From ecfcf4288854788485c1d65a2f0e9044e0cddb65 Mon Sep 17 00:00:00 2001 From: choisunmi00 <81906078+choisunmi00@users.noreply.github.com> Date: Mon, 9 Sep 2024 14:42:29 +0900 Subject: [PATCH 01/62] Update _config.yml --- _config.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/_config.yml b/_config.yml index af7d57221b02..4f9797c29bbb 100644 --- a/_config.yml +++ b/_config.yml @@ -12,17 +12,17 @@ # theme : "minimal-mistakes-jekyll" # remote_theme : "mmistakes/minimal-mistakes" -minimal_mistakes_skin : "default" # "air", "aqua", "contrast", "dark", "dirt", "neon", "mint", "plum", "sunrise" +minimal_mistakes_skin : "aqua" # "default", "air", "aqua", "contrast", "dark", "dirt", "neon", "mint", "plum", "sunrise" # Site Settings -locale : "en-US" +locale : "ko" rtl : # true, false (default) # turns direction of the page into right to left for RTL languages title : "Site Title" title_separator : "-" subtitle : # site tagline that appears below site title in masthead -name : "Your Name" +name : "Choi Sunmi" description : "An amazing website." -url : # the base hostname & protocol for your site e.g. "https://mmistakes.github.io" +url : "https://choisunmi00.github.io" baseurl : # the subpath of your site, e.g. "/blog" repository : # GitHub username/repo-name e.g. "mmistakes/minimal-mistakes" teaser : # path of fallback teaser image, e.g. "/assets/images/500x300.png" From 87594a85153a4c05315b23586085419bb1fb2fe1 Mon Sep 17 00:00:00 2001 From: choisunmi00 <81906078+choisunmi00@users.noreply.github.com> Date: Mon, 9 Sep 2024 14:50:46 +0900 Subject: [PATCH 02/62] Update _config.yml --- _config.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/_config.yml b/_config.yml index 4f9797c29bbb..835c7e2126c7 100644 --- a/_config.yml +++ b/_config.yml @@ -12,7 +12,7 @@ # theme : "minimal-mistakes-jekyll" # remote_theme : "mmistakes/minimal-mistakes" -minimal_mistakes_skin : "aqua" # "default", "air", "aqua", "contrast", "dark", "dirt", "neon", "mint", "plum", "sunrise" +minimal_mistakes_skin : "air" # "default", "air", "aqua", "contrast", "dark", "dirt", "neon", "mint", "plum", "sunrise" # Site Settings locale : "ko" From d8c2f95326685dec497b7f51ac8516421bfdfb6f Mon Sep 17 00:00:00 2001 From: choisunmi00 <81906078+choisunmi00@users.noreply.github.com> Date: Mon, 9 Sep 2024 14:53:36 +0900 Subject: [PATCH 03/62] Update _config.yml --- _config.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/_config.yml b/_config.yml index 835c7e2126c7..064b1fbe92c1 100644 --- a/_config.yml +++ b/_config.yml @@ -12,7 +12,7 @@ # theme : "minimal-mistakes-jekyll" # remote_theme : "mmistakes/minimal-mistakes" -minimal_mistakes_skin : "air" # "default", "air", "aqua", "contrast", "dark", "dirt", "neon", "mint", "plum", "sunrise" +minimal_mistakes_skin : "contrast" # "default", "air", "aqua", "contrast", "dark", "dirt", "neon", "mint", "plum", "sunrise" # Site Settings locale : "ko" From 2d1441790ed4675ce9972de65d48da0e781d89cc Mon Sep 17 00:00:00 2001 From: choisunmi00 <81906078+choisunmi00@users.noreply.github.com> Date: Mon, 9 Sep 2024 14:59:24 +0900 Subject: [PATCH 04/62] Update _config.yml --- _config.yml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/_config.yml