payload: dict[str, Any]) -> StepResponse:
|
| 114 |
+
"""Execute an action in the current episode.
|
| 115 |
|
| 116 |
+
Accepts a raw JSON body and validates it into an ``Action``.
|
| 117 |
+
If validation fails, the error is recorded in the environment
|
| 118 |
+
instead of returning an HTTP 422.
|
| 119 |
"""
|
| 120 |
+
from pydantic import ValidationError
|
| 121 |
+
from environment.models import Reward
|
| 122 |
+
|
| 123 |
+
try:
|
| 124 |
+
action = Action(**payload)
|
| 125 |
+
except (ValidationError, TypeError) as exc:
|
| 126 |
+
# Gracefully absorb bad payloads instead of crashing with HTTP 422
|
| 127 |
+
_log("STEP", endpoint="/step", action_type="invalid", error=str(exc))
|
| 128 |
+
error_msg = f"Invalid action payload: {exc}"
|
| 129 |
+
_env._errors_so_far.append(error_msg)
|
| 130 |
+
_env._step_count += 1
|
| 131 |
+
|
| 132 |
+
obs = _env._build_observation()
|
| 133 |
+
reward = Reward(
|
| 134 |
+
value=0.0,
|
| 135 |
+
signals={"error": 1.0},
|
| 136 |
+
done=False,
|
| 137 |
+
info={"error": error_msg},
|
| 138 |
+
)
|
| 139 |
+
return StepResponse(
|
| 140 |
+
observation=obs,
|
| 141 |
+
reward=reward,
|
| 142 |
+
done=False,
|
| 143 |
+
info={"error": error_msg},
|
| 144 |
+
)
|
| 145 |
+
|
| 146 |
_log("STEP", endpoint="/step", action_type=action.action_type)
|
| 147 |
try:
|
| 148 |
obs, reward, done, info = _env.step(action)
|
test_inference.py
DELETED
|
@@ -1,26 +0,0 @@
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|
| 1 |
-
import sys
|
| 2 |
-
sys.path.insert(0, ".")
|
| 3 |
-
from inference import SYSTEM_PROMPT, TASK_IDS, _parse_json, _build_user_prompt
|
| 4 |
-
from environment import Action
|
| 5 |
-
|
| 6 |
-
print("Imports OK")
|
| 7 |
-
print("Tasks:", TASK_IDS)
|
| 8 |
-
|
| 9 |
-
# Test JSON parsing
|
| 10 |
-
j = _parse_json('{"action_type": "submit_note", "soap_note": {"subjective": "S", "objective": "O", "assessment": "A", "plan": "P"}}')
|
| 11 |
-
print("Parse OK:", j["action_type"])
|
| 12 |
-
|
| 13 |
-
# Test markdown fence stripping
|
| 14 |
-
fenced = '```json\n{"action_type": "submit_note", "soap_note": {"subjective": "S", "objective": "O", "assessment": "A", "plan": "P"}}\n```'
|
| 15 |
-
j2 = _parse_json(fenced)
|
| 16 |
-
print("Fence strip OK:", j2["action_type"])
|
| 17 |
-
|
| 18 |
-
# Test Action creation from parsed output
|
| 19 |
-
action = Action(**j2)
|
| 20 |
-
print("Action created:", action.action_type, "/ sections:", list(action.soap_note.model_fields.keys()))
|
| 21 |
-
|
| 22 |
-
# Test prompt building
|
| 23 |
-
p = _build_user_prompt("Hello doctor", {"name": "Test", "age": 30})
|
| 24 |
-
print("Prompt len:", len(p), "chars")
|
| 25 |
-
|
| 26 |
-
print("\nAll checks passed.")
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test_output.txt
DELETED
|
@@ -1,9 +0,0 @@
|
|
| 1 |
-
|
| 2 |
-
--- Sub-signal unit tests ---
|
| 3 |
-
[OK] conciseness(short): got=1.0 want=1.0
|
| 4 |
-
[OK] conciseness(long) : got=0.0 want=0.0
|
| 5 |
-
[OK] safe_lang(clean) : got=1.0 want=1.0
|
| 6 |
-
[OK] safe_lang(unsafe) : got=0.0 want=0.0
|
| 7 |
-
[OK] format_valid(ok) : got=1.0 want=1.0
|
| 8 |
-
[OK] format_valid(bad) : got=0.0 want=0.0
|
| 9 |
-
[OK] format_valid(clfy): got=1.0 want=1.0
|
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|
test_reward.py
DELETED
|
@@ -1,75 +0,0 @@
|
|
| 1 |
-
import sys
|
| 2 |
-
sys.path.insert(0, ".")
