Log
A working ledger of what I am building, writing, and wrestling with.
Sep 2026
UC activity manuscript, under review
Submitted the Bayesian multilevel manuscript on 27 September. The study combines MR enterography features with faecal calprotectin to estimate endoscopic activity in individual colonic segments, in a prospective cohort of 49 adults with UC and 245 segments. It is now under review. Study page.
UC MRE
Sep 2026
Motility manuscript, accepted
On 24 September the colonic motility manuscript was accepted for publication in Inflammatory Bowel Diseases. DOI to follow. Study page.
UC MRE
Sep 2026
Clinical research ethics course, started
Started the NIH course Ethical and Regulatory Aspects of Clinical Research on 23 September. It runs for seven weeks.
research ethics
Aug 2026
Radiopaedia, daily
Since August I have been taking Radiopaedia courses. I watch and learn from them every day.
radiology
Aug 2026
Motility manuscript, major revision
Completed a major revision of the motility manuscript. The revision narrowed “motility” to what GIQuant actually measures: regional bowel-wall deformation, not transit or propulsion.
UC MRE
Aug 2026
UC activity manuscript, circulated
Completed the Bayesian multilevel manuscript and sent it to co-authors for a final review before submission.
UC MRE
Jul 2026
Loop engineering?
Looked into where a verification loop actually belongs in the lineage pipeline. Landed on Stage 6 selection as the right place for it, and just as clearly on writing as the wrong one.
agentic systems
Jul 2026
Content format taxonomy, drafted
Worked out a full backlog of content formats the tooling could support: lineage pieces, pipeline meta-posts, living reference pages, methods close reads, a reproducibility ledger. Filed it as backlog, not a prerequisite. The first piece still comes first.
content strategy
Jun 2026
Lineage module, stages 3 through 6 built
Reframed the pruner after similarity-based cuts failed to separate on-thread from off-thread papers. The distinction turned out to be structural and temporal, not topical. Stage 6 shipped as a two-step selection-plus-narration system with a strict anti-hallucination contract.
lineage
Jun 2026
Corpus persistence, diagnosed
Untracking papers.db to stop binary merge conflicts quietly broke corpus accumulation along with it. Fixed the conflict, lost the persistence, now rebuilding the data branch and reseeding from Zotero.
ibd-digest
Jun 2026
Risk Stratifier app, v0.5.0
Moved the app to a single artifact-driven design, so it now loads directly from the notebook’s exported JSON. Pushed a UI cleanup alongside it and cut a new Zenodo release.
Streamlit
Jun 2026
Methods and Results, drafted
Worked through the manuscript’s Methods and Results paragraph by paragraph.
manuscript
Jun 2026
ESGAR 2026, presented
Dr. Bhatnagar presented the work in Montpellier on June 11th and it landed well.
ESGAR 2026
Jun 2026
ibd-reports, section-splitter bug fixed
Found a quiet parsing bug where soft line breaks were hiding section headers on later lines. Fixed it and re-ran the affected phases; recovered dozens of impressions that had gone missing.
radiology reports
Jun 2026
ibd-reports, duplicate review closed out
Manually reviewed thousands of fuzzy-matched filename clusters to confirm genuine multi-report patients versus false merges. Tedious, but it locks the input.
radiology reports
Jun 2026
ibd-reports, de-identification validated
Passed the second manual validation layer on the de-identification scrub with a clean stratified read. Locked the design for the final anonymous-ID rekey.
de-identification
May 2026
Activity project, manuscript start
Started structuring the manuscript. The first pass is always the longest.
multilevel modeling
May 2026
ibd-digest, shipped
Automated literature workflow on GitHub Actions, semantic embeddings to surface newly published IBD imaging papers each day. Letting it run for a few days before deciding the next steps.
GitHub Actions
May 2026
ESGAR 2026
Closed out slides for two first-author orals at ESGAR 2026 in Montpellier and sent to co-authors.
ESGAR 2026
May 2026
Motility manuscript, submission queued
The manuscript reached a submission-ready draft. We decided to circulate it for one final read by all authors after ESGAR 2026. The delay bothers me, but the paper will be better for it.
UC MRE
May 2026
Edge cases on a clinical extraction pipeline
Spent a few days handling legacy formatting in historical reports that breaks naive parsing. Most of the work in agentic systems lives here, not in the model calls.
agentic systems
Apr 2026
Motility manuscript, final pass
Last structural revisions and cross-site checks before submission. The hardest part has been trimming a well-written paragraph.
UC MRE
Mar 2026
Personal site, live
Quarto build, custom theme, treated as both a professional presence and a digital garden. The harder decision was structural, not technical: deciding what counts as ready to publish.
Quarto
Last updated: October 2026. Updated as work ships or stalls.