b/_config.yml index 064b1fbe92c1..77033fdd8893 100644 --- a/_config.yml +++ b/_config.yml @@ -17,8 +17,8 @@ minimal_mistakes_skin : "contrast" # "default", "air", "aqua", "contrast", "d # Site Settings locale : "ko" rtl : # true, false (default) # turns direction of the page into right to left for RTL languages -title : "Site Title" -title_separator : "-" +title : "Blog" +title_separator : "*" subtitle : # site tagline that appears below site title in masthead name : "Choi Sunmi" description : "An amazing website." @@ -113,11 +113,11 @@ analytics: # Site Author author: - name : "Your Name" + name : "Choi Sunmi" avatar : # path of avatar image, e.g. "/assets/images/bio-photo.jpg" - bio : "I am an **amazing** person." - location : "Somewhere" - email : + bio : #"I am an **amazing** person." + location : # "Somewhere" + email : "ebebeb@gmail.com" links: - label: "Email" icon: "fas fa-fw fa-envelope-square" From 6cc14c90b14eb152ca3a39cc0a816cf0ab093392 Mon Sep 17 00:00:00 2001 From: choisunmi00 <81906078+choisunmi00@users.noreply.github.com> Date: Wed, 20 Nov 2024 17:08:01 +0900 Subject: [PATCH 05/62] Update _config.yml --- _config.yml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/_config.yml b/_config.yml index 77033fdd8893..aa9ec87c99f2 100644 --- a/_config.yml +++ b/_config.yml @@ -20,9 +20,9 @@ rtl : # true, false (default) # turns direction of the page title : "Blog" title_separator : "*" subtitle : # site tagline that appears below site title in masthead -name : "Choi Sunmi" -description : "An amazing website." -url : "https://choisunmi00.github.io" +name : # "Choi Sunmi" +description : # "An amazing website." +url : # "https://choisunmi00.github.io" baseurl : # the subpath of your site, e.g. "/blog" repository : # GitHub username/repo-name e.g. "mmistakes/minimal-mistakes" teaser : # path of fallback teaser image, e.g. "/assets/images/500x300.png" @@ -113,11 +113,11 @@ analytics: # Site Author author: - name : "Choi Sunmi" + name : # "Choi Sunmi" avatar : # path of avatar image, e.g. "/assets/images/bio-photo.jpg" bio : #"I am an **amazing** person." location : # "Somewhere" - email : "ebebeb@gmail.com" + email : # "ebebeb@gmail.com" links: - label: "Email" icon: "fas fa-fw fa-envelope-square" From 50d87ac4914876e5fd07ad2e62ce104a843d058f Mon Sep 17 00:00:00 2001 From: choisunmi00 <81906078+choisunmi00@users.noreply.github.com> Date: Wed, 20 Nov 2024 17:13:06 +0900 Subject: [PATCH 06/62] Create reguloGPT.md --- _posts/reguloGPT.md | 214 ++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 214 insertions(+) create mode 100644 _posts/reguloGPT.md diff --git a/_posts/reguloGPT.md b/_posts/reguloGPT.md new file mode 100644 index 000000000000..b11a79785b3c --- /dev/null +++ b/_posts/reguloGPT.md @@ -0,0 +1,214 @@ +--- +layout: single +title: reguloGPT +--- + +# 논문 리뷰: reguloGPT +{: .no_toc } +[reguloGPT: Harnessing GPT for Knowledge Graph Construction of Molecular Regulatory Pathways ](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10836076/) + +## Table of contents +{: .no_toc .text-delta } + +1. TOC +{:toc} + +--- +## Background + +- MRP: Molecualr Regulartory Pathways(분자 조절 경로). +- KG: Knowledge Graph(지식 그래프). 