|
| 3 |
-
|
| 4 |
-
from environment import ClinicalNoteScribeEnv, Action, SOAPNote
|
| 5 |
-
from environment.reward import (
|
| 6 |
-
compute_reward, _conciseness_bonus, _safe_language_score, _format_valid,
|
| 7 |
-
WORD_LIMIT, FREE_STEPS, STEP_PENALTY_RATE, ERROR_PENALTY_RATE,
|
| 8 |
-
)
|
| 9 |
-
|
| 10 |
-
def check(label, got, want):
|
| 11 |
-
ok = abs(got - want) < 1e-6
|
| 12 |
-
sym = "OK" if ok else "FAIL"
|
| 13 |
-
print(f" [{sym}] {label}: got={got} want={want}")
|
| 14 |
-
return ok
|
| 15 |
-
|
| 16 |
-
short_note = SOAPNote(
|
| 17 |
-
subjective="Headache and runny nose for 5 days.",
|
| 18 |
-
objective="BP 118/76, HR 72, afebrile, clear lungs.",
|
| 19 |
-
assessment="Viral URI.",
|
| 20 |
-
plan="DayQuil, fluids, rest. Follow up if fever develops.",
|
| 21 |
-
)
|
| 22 |
-
long_note = SOAPNote(subjective=" ".join(["word"] * (WORD_LIMIT + 1)), objective="O", assessment="A", plan="P")
|
| 23 |
-
unsafe_note = SOAPNote(subjective="Patient definitely has pneumonia.", objective="O", assessment="A", plan="P")
|
| 24 |
-
empty_note = SOAPNote(subjective="", objective="O", assessment="A", plan="P")
|
| 25 |
-
|
| 26 |
-
submit_ok = Action(action_type="submit_note", soap_note=short_note)
|
| 27 |
-
submit_bad = Action(action_type="submit_note", soap_note=empty_note)
|
| 28 |
-
clarify = Action(action_type="request_clarify", clarify_question="fever?")
|
| 29 |
-
|
| 30 |
-
print("\n--- Sub-signal unit tests ---")
|
| 31 |
-
check("conciseness(short)", _conciseness_bonus(short_note), 1.0)
|
| 32 |
-
check("conciseness(long) ", _conciseness_bonus(long_note), 0.0)
|
| 33 |
-
check("safe_lang(clean) ", _safe_language_score(short_note), 1.0)
|
| 34 |
-
check("safe_lang(unsafe) ", _safe_language_score(unsafe_note), 0.0)
|
| 35 |
-
check("format_valid(ok) ", _format_valid(submit_ok), 1.0)
|
| 36 |
-
check("format_valid(bad) ", _format_valid(submit_bad), 0.0)
|
| 37 |
-
check("format_valid(clfy)", _format_valid(clarify), 1.0)
|
| 38 |
-
|
| 39 |
-
print("\n--- grader=1.0, steps=2, errors=0 → expect value=1.0 ---")
|
| 40 |
-
r = compute_reward(submit_ok, grader_score=1.0, step_count=2, errors_so_far=[])
|
| 41 |
-
check("value ", r.value, 1.0)
|
| 42 |
-
check("grader_score wt ", r.signals["grader_score"], 0.60)
|
| 43 |
-
check("conciseness wt ", r.signals["conciseness_bonus"], 0.10)
|
| 44 |
-
check("safe_lang wt ", r.signals["safe_language_score"], 0.15)
|
| 45 |
-
check("format_valid wt ", r.signals["format_valid"], 0.15)
|
| 46 |
-
check("step_penalty ", r.signals["step_penalty"], 0.0)
|
| 47 |
-
check("error_penalty ", r.signals["error_penalty"], 0.0)
|
| 48 |
-
|
| 49 |
-
print("\n--- grader=1.0, steps=5 (+2 extra) → expect deduct 0.10 ---")
|
| 50 |
-
r2 = compute_reward(submit_ok, grader_score=1.0, step_count=5, errors_so_far=[])
|
| 51 |
-
check("step_penalty ", r2.signals["step_penalty"], -(2 * STEP_PENALTY_RATE))
|
| 52 |
-
check("value ", r2.value, round(1.0 - 2 * STEP_PENALTY_RATE, 4))
|
| 53 |
-
|
| 54 |
-
print("\n--- grader=1.0, steps=2, errors=2 → expect deduct 0.20 ---")
|
| 55 |
-
r3 = compute_reward(submit_ok, grader_score=1.0, step_count=2, errors_so_far=["e1", "e2"])
|
| 56 |
-
check("error_penalty ", r3.signals["error_penalty"], -(2 * ERROR_PENALTY_RATE))
|
| 57 |
-
check("value ", r3.value, round(1.0 - 2 * ERROR_PENALTY_RATE, 4))
|
| 58 |
-
|
| 59 |
-
print("\n--- all bad signals → expect value clamped to 0.0 ---")
|
| 60 |
-
bad_note = SOAPNote(subjective=" ".join(["word"] * 500) + " Patient definitely has cancer.", objective="", assessment="A", plan="P")
|
| 61 |
-
bad_act = Action(action_type="submit_note", soap_note=bad_note)
|
| 62 |
-
r4 = compute_reward(bad_act, grader_score=0.0, step_count=10, errors_so_far=["e1","e2","e3"])
|
| 63 |
-
check("value clamped ", r4.value, 0.0)
|
| 64 |
-
|
| 65 |
-
print("\n--- end-to-end env: clarify(step1) then submit(step2) ---")
|
| 66 |
-
env = ClinicalNoteScribeEnv()
|
| 67 |
-
env.reset("easy_routine_checkup")
|
| 68 |
-
_, rc, dc, _ = env.step(Action(action_type="request_clarify", clarify_question="did the patient report any fever?"))
|
| 69 |
-
check("clarify done=False", float(dc), 0.0)
|
| 70 |
-
_, rs, ds, _ = env.step(submit_ok)
|
| 71 |
-
check("submit done=True ", float(ds), 1.0)
|
| 72 |
-
assert 0.0 <= rs.value <= 1.0
|
| 73 |
-
print(f" Final value: {rs.value}")
|
| 74 |
-
print(f" Signals: { {k:v for k,v in rs.signals.items() if not k.startswith('_')} }")
|
| 75 |
-
print("\nAll done.")
|
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