Weekly Report — 2026-W06 (2026-02-02 ~ 2026-02-08)

This week (2026-02-06~07) work focused on two main tracks: first, a systematic root-cause analysis of the ARI performance gap between the MIHD project’s staig_fusion and the original STAIG (0.21 → target 0.56), identifying and quantifying five key implementation differences and completing the code-level strict-alignment override refactor; second, an engineering upgrade to the benchmark tool — fixing a bar chart rendering bug in reports, implementing an end-to-end GitHub Pages auto-publish pipeline, and adding interactive CLI upload functionality. Additionally, one TOEFL English speaking practice session was recorded (personal study).

Weekly Overview

Metric	Value
Date Range	2026-02-02 ~ 2026-02-08
Active Days	1 / 7
Total Conversations	2
Projects Involved	2
Completed Tasks	7
In-Progress Tasks	2
Total Tokens	88,552,896
Total Cost	$28.25
Claude Code Tokens	4,682,683
Claude Code Cost	$1.00
Codex Tokens	83,870,213
Codex Cost	$27.25
Daily Average Cost	$14.12

Project Progress

MIHD / STAIG Fusion (1 day active) — 🔄 active

Completed:

Systematically compared the original STAIG notebook with the MIHD implementation, identified five quantifiable key differences and ranked them by priority
Identified the most critical root cause: full-resolution image (13332×13332) coordinates were still multiplied by the hires scale factor (0.15), causing patch sampling to deviate severely from tissue regions
Completed code refactoring for strict semantic alignment of staig_fusion (4 core files), implementing default mclust, raw HVG features, STAIG hyperparameter profile, and spatial majority vote refinement
Fixed the silent fallback from mclust to kmeans when mclust is unavailable; added pre-validation of embedding shape
Identified reversed gene preprocessing order (MIHD: HVG → normalize/log/scale; original STAIG: reverse order)

Blockers:

⚠️ Coordinate scale mismatch is the highest-priority fix; runtime validation after the refactor is still pending
⚠️ Root cause of the mclust dimension is zero error (which upstream step produces an empty embedding) is pending confirmation from the next run
⚠️ rpy2 and R mclust packages are not fully installed in the HPC environment; the silent fallback risk has not been fully eliminated

Benchmark Tool (gadget) (1 day active) — 🔄 active

Completed:

Fixed the bar chart rendering bug where high scores produced short bars (pinned Plotly JS CDN version, forced list type, set rangemode='tozero')
Implemented a complete GitHub Pages public submission pipeline: relay validation/deduplication/sanitization → repository_dispatch → queue files → daily batch processing → auto-deployment
Added scripts/ingest_submissions.py (validation/deduplication/cleaning) and scripts/submit_result.py
Implemented three GitHub Actions workflows (accept-submission, daily-publish, pages-deploy)
Added interactive upload prompt to the benchmark CLI, supporting --upload/--no-upload flags and environment variable configuration
Removed the Historical Trends section and fixed an AttributeError

Blockers:

⚠️ Low GPU utilization issue (both CPU and GPU underutilized, single-threaded I/O wait bottleneck) is not fully resolved; awaiting user’s choice of optimization approach

English Study (TOEFL) (1 day active) — 🔄 active

Completed:

Completed TOEFL integrated speaking Task 4 practice (Bystander Effect), scored 4.5/5
Practiced 4 tasks this week in total, with scores improving from 3.5 to 4.5; the main weakness is subject-verb agreement grammar errors

Key Tasks

✅ Diagnose the ARI/NMI performance gap between STAIG fusion and the original STAIG (2026-02-06) — Systematically compared two code paths, identified and quantified five root causes: ① full-resolution image coordinate scale mismatch (most critical); ② silent mclust downgrade to kmeans; ③ reversed gene preprocessing order; ④ pseudo-label cluster count 300 vs 80; ⑤ hyperparameters not fully aligned
✅ Implement GitHub Pages auto-publish pipeline (2026-02-06) — Added relay architecture and three GitHub Actions workflows, achieving end-to-end public data collection, deduplication, cleaning, and auto-publishing
🔄 Implement strict alignment override refactor for STAIG fusion (2026-02-06) — Modified 4 core files for strict STAIG semantic alignment; syntax validation passed, but encountered mclust dimension error at runtime; full validation pending
✅ Fix benchmark report bar chart rendering bug (2026-02-06) — Pinned Plotly JS CDN version to 3.3.1, converted Series to list, set rangemode='tozero'; completely resolved the high-score short-bar issue
🔄 Fix mclust dimension is zero runtime error (2026-02-06) — Added pre-validation of embedding shape at the Python level (2D, non-zero rows/columns, sample count ≥ cluster count); root cause pending confirmation from next run
✅ Add interactive upload prompt to benchmark CLI (2026-02-06) — Prompts user after run to confirm upload; supports --upload/--no-upload/--relay-url flags and BENCHMARK_RELAY_URL environment variable

