Lab Website Memory

Distilled 2026-04-10 20:44 UTC

Recent Changes

• Colin et al. publication update (2026-03-11): Updated arXiv preprint for interpretability paper from v1 to v2 (https://arxiv.org/abs/2411.03993v2). Title: “Choosing the right basis for interpretability: Psychophysical comparison between neuron-based and dictionary-based representations.” Changes synced across publications_by_year.json, officialPublicationUrls.js, and serre_lab_publications.bib.

• Highlights section removal (2026-03-11): Removed the new Highlights section from home page (index.html) after it replaced previous highlights unintentionally. The “Selected Recent Publications” section was kept as the main feature list. No separate highlights needed.

Key Files & Locations

• Publications data: src/data/publications_by_year.json (source of truth)
• URL resolver: src/data/officialPublicationUrls.js (title → URL mapping)
• BibTeX: serre_lab_publications.bib (kept in sync with JSON)
• Static dump: public/misc/publications (legacy, synced with JSON)
• Home page: index.html (has “Selected recent publications” section only)

Workflow Notes

• All publication updates go through publications_by_year.json first
• sync_from_central.py keeps lab site aligned with CV’s central publication data
• Avoid adding duplicate publication metadata — use URL resolver for lookups
• Jekyll builds the site from src/ to public/

Distilled 2026-04-17 04:30 UTC

cpsy1950 course site — Week 13 + Week 14 fixes (tserre.github.io)

Week 14 restructuring — An earlier LLM edit had broken the consistency of the Week 14 block with prior weeks (Weeks 8/13). Aligned to the canonical template in cpsy1950/index.md:

• Tuesday summary uses Lecture: / Guest lecture: prefix (not topic-only title).
• Readings reverted from nested <ol> + focus/skim layout to the simpler intro paragraph + <ul> of links (matches Week 8).
• Replaced generic .../assignments placeholder URLs (which look like submission links) with per-assignment Canvas URLs once provided.
• Guest (Victor Boutin) given a homepage line ` — site at https://victorboutin.github.io/` to match Tuckute / VanRullen pattern.

Canvas assignment IDs added (Week 14):

• W14 Reading Response (Tue 4/21): https://canvas.brown.edu/courses/1101742/assignments/8113914
• W14 Reflection (Sun 4/26): https://canvas.brown.edu/courses/1101742/assignments/8113915
• Removed stale cpsy1950/week14-rubrics.md file that was sitting in the repo.

Week 13 — Tuckute guest lecture materials:

• Copied slides into site tree: ~/Downloads/Tuckute_Language_network_LLMs_Brown_sh.pdf → personal/website/assets/cpsy1950/Tuckute_Language_network_LLMs_Brown_sh.pdf. ~66 MB; GitHub warned ≥50 MB — consider Git LFS if more large assets come. cp -f is the keep-in-sync step when the file is updated in Downloads.
• Added Slides (PDF) + Lecture capture line in Tue 4/14 entry using the same 📑 Slides · Lecture capture pattern as earlier weeks. Zoom play URL uses the short token form (/rec/play/<token>), stripping the long query string (works fine; revert to full URL only if browser issues).

Week 14 — VanRullen guest lecture (Thu 4/16) lecture capture:

• Zoom recording URL added to Thu 4/16 entry: https://brown.zoom.us/rec/share/Dh6myqJFRT-3kYoYJPZ7G4pIGqXtRzTq05KMS84bkJatb7Q4CxEPdIYKDz0SK4EJ.M_w8D7_v23XlZ-c6

Repo/push note: session also did a batched “push to gh” covering 4 repos — tserre.github.io (this one, incl. the 62 MB Tuckute PDF which tripped GitHub’s >50 MB warning; 2 high-severity Dependabot alerts pending at https://github.com/tserre/tserre.github.io/security/dependabot), serre-lab/prj_papers (fossils paper), Singapore_GlobalAI (grant), prj_cv. All clean of secrets and no PLOS PDFs.

Conventions reinforced

• Per-assignment Canvas URLs preferred over bare /assignments page.
• Guest lecture entries should carry: homepage link · slides (PDF) · lecture capture — all three, matching existing Week 13 pattern.
• Tuesday vs Thursday sessions keep Lecture: / Guest lecture: prefixes in the <details> summary.

