Automating Clinical Data Analysis: The Pipeline From Hospital Exports to Paper Drafts

Automating Clinical Data Analysis: The Pipeline From Hospital Exports to Paper Drafts I've been building Data2Paper — a tool that turns research data into complete paper drafts. The latest challenge: handling clinical datasets from hospital systems. If you've never worked with hospital data exports, here's what makes them... fun. The input problem A typical clinical data export looks like this: PatientID | Age | Sex | HbA1c | SBP | DBP | eGFR | Dx | AdmDate | DisDate | Status 001 | 67 | M | 8.2 | 145 | 92 | | T2DM | 2024-01-15 | 01/25/2024 | alive 002 | 54 | F | | 128 | 78 | 85 | 2型糖尿病 | 20240203 | 2024-02-10 | 003 | -5 | M | 7.1 | 300 | 85 | 92 | type 2 DM | 2024-03-01 | 2024-03-08 | dead Notice: three different date formats in the same column, the same diagnosis coded three different ways, an obviously wrong age, a systolic BP that's probably a data entry error, missing values that could mean "not tested" or "not recorded," and mixed languages. This is normal. Every clinical research