Issues & Solutions

1. MIHD staig_fusion ARI (0.21/0.4849) far below original STAIG (0.562), root cause unknown [MIHD / STAIG Fusion] (2026-02-06)

Solution: Systematically compared two code paths and identified five root causes ranked by priority: ① full-resolution image (13332×13332) coordinates still multiplied by the hires scale factor (0.15), causing patch sampling to deviate severely from tissue regions (most critical); ② mclust unavailable on HPC, causing silent downgrade to kmeans; ③ reversed gene preprocessing order; ④ pseudo-label cluster count 300 vs 80; ⑤ hyperparameters not fully aligned

2. Plotly bar chart rendering error: high scores display as short bars, visual logic inverted [Benchmark Tool] (2026-02-06)

Solution: Root cause: Plotly 6.x uses binary-encoded array serialization, which is incompatible with older CDN versions. Fix: pin the CDN version to match the Python package version (3.3.1), force passing Python lists, and set rangemode='tozero'

3. Strict STAIG mode silently overrides the visual encoder to UNI; user assumed UNI2 was in use — opaque behavior [MIHD / STAIG Fusion] (2026-02-06)

Solution: Added an explicit encoder override notice to the logs; the UNI2 progress bar not appearing was because UNI was actually running

4. `create_trend_chart` AttributeError: method was commented out but still called in `generate_html` [Benchmark Tool] (2026-02-06)

Solution: Added a stub method returning an empty chart and completely removed the call site from the caller code

Learnings

Architecture

The correct layered architecture for a public GitHub Pages submission pipeline: public users → relay (validation/rate limiting/sanitization) → repository_dispatch → queue files → daily batch processing (deduplication/cleaning/CSV append) → commit/push → Pages auto-deployment. The relay middle layer is the critical isolation point that protects repository write access.
Interface names must semantically match their actual behavior exactly: the name staig_fusion implicitly promises STAIG-equivalent semantics; allowing major behavioral differences in defaults causes many hidden errors. Global override behaviors (such as forcing the encoder to UNI) must be explicitly surfaced in logs.

Debugging

Plotly 6.x defaults to binary-encoded array serialization, which causes bar length parsing errors when the CDN version is outdated. Fix: strictly pin the CDN version to match the Python package version, and always pass Python lists instead of pandas Series.
Simultaneously low CPU and GPU utilization indicates the process is blocked on single-threaded I/O, not compute. The performance bottleneck in visual feature extraction is typically data preprocessing (patch sampling), not the model forward pass.
R interface errors (e.g., mclust) are not intuitive when surfaced in Python; add thorough pre-validation on the Python side with clear error messages including shape information. When an R package is unavailable and silent degradation occurs, an explicit warning is mandatory — algorithm behavior must never change silently.

Domain Knowledge

Five quantifiable key implementation differences exist between MIHD and the original STAIG (ranked by priority): ① full-resolution image coordinate scale mismatch (most critical); ② silent mclust downgrade; ③ reversed gene preprocessing order; ④ pseudo-label cluster count difference; ⑤ hyperparameter and image transform differences. The ARI gap (0.21 → 0.56) is primarily driven by ①②③.

AI Usage Notes

Effective patterns:

✓ Systematic cross-repository code comparison: line-by-line comparison of two codebases to quantify and rank multiple implementation differences by priority
✓ Multi-round tool calls complemented by human observation: AI discovered the coordinate scale issue (technical detail); user discovered the UNI/UNI2 encoder override issue (runtime observation) — forming a complementary workflow
✓ Architectural design collaboration: human provided the core security intuition (pre-upload confirmation, secure isolation); AI translated it into a complete, executable technical architecture

Limitations:

