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Hi @oeway, Thank you for the draft PR. Source code files can go in the upper-level notebooks folder of the repo, and your chapter can link to them as a reference. Your assets folder makes sense for your images, and if any of your source code should be less prominent, leaving it there as well is an option. The draft so far has a lot of interesting information. We suggest expanding the intro paragraphs a bit to give an expanded road map of the chapter. This will be helpful for readers who may know very little about LLMs beyond ChatGPT's existence. We also suggest as you refine the text making sure that terms are well defined for inexperienced readers. We will wait on fully editing the draft until you tell us it is ready for review. All the best, |
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Hi @oeway, We wanted to briefly follow up on the status of your draft PR. You had mentioned wanted to work on the draft more before a full review. Please let us know when this draft is ready, and we will be happy to take a look. Thank you, |
# Conflicts: # docs/3-llms.qmd # docs/references.bib
- Fix critical factual error: LLM training description now correctly describes autoregressive next-token prediction (was incorrectly describing BERT-style masked prediction) - Remove fabricated VLM confidence scores (95.0%, 90.0%, 85.0%); replace with honest qualitative description - Add missing citations: hallucination rates (Chelli et al. 2024, JMIR), EIMS microscope system (Huang et al. 2025, bioRxiv) - Add 2026 citations: Wang et al. (Nat Biomed Eng) for LLM coding benchmarks, Li et al. (Nat Biotech) for agentic AI in biomedical research, Qu et al. (Nat Biomed Eng) for CRISPR-GPT - Reduce redundancy: SWE-bench stats consolidated from 5 mentions to 2, VLM generalization demo deduplicated across sections - Fix AI-generated style: replace ~15 instances of "remarkable", "dramatic", "transformative" with precise language; tighten formulaic transitions and reduce hype throughout - Verified chapter compiles with Quarto 1.6.42 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
…reduce hype
- Section 3.1: Merged redundant "Complexity Challenge" and "Overwhelming Landscape" subsections;
removed overstated claims ("cannot be overstated", "paradigm shift", "profound")
- Section 3.2: Improved LLM intro paragraph; renamed "Promise and Current Limitations" to
"What LLM Code Generation Can and Cannot Do Today" with more specific content
- Section 3.3: Enriched Function Calling section with motivating problem, detailed MCP
explanation with microscopy example, expanded Trust Escalation discussion
- Section 3.4: Rewrote VLM intro for clarity; expanded limitations subsection with
cost/speed specifics; added vision-guided programming paragraph
- Section 3.5: Tightened agent intro (removed "qualitative leap"); condensed harness
engineering and execution environment paragraphs; improved computer use precision
- Section 3.6: Added concrete calcium imaging example; toned down "revolution" language
- Sections 3.7-3.9: Minor tightening of opening paragraphs, improved precision
- Global: Removed remaining hype words, improved scientific precision throughout
- Verified: Quarto build succeeds (only expected @sec-10 warning)
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
…essibility - Remove vision-guided programming duplication (was described twice in 3.4) - Remove MCP/Linux Foundation duplication between 3.3 and 3.5 (now cross-refs) - Simplify memory systems paragraph with microscopy-specific example - Tighten Dynamic Code Generation subsection (overlapped with 3.2 and 3.6) - Restructure agent ecosystem callout box by category instead of flat list - Tighten conclusion — remove grandiose phrasing - Fix awkward "can barely do extrapolation" phrasing in 3.1 - Replace "quiet revolution" cliché in 3.6 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
…hter conclusion - Fix overclaiming: 'human-level' → 'expert-level on well-represented types'; logprob ≠ calibrated confidence; 'not science fiction' → measured framing - Tone: remove celebrity attributions (Karpathy, Tobi Lutke, OpenAI team); contextualize 'vibe coding'; replace spreadsheet analogy with microscopy one - Clarify SmartEM/pySTED are ML-based, not LLM agents - Add reproducibility paragraph to Section 3.6 (ephemeral software) - Add validation caveat to 'within minutes' and 'nearly free' claims - Slim Section 3.5 validation callout to cross-reference §3.8 - Tighten conclusion: reduce recap, add synthesis on what changed (narrow task automation → intent-driven interaction), weave cross-refs into prose - Soften 'emerging' tier in hype check; add conditional tense to §3.6 - Hedge VLM benchmark claim; date-stamp Gemini CLI free tier - Quarto build verified (only expected @sec-10 warning) Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
…, expanded conclusion Major changes: - Section 3.1: Tightened extrapolation discussion, shortened figure captions, moved VLM generalization demo to 3.4 where VLMs are properly introduced - Section 3.2: Retitled ImageJ subsection, merged benchmarking + limits - Section 3.3: Added concrete JSON function-call example for microscopists - Section 3.4: Restructured into two focused subsections (interpretation + capabilities/limits), integrated VLM generalization from 3.1 - Section 3.5: Consolidated agent architecture, rewrote Omega/BioImage.IO descriptions to focus on paradigm not features, noted EIMS is preprint - Section 3.6: Strengthened reproducibility discussion, added institutional knowledge concern, integrated software-obsolescence discussion from 3.8 - Section 3.7: Added prompt engineering tips, fixed FUCCI biology (S-phase = co-expression), added FUCCI citation, added data privacy callout, added coding agent comparison table - Section 3.8: Split reproducibility/bias into separate subsections, developed skills atrophy with concrete FUCCI scenario, sharpened hype-check tiers - Section 3.9: Expanded from 3 paragraphs to proper 5-paragraph synthesis - AI Disclosure: More specific about models and roles - Global: Reduced 'substantially'/'fundamentally' overuse, varied sentence structure, removed formulaic patterns, standardized BioImage.IO naming Net: 267 insertions, 288 deletions (21 lines shorter, richer content) Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
…ures - Added Claude Code, Gemini CLI, Codex to AI Agents row in model evolution table - Added intent-driven microscopy Excalidraw diagram - Updated glossary entries - Added CLAUDE.md project development guide Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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Hi all — apologies for the long delay on this. The draft for Chapter 3 has gone through several rounds of revision and should be in good shape now. Would appreciate your feedback whenever you get a chance. Thanks! |
These are local development config files and should not be in the repo. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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Hi @ScientistRachel and @opp1231 while I am still working on this, maybe you can give me some hint on how we should attach source code files? In my case I have some python code to generate data for figures, train models, which is not meant for show to the readers, but they can check in details if needed. In this case can I leave it as some python files? where should place them? also where should I place figures? I have them in a separate folders. Please comment if you see changes needed regarding these.
Content-wise, it's a dump of everything right now, need a bit more work on re-org and polishing, will do with a postdoc in my group.