Distilled 2026-04-18 04:30 UTC

cpsy1950 sidebar alignment

File: _data/cpsy1950/structure.yml drives the course site’s left-sidebar menu for layout: course-sidebar pages.

Change: Renamed “W13 - Guest lectures” → “W13 - Frontier topics” and “W14 - Guest lectures” → “W14 - Frontier topics” so the sidebar labels match the schedule headings in cpsy1950/index.md (both read “Frontier topics in NeuroAI”).

Rule: sidebar entries in _data/cpsy1950/structure.yml should stay in sync with the ### Week N headings in cpsy1950/index.md. When a schedule heading changes, also update the sidebar label.

Pushed to tserre.github.io in the same session.

Distilled 2026-04-20 04:30 UTC

Safety rule: exam materials NEVER live in this (public) repo

tserre.github.io is a public GitHub Pages repo. During a ~/Work backup audit on 2026-04-19, a cpsy1950/final-exam/ folder was spotted as untracked in this repo with actual exam content (blueprint, questions, answer key, fake-paper PDF). Thomas deleted it on the spot and moved the materials to the private tserre/cpsy1950 repo under internal/.

Rule: any file with “exam”, “rubric+samples”, “answer-key”, “final-*” naming must go to ~/Work/teaching/cpsy1950/internal/ (private repo), never anywhere under ~/Work/personal/website/. Grading spreadsheets were already in .gitignore for this repo — the same caution applies to any graded-work content.

CV asset auto-update

When the CV is regenerated, a copy of latex/serre_cv.pdf gets pushed into this repo at assets/serre_cv.pdf so the public download link stays current. Expect a small commit here every time the CV repo ships a rebuild.

Distilled 2026-04-21 02:00 UTC

Brown library proxy URL migration. Brown moved from their legacy EZproxy host revproxy.brown.edu to the OCLC-hosted EZproxy brown.idm.oclc.org. Both use the same hyphenated-hostname convention (www-nature-com.brown.idm.oclc.org), so a pure string swap of revproxy.brown.edu → brown.idm.oclc.org is safe — subdomain prefixes transfer unchanged.

Files updated in this repo: cpsy1950/index.md (9), cpsy1950/syllabus.md (3), _data/cpsy1950/schedule.yml (4), _data/cpsy1950/readings.yml (2). Committed as c12686d on master in tserre/tserre.github.io.

Action item: spot-check one or two proxied links from the cpsy1950 readings list before next class to confirm OCLC host resolves for Brown credentials. Dependabot flagged 2 high-severity alerts on tserre.github.io default branch (unrelated); review at https://github.com/tserre/tserre.github.io/security/dependabot when time allows.

Distilled 2026-04-22 04:30 UTC

cpsy1950 Week 14 Tue lecture — Slides + Panopto added (2026-04-21)

Two incremental updates to cpsy1950/index.md, Week 14 Tuesday 4/21 block (“The role of feedback in biological and artificial vision”):

• Slides link (Google Slides): https://docs.google.com/presentation/d/13vkYs1nYExpOY4bi03koeweiuxT4GEaE5Cd-3FHZ6u8/edit?usp=sharing — commit f6bfad3 on master in tserre/tserre.github.io.
• Panopto lecture capture (one-link-per-push workflow): https://brown.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=5b74eb9c-6077-4576-933c-b43301314ef1 — placed next to the Slides link using the canonical 📑 Slides · Lecture capture pattern, pushed separately.

Notes:

• Tuesday CPSY1950 sessions are recorded to Panopto (Brown-hosted), Thursday guest lectures have previously used Zoom share recordings — both are valid, just different hosts. Use whichever URL the instructor/guest provides.
• Distilled memory file is explicitly included in git add when Thomas says “push to gh” — this is the expected behavior (auto-staged like other “reasonable files”), not a stray file.

Lab-website (serre-lab/Lab-Website, ~/Work/research/lab-website/) — Selected Publications card swap

Replaced the “Deceptive learning in histopathology” card in the Selected Recent Publications grid on the Home page with the newer Calvert et al. 2026 spinal-cord paper:

• Title: “Perilesional neuromodulation replaces lost sensorimotor function in persons with spinal cord injury”
• Authors: J.S. Calvert et al.
• Venue: Nature Biomedical Engineering, 2026
• Source of truth for citation details: src/data/publications_by_year.json (already had the full record + Nature URL). Always pull metadata from this file rather than typing by hand — ensures consistency with the publications page.

