UCLA DATA Predicates file #23
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (3)
src/MEDS_DEV/datasets/UCLA/anemia.yaml (3)
1-4: LGTM! Minor formatting fix needed.The description clearly explains the task's purpose and inclusion criteria. However, there's a trailing space on line 2 that should be removed.
Apply this diff to fix the formatting issue:
- This task predicts whether the patient will have abnormal _hemoglobin_ values within a 24-hour window for a given patient. + This task predicts whether the patient will have abnormal _hemoglobin_ values within a 24-hour window for a given patient.🧰 Tools
🪛 yamllint
[error] 2-2: trailing spaces
(trailing-spaces)
6-31: LGTM! Consider adding a comment for clarity.The predicates are well-defined and logically structured. The use of different codes for hemoglobin (LAB//220228//g/dl and LAB//50811//g/dL) is noted and might indicate different measurement methods or units.
Consider adding a brief comment explaining the reason for using two different hemoglobin codes. This would improve clarity for future maintainers. For example:
# Hemoglobin codes for different measurement methods or units hemoglobin_1: code: LAB//220228//g/dl hemoglobin_2: code: LAB//50811//g/dL
35-51: LGTM! Consider adding a comment for consistency.The windows are well-defined and align perfectly with the task description. The input and target windows are appropriately set to 24 hours each, with correct inclusivity settings to prevent overlap.
For consistency with the predicates section, consider adding a brief comment explaining the purpose of each window. For example:
windows: # Input window: 24-hour period for initial hemoglobin measurement input: # ... (existing code) # Target window: subsequent 24-hour period for predicting abnormal hemoglobin target: # ... (existing code)
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📒 Files selected for processing (1)
- src/MEDS_DEV/datasets/UCLA/anemia.yaml (1 hunks)
🧰 Additional context used
🪛 yamllint
src/MEDS_DEV/datasets/UCLA/anemia.yaml
[error] 2-2: trailing spaces
(trailing-spaces)
🔇 Additional comments (2)
src/MEDS_DEV/datasets/UCLA/anemia.yaml (2)
33-33: LGTM!The trigger
lab_startis appropriately defined and aligns with the task description of initiating the prediction when a lab measurement is taken.
1-51: Great job! File approved with minor suggestions.This YAML file is well-structured and clearly defines the task for predicting abnormal hemoglobin values. The predicates, trigger, and windows are logically organized and align with the task description. The minor suggestions provided earlier (removing a trailing space, adding clarifying comments) will further enhance the file's readability and maintainability.
🧰 Tools
🪛 yamllint
[error] 2-2: trailing spaces
(trailing-spaces)
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@Simonlee711 is this ready for review, or should we convert it to a draft for now? I'm going through outstanding PRs to make sure I'm not blocking anything that needs my review. If it is ready for review, go ahead and add me as a reviewer and try to fix the PR check that is failing. I'm happy to have a call to help you get that set up to run automatically on commit for you. |
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@Simonlee711 if you fix the PR workflow errors this is likely ready to go in. Note you can set up pre-commit to run locally and automatically fix issues by installing pre-commit then running |
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@Simonlee711 @mmcdermott I fixed the pre-commit errors. Maybe we can merge this and then update later as per #31 (@Simonlee711 maybe you could also take a look at that PR to see if you have any suggestions for what information new dataset PRs should have, and see if UCLA dataset has that information available). |
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Actionable comments posted: 1
🧹 Outside diff range and nitpick comments (1)
src/MEDS_DEV/datasets/UCLA/anemia.yaml (1)
1-4: Enhance description with specific clinical criteria.The description should explicitly mention the abnormal hemoglobin threshold (13 g/dL) to make the clinical criteria immediately clear to readers.
description: >- This task predicts whether the patient will have abnormal _hemoglobin_ values within a 24-hour window for a given patient. To be included, patients must have at least one measurement for hemoglobin within a given 24-hour period in the labs table - at UCLA. + at UCLA. Hemoglobin values above 13 g/dL are considered abnormal for this task.
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📒 Files selected for processing (3)
.gitignore(1 hunks)src/MEDS_DEV/datasets/UCLA/README.md(1 hunks)src/MEDS_DEV/datasets/UCLA/anemia.yaml(1 hunks)
✅ Files skipped from review due to trivial changes (1)
- .gitignore
🚧 Files skipped from review as they are similar to previous changes (1)
- src/MEDS_DEV/datasets/UCLA/README.md
🔇 Additional comments (4)
src/MEDS_DEV/datasets/UCLA/anemia.yaml (4)
28-31: LGTM!
The combined predicates are well-organized and correctly use OR logic to handle both hemoglobin codes.
11-15:
Standardize unit formatting across hemoglobin codes.
The units are inconsistently formatted: g/dl vs g/dL. This could lead to confusion or potential issues with data processing.
hemoglobin_1:
- code: LAB//220228//g/dl
+ code: LAB//220228//g/dL
hemoglobin_2:
code: LAB//50811//g/dL#!/bin/bash
# Search for other hemoglobin-related lab codes to ensure completeness
rg -i "hemoglobin.*g/d[lL]" --type yaml33-51: LGTM! Verify window configuration with existing tasks.
The window configuration is well-structured with appropriate time ranges and non-overlapping windows. The labeling strategy is correct.
#!/bin/bash
# Search for similar window configurations in other tasks for consistency
rg -A 10 "windows:" --type yaml7-9: Verify the lab code regex pattern.