개체, 사건 또는 개념과 같은 실체에 대한 상호 연결된 설명 모음 +- end-to-end learning: 입력에서 출력까지 파이프라인 네트워크 없이 신경망으로 한 번에 처리. 양끝단 상에서 라벨링된 데이터가 많을 때 잘 동작하는 경향이 있다. +- m6A(N6-methyladenosine): mRNA(단백질 설계도)에 부여하는 화학적 변형. 유전자 발현을 조절하기 위한 기작. +- ICL: in-context learning. +- outdegree: 방향성 그래프에서 node로부터 시작하는 고유한 edge. +{: .fs-3 } + +## 0. Abstract + +- Motivation: MRP에 대한 KG 구축이 현재로선 미미하다. + +- Results: reguloGPT의 문헌에서 생물학적 지식 추출 가능성 + reguloGPT 통한 예측 -> m6A-KG 구축 -> m6A 조절 메커니즘 밝힘. + 컨텍스트 인식 관계형 그래프 도입 / m6A 제목 및 벤치마크 데이터 세트 제작 + G-Eval 체계: 성능 평가 위해 GPT-4를 활용. 기존 주석 기반 평가와 일치. + +- Availability and implementation: + reguloGPT의 소스 코드, m6A 관련 제목 및 벤치마크 데이터 세트, m6A-KG + https://github.com/Huang-AI4Medicine-Lab/reguloGPT + +- Key words: MRP, KG, GPT, In Context Learning, m6A mRNA Methylation + +## 1. Introduction + +- 왜 필요한가 + MRP: 생물의학 연구 핵심. + KG: MRP를 위한 도구. KG는 복잡한 생물학적 지식을 구조화하여 표현한다. + -> 문헌에서 지식 추출 자동화: NLP(Natural Language Processing) 이용 + +- 현재는 어떤가 + 현재로서는 NLP를 통해 복잡한 MRP를 매핑하기에는 부적절하다. + + ![Fig. 1.](https://www.ncbi.nlm.nih.gov/pmc/articles/instance/10836076/bin/nihpp-2024.01.27.577521v1-f0001.jpg) + METTLL3가 위암의 진행을 조절하는 메커니즘을 전체적으로 설명 + MRP를 위해 이러한 그래프를 얻기 위해서는 기존 NLP, 컨텍스트 식별, NER(Named Entity Recignition), N항 RE(N-ary Relationship Extraction) 필요. + + 여러 시스템이 있지만 N항 RE는 생물의학 분야에서 충분히 탐구되지 못했다. + +- 이 논문에서는 + 주어진 문장에서 m6A methylation의 컨텍스트별 MRP를 위해 컨텍스트 인식 관계형 그래프의 end-to-end 구성에서 GPT-4 기능을 탐구한다. + - 논문의 기여 + 1. end-to-end joint NER, N-ary 위한 reguloGPT, GPT-4 구동 ICL prompt 제안. + reguloGPT에 대한 기준선인 few-shot 및 CoT 프롬프트 설계 + 2. 컨텍스트 인식 관계형 그래프 표현 도입 + 3. 벤치마크 데이터 세트 구축 + 4. 프롬프트의 성능 평가 + 5. G-Eval 체계 도입: 프롬프트를 활용하여 추출된 그래프를 평가 + 6. m6A-KG 구축: 2013-2023년 PubMed에서 수집한 문헌 제목에 reguloGPT 적용 + +## 2. Methods + +- reguloGPT: end-to-end 추출 위해 GPT-4 기반 ICL 활용. 6개의 모듈을 포함한다. + + ![Fig. 2.](https://www.ncbi.nlm.nih.gov/pmc/articles/instance/10836076/bin/nihpp-2024.01.27.577521v1-f0002.jpg) + PubMed에서 컨텍스트 인식 KG를 구축하기 쉽도록 reguloGPT를 설계 + +### A. reguloGPT에 대한 ICL 프롬프트 + ![Fig. 3.](https://www.ncbi.nlm.nih.gov/pmc/articles/instance/10836076/bin/nihpp-2024.01.27.577521v1-f0003.jpg) + +1) 기준 프롬프트 (A): 지침, 정의 및 출력 형식을 포함한 기준 프롬프트 + 1 - 작업 목표 제시 + 2 - node, edge, context, inferred edge 를 포함하여 컨텍스트 인식 관계형 그래프의 구성요소 정의 + 3 - 출력 형식. + +2) Few-shot 프롬프트 (B): 대상 문장과 출력(context, nodes, direct edges, inferred edges) + 1 - 지시, 2 - 정의, 3 - 데모, 4 - 출력의 형식 + 기준 프롬프트와 달리 정의 뒤에 추가 데모 섹션이 포함되어 있음. + +3) Chain-of-Thoughts(CoT) 프롬프트 (C): + LLM에게 복잡하고 논리적인 응답 장려. 중간 추론 단계를 사고의 사슬로 추가. + +### B. 벤치마크 및 지식 그래프 생성을 위한 데이터 세트 구축 + +- m6A 연구와 관련된 문헌의 제목 추출: PubMed, PtbTator 검색 및 사용. + 완전한 문장, 여러 유전자에 대한 참조를 포함하는 제목 -> m6A와 유전자/단백질 사이의 경로 매핑 + +1. 벤치마크 데이터세트에 대한 주석 방법 + 컴퓨터 과학과 생물의학 분야 전문가 5명을 주석자로 삼고 400개의 제목에 주석을 닮. 세 단계를 거침. + a. 연습 주석 단계 + b. 그룹 주석 단계 + c. 심사 단계 + +2. 주석 지침 + 연습 주석 단계에서의 기본 지침 요약 + +### C. nodes, predicates, context의 정규화 + +- node, context 정규화: Gilda, Gene Ontoloy knowledgebase. +- predicates 정규화: Ontological predicate definition. +- 관계 정규화: GPT-4 적용 및 수동 평가. + +### D. m6A-KG 구축 + +- 400개 제목의 벤치마크 데이터 세트 외에 PubTator에서 MRP에 관한 제목 968개 추가 추출. + 정규화된 관계 그래프를 벤치마크 데이터 세트의 그래프와 통합. + 포괄적인 KG인 m6A-KG 구축. + +- Neo4j를 이용한 KG 시각화 및 조작 + +### E. 