Structural notes for future edits on this repo:

• Home page publication cards live in src/pages/Home/Home.tsx as hard-coded <div className="highlight-card"> blocks — they are NOT auto-generated from publications_by_year.json. To swap/add/remove a card, edit Home.tsx directly.
• Journal names on these cards are run through a shortenJournalName() helper (also in Home.tsx) that maps full names to display abbreviations (e.g. 'Attention, Perception, & Psychophysics' → 'Atten Percept Psychophys'). To abbreviate a new journal, add an entry to that map — don’t hand-edit the card text. Added 'Nature Biomedical Engineering': 'Nature BME' in this session.
• Commits landed on main in serre-lab/Lab-Website; most recent: 4327ebb (“Abbreviate Nature Biomedical Engineering to Nature BME”).

Conventions reinforced

• Weekly lecture updates pattern for cpsy1950/index.md: (1) pre-class, add Slides link; (2) post-class, add Lecture capture link next to it with ` · ` separator. Two separate commits is fine and is the actual workflow.
• On the lab website, publication card edits on Home.tsx must be kept consistent with publications_by_year.json; the JSON is the source of truth for citation strings, URLs, and year.

Distilled 2026-04-27 04:30 UTC

Lab-website (serre-lab/Lab-Website) — SciComm card added for Brown news on LLM “understanding”

Prepended a new entry to src/data/scicomm.json (newest-first ordering) for the Brown News piece “Do AI language models ‘understand’ the real world? On a basic level, they do, a new study finds” (2026-04-22, Kevin Stacey). Lepori / Serre / Pavlick, ICLR 2026 mechanistic-interpretability work classifying events as commonplace / improbable / impossible / nonsense.

• Link: https://www.brown.edu/news/2026-04-22/artificial-intelligence-understanding-real-world
• Image: Pulled the page’s og:image (neuralnets.jpg on brown.edu) — same pattern as prior Brown news entries.
• Commit: 739ac6c on main in serre-lab/Lab-Website. Pushed cleanly.

Reinforced workflow conventions

• Media page entries are sourced from src/data/scicomm.json and rendered by src/pages/SciComm/SciComm.tsx. Order is newest first — always prepend, don’t append.
• For Brown News (and similar) pieces, lift the hero image from og:image rather than typing one by hand: curl -sL <url> | grep og:image then HTML-decode the URL. Keeps cards consistent with the source page.
• After editing JSON data files (scicomm.json, publications_by_year.json), always validate with node -e "JSON.parse(require('fs').readFileSync('<path>'))" before committing — silent JSON parse errors break the build.
• Dependabot still has open high-severity alerts on tserre.github.io (unrelated to this commit but still pending — see 2026-04-21 entry).

Distilled 2026-05-08 04:30 UTC

Dependabot fix on tserre.github.io (Jekyll site)

Resolved 2 high-severity Dependabot alerts on tserre/tserre.github.io (the personal Jekyll site, not the React lab-website). The alerts surfaced on a previous push and were noted as pending in the 2026-04-21 entry. Fixed in this session.

What was vulnerable:

• addressable — needed ≥ 2.9.0 for the template-pattern ReDoS issue.
• json — lockfile had 2.15.2; needed ≥ 2.15.2.1.
• kramdown — already on 2.5.x but bumped to 2.5.2 to stay clearly clear of the advisory range.

Fix command (idempotent — Gemfile.lock-only change, no Gemfile edit):

cd ~/Work/personal/website
bundle update addressable json kramdown rexml webrick

Resulting versions: addressable 2.9.0, json 2.19.5, kramdown 2.5.2, public_suffix 7.0.5, webrick 1.9.2.

Validation steps run (and worth keeping as a checklist):

• bundle audit check → no advisories (install with gem install bundler-audit if missing).
• bundle exec jekyll build → succeeds; existing Liquid/Sass deprecation warnings unchanged. No new warnings introduced.

Commit: 8859d24 on master in tserre/tserre.github.io: fix(deps): address Dependabot alerts (addressable, json, kramdown). After ~5s wait, gh api repos/tserre/tserre.github.io/dependabot/alerts returns those alerts as state: fixed.

Optional follow-up not done yet: wire bundle audit check (and jekyll build) into .github/workflows/ so this drift is caught at PR time instead of by Dependabot after the fact. Worth doing on the next quiet maintenance pass — the Gemfile.lock churn pattern repeats every few months.