The pattern ^LABS//.* appears overly broad and might match unintended lab codes. Consider making it more specific to match only hemoglobin-related lab codes.
| abnormal_hemoglobin_1: | ||
| code: LAB//220228//g/dl | ||
| value_min: null | ||
| value_max: 13 | ||
| value_max_inclusive: False | ||
| abnormal_hemoglobin_2: | ||
| code: LAB//50811//g/dL | ||
| value_min: null | ||
| value_max: 13 | ||
| value_max_inclusive: False | ||
|
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🛠️ Refactor suggestion
Consider using YAML anchors to reduce predicate duplication.
The abnormal hemoglobin predicates share identical configuration except for the code. Consider using YAML anchors to reduce duplication and maintain consistency.
+ # Define the base abnormal configuration
+ abnormal_config: &abnormal_base
+ value_min: null
+ value_max: 13
+ value_max_inclusive: False
+
abnormal_hemoglobin_1:
code: LAB//220228//g/dl
- value_min: null
- value_max: 13
- value_max_inclusive: False
+ <<: *abnormal_base
abnormal_hemoglobin_2:
code: LAB//50811//g/dL
- value_min: null
- value_max: 13
- value_max_inclusive: False
+ <<: *abnormal_base📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| abnormal_hemoglobin_1: | |
| code: LAB//220228//g/dl | |
| value_min: null | |
| value_max: 13 | |
| value_max_inclusive: False | |
| abnormal_hemoglobin_2: | |
| code: LAB//50811//g/dL | |
| value_min: null | |
| value_max: 13 | |
| value_max_inclusive: False | |
| # Define the base abnormal configuration | |
| abnormal_config: &abnormal_base | |
| value_min: null | |
| value_max: 13 | |
| value_max_inclusive: False | |
| abnormal_hemoglobin_1: | |
| code: LAB//220228//g/dl | |
| <<: *abnormal_base | |
| abnormal_hemoglobin_2: | |
| code: LAB//50811//g/dL | |
| <<: *abnormal_base |
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Actionable comments posted: 1
🧹 Outside diff range and nitpick comments (2)
src/MEDS_DEV/datasets/UCLA/predicates.yaml (2)
12-15: Maintain consistent abbreviation documentationSimilar to the ED predicates, consider documenting that ICU stands for Intensive Care Unit for clarity.
The regex patterns are consistent with other predicates, which is good.
1-18: Add file-level documentationConsider adding a comment section at the top of the file to document:
- The general structure of predicates
- When to use regex patterns vs direct codes
- Expected format and validation rules for data after "//"
- Examples of valid values for each predicate type
This will help maintain consistency as new predicates are added.
Would you like me to help draft this documentation?
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src/MEDS_DEV/datasets/UCLA/predicates.yaml(1 hunks)
🔇 Additional comments (2)
src/MEDS_DEV/datasets/UCLA/predicates.yaml (2)
17-18: Verify the different pattern for death predicate
The death predicate uses a direct code "MORTALITY" instead of a regex pattern with prefix like other predicates. Please verify:
- Is this intentional?
- Should it follow the same pattern format as others (e.g., "^MORTALITY//")?
- Are there any specific requirements that necessitate this different format?
Let's check for similar usage patterns:
#!/bin/bash
# Check for other direct code usage vs regex patterns
echo "Checking for direct code usage:"
ast-grep --pattern 'code: $VALUE'
echo -e "\nChecking for regex pattern usage:"
ast-grep --pattern 'code: { regex: $_}'7-10: Consider standardizing naming convention
The abbreviation "ED" might not be immediately clear to all developers. Consider either:
- Using the full form "EMERGENCY_DEPARTMENT" to match the verbosity of other predicates
- Adding a comment documenting that ED stands for Emergency Department
Let's check if "ED" abbreviation is consistently used across the codebase:
| hospital_admission: | ||
| code: { regex: "^HOSPITAL_ADMISSION//.*" } | ||
| hospital_discharge: | ||
| code: { regex: "^HOSPITAL_DISCHARGE//.*" } |
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💡 Codebase verification
Documentation needed for predicate pattern format
The regex patterns for hospital events are consistently implemented across multiple datasets (UCLA, MIMIC-IV), but there's no documentation explaining:
- The expected format after the "//" delimiter
- Example valid strings
- Purpose of this pattern structure
This documentation would be valuable since:
- The README.md is currently minimal with just TODOs
- The pattern is used across multiple datasets
- No examples or explanations exist in the codebase
🔗 Analysis chain
Consider documenting the expected format after "//"
The regex patterns for hospital events look good, but it would be helpful to document:
- The expected format of data after "//"
- Examples of valid strings
Let's check if there are any existing examples or documentation:
The previous search revealed that this pattern is consistently used across multiple datasets (MIMIC-IV, UCLA, AUMCdb). Let's check for documentation and example usage to make a more informed decision about whether documentation is really needed.
Let's check the README content and actual usage examples to make a final determination about whether documentation is needed.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Search for examples or documentation of these patterns
rg -i "HOSPITAL_(ADMISSION|DISCHARGE)//" --type md
Length of output: 6849
Script:
#!/bin/bash
# Let's check for any documentation files in the UCLA dataset directory
fd -e md -e txt . src/MEDS_DEV/datasets/UCLA/
# Also check for any comments or documentation in the predicates file
cat src/MEDS_DEV/datasets/UCLA/predicates.yaml
# Check if there are any test files that might show example usage
fd test src/MEDS_DEV/datasets/UCLA/
Length of output: 591
Script:
#!/bin/bash
# Let's check the README for any documentation about these patterns
cat src/MEDS_DEV/datasets/UCLA/README.md
# Also check if there are any examples in the codebase showing how these patterns are used
rg "HOSPITAL_ADMISSION//" -A 1 -B 1
Length of output: 807
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