평가 및 지표 기준 + +1) 벤치마크 데이터 세트 평가 + Precision 및 F1 score 지표 + + 예측된 node 및 edge를 평가하는 기준 + a. True positive: GPT-4의 예측 node가 벤치마크 주석과 완전히 일치할 경우 + b. False positive: node나 edge가 잘못 추출될 경우 혹은 node는 일치하지만 서술어가 올바르지 않거나 추출되지 않았을 경우 + c. False negative: 모든 node와 edge에 대한 예측이 일치하지 않았을 경우 + + +3) G-Eval 체계 + 수동 주석 작업을 자동화하기 위해 LLM 사용. + 프레임워크 GPT-4-evaluation 제안. + + ![Fig. 4.](https://www.ncbi.nlm.nih.gov/pmc/articles/instance/10836076/bin/nihpp-2024.01.27.577521v1-f0004.jpg) + 평가를 위한 G-Eval 프롬프트 / A: 컨텍스트 평가, B: 그래프 평가 + +## 3. Results + +### A. 벤치마크 데이터 세트의 주석 +- m6A 연구 논문 400개의 제목에 대한 컨텍스트 인식 그래프에 주석을 닮. +- 데이터 세트의 정규화된 컨텍스트에서 24개의 다른 TCGA 암 유형을 추출할 수 있었음. + +### B. 우수한 성능의 reguloGPT + +- 평가 위해 REACH, EIDOS 알고리즘 선택 + (두 알고리즘 모두 컨텍스트를 추출하도록 설계된 것은 아님) + + ![Table 1.](https://www.biorxiv.org/content/biorxiv/early/2024/01/30/2024.01.27.577521/T1.medium.gif) + 각 프롬프트의 성능을 알고리즘과 비교하여 평가 (컨텍스트 평가는 제외) / CoT 프롬프트가 가장 효과적 + +- 예시1 + "m6A 메틸트랜스퍼라제 METTL3는 LEF1의 m6A 수준을 조절하여 골육종 진행을 촉진한다" (PMID: 31253399) + 컨텍스트: 골육종 + REACH: (METTL3, STIMULATES, LEF1 수준) + EIDOS: (m6A 메틸트랜스퍼라제 METTL3, STIMULATES, 골육종 진행) + reguloGPT: 골육종 및 올바른 3개의 직접 edge 및 1개의 간접 3edge 관계 추출 성공 + +- 예시2 + "elF3i는 PHGDH 번역 증강을 통해 대장암 세포 생존을 촉진한다" (PMID: 37611825) + reguloGPT: 컨텍스트는 대장암 세포, 세 개의 삼중항 식별. (PHGDH, STIMULATES, 생존) 까지. + REACH: 한 개의 삼중항 (elF3i, STIMULATES, 세포 생존) + EIDOS: 두 개의 삼중항(elF3i, AUGMENTS, PHGDG 번역), (elF3i, STIMULATES, 대장암 세포 생존) + +- few-show prompt의 조건 무시 문제 + "Suppression of m6A reader Ythdf2 promotes hematopoietic stem cell expansion" (PMID: 30065315) + "Silencing METTL3 inhibits the proliferation and invasion of osteosarcoma by regulating ATAD2" (PMID: 32044716) + +### C. G-Eval 평가는 수동 평가와 일치 + +- G-Eval 평가의 score 범위는 1~5. 사람 주석 평가와의 유사성. + + ![Table 2.](https://www.biorxiv.org/content/biorxiv/early/2024/01/30/2024.01.27.577521/T2.medium.gif) + CoT 프롬프트가 가장 우수. + +## 4. m6A-KG, A context-aware KG of m6A regulatory fuctions + +### A. reguloGPT를 이용한 m6A-KG 구축 + +- 포괄적인 m6A-KG에서 가장 연결 차수가 높은 m6(827)는 그래프의 중심이 된다. + 차수별 상위 node에는 METTL3(436), METTL14(122)와 같은 주요 m6A writers, ALKBH5(166) 및 FTO(222)와 같은 erasers, YTHDF2(127) 및 YTHDF1(109)과 같은 readers가 포함된다. + 이는 m6A의 조절 기능에서 중요한 역할을 강조한다. + 세포 증식과 신생물 전이를 나타내는 node도 높은 수준을 보이며, m6A가 이러한 종양 관련 표현형에 상당한 영향을 미친다는 것을 나타낸다. + +### B. m6-KG의 구조는 분자 조절 경로의 구조를 반영 + +- MRP의 아키텍처를 따르는지 알아보기 위한 node 분류 그룹: + m6A, WERs, GO/pathway, genes/proteins, 기타(H, M, L) + +- 다양한 범주 node의 outdegree-rate + + ![Fig. 5.](https://www.ncbi.nlm.nih.gov/pmc/articles/instance/10836076/bin/nihpp-2024.01.27.577521v1-f0005.jpg) + m6A와 WERs(Writers, Erasers, Readers)는 핵심 조절자. + GO/pathwat node는 하류 조절자. + gene/protein node는 그 둘을 잇는 중간자. + + other node의 경우 + other(L)은 질병 표현형 또는 결과 정의. + other(H)는 화학적 자극 또는 환경적 자극. + + => MRP의 특징 + +### C. m6A-KG는 다양한 암 유형에서 m6 기능의 독특한 메커니즘을 보여준다 + +- m6A 조절 기능에 대해 알 수 있다. + m6A 조절자, 질병 표현형, 종양 전이 관여, 종양 억제 유전자의 암 의존적 조절 등 조절 메커니즘을 KG를 통해 해석할 수 있다. + +## 5. Conclusion + +- reguloGPT: MRP 영역에서 KG의 end-to-end 구축을 위한 GPT-4의 새로운 응용 프로그램. +- ICL 프롬프팅 개발. +- 벤치마크 데이터베이스에 대한 reguloGPT의 효능 평가, G-Eval 평가와 사람 주석의 유사성. +- m6A-KG 구축: MRP 구조 반영. 