✗ Incomplete fixes: when removing the trend chart, the first pass only removed the call site without handling the function definition, requiring a second fix
✗ Prone to missing existing global override logic: when adding the UNI2 tqdm progress bar, failed to notice that strict mode would force-override the visual encoder
✗ Did not proactively check available modules in the HPC environment (e.g., scanpy), causing ModuleNotFoundError during validation and adding extra debug iterations
✗ Offered multiple solution options for the low GPU utilization issue but did not proactively suggest profiling tools (py-spy, nvprof) to precisely locate the actual bottleneck

Next Week Outlook

Top priority next week is validating the runtime effect of the STAIG strict-alignment refactor: ① fix the coordinate scale mismatch (full-resolution images should no longer be multiplied by the hires scale factor) — this is the most critical step for improving ARI; ② confirm and fix the upstream root cause of the mclust dimension is zero error; ③ install rpy2 and the R mclust package to eliminate the silent fallback risk in the HPC environment. For the benchmark tool, optionally advance GPU utilization optimization (DataLoader multiprocessing or pre-extracted patch cache). For English study, continue targeted practice on grammar weaknesses such as subject-verb agreement.

Token Usage Statistics

Daily Cost Trend

Date	Tokens (M)	Cost ($)
2026-02-06	51.6	16.44
unknown	36.9	11.81

Peak day: 2026-02-06 — $16.44 / 51.6M tokens

Claude Code

Metric	Value
Total Tokens	4,682,683
Input Tokens	309
Output Tokens	542
Cache Write	459,558
Cache Read	4,222,274
Total Cost	$1.00

Model Usage Distribution

Model	Cost ($)	Input Tokens	Output Tokens
claude-haiku-4-5-20251001	1.00	309	542

Codex

Metric	Value
Total Tokens	83,870,213
Input Tokens	83,524,009
Output Tokens	346,204
Reasoning Tokens	156,104
Cache Read	78,577,792
Total Cost	$27.25

Model Usage Distribution

Model	Cost ($)	Input Tokens	Output Tokens	Reasoning Tokens
gpt-5.3-codex	7.15	59,503,049	248,276	122,926
gpt-5.2-codex	4.96	24,020,960	97,928	33,178

Weekly Report — 2026-W06 (2026-02-02 ~ 2026-02-08)#

Weekly Overview#

Project Progress#

MIHD / STAIG Fusion (1 day active) — 🔄 active#

Benchmark Tool (gadget) (1 day active) — 🔄 active#

English Study (TOEFL) (1 day active) — 🔄 active#

Key Tasks#

Issues & Solutions#

1. MIHD staig_fusion ARI (0.21/0.4849) far below original STAIG (0.562), root cause unknown [MIHD / STAIG Fusion] (2026-02-06)#

2. Plotly bar chart rendering error: high scores display as short bars, visual logic inverted [Benchmark Tool] (2026-02-06)#

3. Strict STAIG mode silently overrides the visual encoder to UNI; user assumed UNI2 was in use — opaque behavior [MIHD / STAIG Fusion] (2026-02-06)#

4. create_trend_chart AttributeError: method was commented out but still called in generate_html [Benchmark Tool] (2026-02-06)#

Learnings#

Architecture#

Debugging#

Domain Knowledge#

AI Usage Notes#

Next Week Outlook#

Token Usage Statistics#

Daily Cost Trend#

Claude Code#

Model Usage Distribution#

Codex#

Model Usage Distribution#

Weekly Report — 2026-W06 (2026-02-02 ~ 2026-02-08)

Weekly Overview

Project Progress

MIHD / STAIG Fusion (1 day active) — 🔄 active

Benchmark Tool (gadget) (1 day active) — 🔄 active

English Study (TOEFL) (1 day active) — 🔄 active

Key Tasks

Issues & Solutions

1. MIHD staig_fusion ARI (0.21/0.4849) far below original STAIG (0.562), root cause unknown [MIHD / STAIG Fusion] (2026-02-06)

2. Plotly bar chart rendering error: high scores display as short bars, visual logic inverted [Benchmark Tool] (2026-02-06)

3. Strict STAIG mode silently overrides the visual encoder to UNI; user assumed UNI2 was in use — opaque behavior [MIHD / STAIG Fusion] (2026-02-06)

4. `create_trend_chart` AttributeError: method was commented out but still called in `generate_html` [Benchmark Tool] (2026-02-06)

Learnings

Architecture

Debugging

Domain Knowledge

AI Usage Notes

Next Week Outlook

Token Usage Statistics

Daily Cost Trend

Claude Code

Model Usage Distribution

Codex

Model Usage Distribution