컨텍스트와 PubMed ID를 통합하는 고유한 컨텍스트 인식 edge가 특징. + 컨텍스트별 조절 이해, 데이터의 추적성과 검증 개선. +- 향후 연구: edge와 컨텍스트에 대한 개선된 정규화 체계, 체계적인 G-Eval 평가 및 관계 추출 탐구. From 0564e160056371063c87ec99d1bee58871a7af01 Mon Sep 17 00:00:00 2001 From: choisunmi00 <81906078+choisunmi00@users.noreply.github.com> Date: Wed, 20 Nov 2024 17:15:19 +0900 Subject: [PATCH 07/62] Rename reguloGPT.md to 2024-11-20-reguloGPT.md --- _posts/{reguloGPT.md => 2024-11-20-reguloGPT.md} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename _posts/{reguloGPT.md => 2024-11-20-reguloGPT.md} (100%) diff --git a/_posts/reguloGPT.md b/_posts/2024-11-20-reguloGPT.md similarity index 100% rename from _posts/reguloGPT.md rename to _posts/2024-11-20-reguloGPT.md From 34be11fb71dcb33e524c933eb9b2b319c3f9c9ea Mon Sep 17 00:00:00 2001 From: choisunmi00 Date: Wed, 20 Nov 2024 17:27:06 +0900 Subject: [PATCH 08/62] Update _config.yml --- _config.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/_config.yml b/_config.yml index aa9ec87c99f2..7469c03ab34f 100644 --- a/_config.yml +++ b/_config.yml @@ -15,14 +15,14 @@ minimal_mistakes_skin : "contrast" # "default", "air", "aqua", "contrast", "dark", "dirt", "neon", "mint", "plum", "sunrise" # Site Settings -locale : "ko" +locale : "ko-KR" rtl : # true, false (default) # turns direction of the page into right to left for RTL languages title : "Blog" -title_separator : "*" +title_separator : "|" subtitle : # site tagline that appears below site title in masthead -name : # "Choi Sunmi" +name : "Choi Sunmi" description : # "An amazing website." -url : # "https://choisunmi00.github.io" +url : "https://choisunmi00.github.io" baseurl : # the subpath of your site, e.g. "/blog" repository : # GitHub username/repo-name e.g. "mmistakes/minimal-mistakes" teaser : # path of fallback teaser image, e.g. "/assets/images/500x300.png" From defb0d1a2d8eeb4392db56d5b30aaa719df239c3 Mon Sep 17 00:00:00 2001 From: choisunmi00 Date: Wed, 20 Nov 2024 18:00:37 +0900 Subject: [PATCH 09/62] Update _config.yml --- _config.yml | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/_config.yml b/_config.yml index 7469c03ab34f..4149c9fa8f52 100644 --- a/_config.yml +++ b/_config.yml @@ -28,7 +28,7 @@ repository : # GitHub username/repo-name e.g. "mmistakes/minimal-m teaser : # path of fallback teaser image, e.g. "/assets/images/500x300.png" logo : # path of logo image to display in the masthead, e.g. "/assets/images/88x88.png" masthead_title : # overrides the website title displayed in the masthead, use " " for no title -breadcrumbs : # true, false (default) +breadcrumbs : true # true, false (default) words_per_minute : 200 enable_copy_code_button : # true, false (default) copyright : # "copyright" name, defaults to site.title @@ -323,3 +323,6 @@ defaults: comments: # true share: true related: true + show_date: true + +date_format: "%Y-%m-%d" From 014cf15efecbaa6d69f08dec7cb8555d1e88d45e Mon Sep 17 00:00:00 2001 From: choisunmi00 Date: Wed, 20 Nov 2024 18:21:22 +0900 Subject: [PATCH 10/62] modify --- _config.yml | 34 +++++++++++++++++----------------- _data/navigation.yml | 6 ++++-- _pages/category-archive.md | 7 +++++++ _posts/2024-11-20-reguloGPT.md | 1 + 4 files changed, 29 insertions(+), 19 deletions(-) create mode 100644 _pages/category-archive.md diff --git a/_config.yml b/_config.yml index 4149c9fa8f52..f6cc334bd094 100644 --- a/_config.yml +++ b/_config.yml @@ -115,7 +115,7 @@ analytics: author: name : # "Choi Sunmi" avatar : # path of avatar image, e.g. "/assets/images/bio-photo.jpg" - bio : #"I am an **amazing** person." + bio : # "I am an **amazing** person." location : # "Somewhere" email : # "ebebeb@gmail.com" links: @@ -141,24 +141,24 @@ author: # Site Footer footer: links: - - label: "Twitter" - icon: "fab fa-fw fa-twitter-square" - # url: - - label: "Facebook" - icon: "fab fa-fw fa-facebook-square" - # url: - - label: "GitHub" - icon: "fab fa-fw fa-github" - # url: + # - label: "Twitter" + # icon: "fab fa-fw fa-twitter-square" + # # url: + # - label: "Facebook" + # icon: "fab fa-fw fa-facebook-square" + # # url: + # - label: "GitHub" + # icon: "fab fa-fw fa-github" + # # url: - label: "GitLab" icon: "fab fa-fw fa-gitlab" - # url: - - label: "Bitbucket" - icon: "fab fa-fw fa-bitbucket" - # url: - - label: "Instagram" - icon: "fab fa-fw fa-instagram" - # url: + url: "https://github.com/choisunmi00" + # - label: "Bitbucket" + # icon: "fab fa-fw fa-bitbucket" + # # url: + # - label: "Instagram" + # icon: "fab fa-fw fa-instagram" + # # url: # Reading Files diff --git a/_data/navigation.yml b/_data/navigation.yml index 6f30866f3bed..8df451e1393e 100644 --- a/_data/navigation.yml +++ b/_data/navigation.yml @@ -1,7 +1,9 @@ # main links main: - - title: "Quick-Start Guide" - url: https://mmistakes.github.io/minimal-mistakes/docs/quick-start-guide/ + - title: "Categoty" + url: /categories/ + # - title: "Quick-Start Guide" + # url: https://mmistakes.github.io/minimal-mistakes/docs/quick-start-guide/ # - title: "About" # url: https://mmistakes.github.io/minimal-mistakes/about/ # - title: "Sample Posts" diff --git a/_pages/category-archive.md b/_pages/category-archive.md new file mode 100644 index 000000000000..9b0c679a9685 --- /dev/null +++ b/_pages/category-archive.md @@ -0,0 +1,7 @@ +--- +title: "Category" +layout: categories +permalink: /categories/ +athor_profile: true +sidebar_main: true +--- \ No newline at end of file diff --git a/_posts/2024-11-20-reguloGPT.md b/_posts/2024-11-20-reguloGPT.md index b11a79785b3c..93751b8b74de 100644 --- a/_posts/2024-11-20-reguloGPT.md +++ b/_posts/2024-11-20-reguloGPT.md @@ -1,6 +1,7 @@ --- layout: single title: reguloGPT +categories: paper --- # 논문 리뷰: reguloGPT From 4629043435db327f6844007c7389014866675b0a Mon Sep 17 00:00:00 2001 From: choisunmi00 Date: Wed, 20 Nov 2024 18:32:17 +0900 Subject: [PATCH 11/62] modify --- _config.yml | 30 +++++++++++++++--------------- _pages/tag-archive.md | 7 +++++++ _posts/2024-11-20-reguloGPT.md | 7 ++++--- 3 files changed, 26 insertions(+), 18 deletions(-) create mode 100644 _pages/tag-archive.md diff --git a/_config.yml b/_config.yml index f6cc334bd094..a88f59e3c46a 100644 --- a/_config.yml +++ b/_config.yml @@ -147,12 +147,12 @@ footer: # - label: "Facebook" # icon: "fab fa-fw fa-facebook-square" # # url: - # - label: "GitHub" - # icon: "fab fa-fw fa-github" - # # url: - - label: "GitLab" - icon: "fab fa-fw fa-gitlab" + - label: "GitHub" + icon: "fab fa-fw fa-github" url: "https://github.com/choisunmi00" + # - label: "GitLab" + # icon: "fab fa-fw fa-gitlab" + # url: # - label: "Bitbucket" # icon: "fab fa-fw fa-bitbucket" # # url: @@ -290,16 +290,16 @@ tag_archive: type: liquid path: /tags/ # https://github.com/jekyll/jekyll-archives -# jekyll-archives: -# enabled: -# - categories -# - tags -# layouts: -# category: archive-taxonomy -# tag: archive-taxonomy -# permalinks: -# category: /categories/:name/ -# tag: /tags/:name/ +jekyll-archives: + enabled: + - categories + - tags + layouts: + category: archive-taxonomy + tag: archive-taxonomy + permalinks: + category: /categories/:name/ + tag: /tags/:name/ # HTML Compression diff --git a/_pages/tag-archive.md b/_pages/tag-archive.md new file mode 100644 index 000000000000..eaf9e8856f61 --- /dev/null +++ b/_pages/tag-archive.md @@ -0,0 +1,7 @@ +--- +title: "Tag" +layout: tags +permalink: /tags/ +athor_profile: true +sidebar_main: true +--- \ No newline at end of file diff --git a/_posts/2024-11-20-reguloGPT.md b/_posts/2024-11-20-reguloGPT.md index 93751b8b74de..38f355bc1c21 100644 --- a/_posts/2024-11-20-reguloGPT.md +++ b/_posts/2024-11-20-reguloGPT.md @@ -2,17 +2,18 @@ layout: single title: reguloGPT categories: paper +toc: true --- # 논문 리뷰: reguloGPT -{: .no_toc } + [reguloGPT: Harnessing GPT for Knowledge Graph Construction of Molecular Regulatory Pathways ](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10836076/) -## Table of contents + --- ## Background From 6a139ca247ed81da3d7e7919669b7b6391e645ec Mon Sep 17 00:00:00 2001 From: choisunmi00 Date: Wed, 20 Nov 2024 18:50:22 +0900 Subject: [PATCH 12/62] modify font --- _pages/404.md | 8 ++++++++ _posts/2024-11-20-reguloGPT.md | 1 + _sass/minimal-mistakes.scss | 3 +++ _sass/minimal-mistakes/_variables.scss | 2 +- 4 files changed, 13 insertions(+), 1 deletion(-) create mode 100644 _pages/404.md diff --git a/_pages/404.md b/_pages/404.md new file mode 100644 index 000000000000..b3025a6053b5 --- /dev/null +++ b/_pages/404.md @@ -0,0 +1,8 @@ +--- +title: "Page Not Found" +excerpt: "Page not found. Your pixels are in another canvas." +sitemap: false +permalink: /404.html +--- + +Sorry, but the page you were trying to view does not exist. diff --git a/_posts/2024-11-20-reguloGPT.md b/_posts/2024-11-20-reguloGPT.md index 38f355bc1c21..8348823cc0f4 100644 --- a/_posts/2024-11-20-reguloGPT.md +++ b/_posts/2024-11-20-reguloGPT.md @@ -3,6 +3,7 @@ layout: single title: reguloGPT categories: paper toc: true +toc_depth: 2 --- # 논문 리뷰: reguloGPT diff --git a/_sass/minimal-mistakes.scss b/_sass/minimal-mistakes.scss index ba9d13d5df2f..5be40467d81b 100644 --- a/_sass/minimal-mistakes.scss +++ b/_sass/minimal-mistakes.scss @@ -35,3 +35,6 @@ @import "minimal-mistakes/archive"; @import "minimal-mistakes/sidebar"; @import "minimal-mistakes/print"; + +/* google fonts */ +@import url('https://fonts.googleapis.com/css2?family=Nanum+Myeongjo&display=swap'); \ No newline at end of file diff --git a/_sass/minimal-mistakes/_variables.scss b/_sass/minimal-mistakes/_variables.scss index 81a3acf7b88f..d16f2e1b2aae 100644 --- a/_sass/minimal-mistakes/_variables.scss +++ b/_sass/minimal-mistakes/_variables.scss @@ -14,7 +14,7 @@ $indent-var: 1.3em !default; /* system typefaces */ $serif: Georgia, Times, serif !default; -$sans-serif: -apple-system, BlinkMacSystemFont, "Roboto", "Segoe UI", +$sans-serif: -apple-system, BlinkMacSystemFont, "Nanum Myeongjo", "Roboto", "Segoe UI", "Helvetica Neue", "Lucida Grande", Arial, sans-serif !default; $monospace: Monaco, Consolas, "Lucida Console", monospace !default; From 58782f72af288ed4204a59405d519857c7d02d9a Mon Sep 17 00:00:00 2001 From: choisunmi00 Date: Thu, 21 Nov 2024 10:18:33 +0900 Subject: [PATCH 13/62] test commit --- _posts/2024-11-20-reguloGPT.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/_posts/2024-11-20-reguloGPT.md b/_posts/2024-11-20-reguloGPT.md index 8348823cc0f4..3bbd816e7999 100644 --- a/_posts/2024-11-20-reguloGPT.md +++ b/_posts/2024-11-20-reguloGPT.md @@ -3,7 +3,7 @@ layout: single title: reguloGPT categories: paper toc: true -toc_depth: 2 +toc_depth: 1 --- # 논문 리뷰: reguloGPT From e2f3871fe668e1724d4bab5c52726cc43a3c401d Mon Sep 17 00:00:00 2001 From: choisunmi00 Date: Thu, 21 Nov 2024 11:20:40 +0900 Subject: [PATCH 14/62] change css --- _config.yml | 5 +++++ _posts/2024-11-20-reguloGPT.md | 16 +++++++--------- _sass/minimal-mistakes/_navigation.scss | 2 +- _sass/minimal-mistakes/_page.scss | 4 ++-- _sass/minimal-mistakes/_variables.scss | 2 ++ _sass/minimal-mistakes/skins/_contrast.scss | 4 ++-- 6 files changed, 19 insertions(+), 14 deletions(-) diff --git a/_config.yml b/_config.yml index a88f59e3c46a..801b13ff3fb9 100644 --- a/_config.yml +++ b/_config.yml @@ -324,5 +324,10 @@ defaults: share: true related: true show_date: true + toc: true + toc_sticky: true + toc_icon: "" + toc_label: Contents + toc_depth: 1 date_format: "%Y-%m-%d" diff --git a/_posts/2024-11-20-reguloGPT.md b/_posts/2024-11-20-reguloGPT.md index 3bbd816e7999..af89e77bd6b7 100644 --- a/_posts/2024-11-20-reguloGPT.md +++ b/_posts/2024-11-20-reguloGPT.md @@ -2,8 +2,6 @@ layout: single title: reguloGPT categories: paper -toc: true -toc_depth: 1 --- # 논문 리뷰: reguloGPT @@ -124,18 +122,18 @@ toc_depth: 1 1) 벤치마크 데이터 세트 평가 Precision 및 F1 score 지표 - 예측된 node 및 edge를 평가하는 기준 - a. True positive: GPT-4의 예측 node가 벤치마크 주석과 완전히 일치할 경우 - b. False positive: node나 edge가 잘못 추출될 경우 혹은 node는 일치하지만 서술어가 올바르지 않거나 추출되지 않았을 경우 - c. False negative: 모든 node와 edge에 대한 예측이 일치하지 않았을 경우 + 예측된 node 및 edge를 평가하는 기준 + a. True positive: GPT-4의 예측 node가 벤치마크 주석과 완전히 일치할 경우 + b. False positive: node나 edge가 잘못 추출될 경우 혹은 node는 일치하지만 서술어가 올바르지 않거나 추출되지 않았을 경우 + c. False negative: 모든 node와 edge에 대한 예측이 일치하지 않았을 경우 -3) G-Eval 체계 +3) G-Eval 체계 수동 주석 작업을 자동화하기 위해 LLM 사용. 프레임워크 GPT-4-evaluation 제안. - ![Fig. 4.](https://www.ncbi.nlm.nih.gov/pmc/articles/instance/10836076/bin/nihpp-2024.01.27.577521v1-f0004.jpg) - 평가를 위한 G-Eval 프롬프트 / A: 컨텍스트 평가, B: 그래프 평가 + ![Fig. 4.](https://www.ncbi.nlm.nih.gov/pmc/articles/instance/10836076/bin/nihpp-2024.01.27.577521v1-f0004.jpg) + 평가를 위한 G-Eval 프롬프트 / A: 컨텍스트 평가, B: 그래프 평가 ## 3. Results diff --git a/_sass/minimal-mistakes/_navigation.scss b/_sass/minimal-mistakes/_navigation.scss index 3ba1b66deaa0..ed4edfe41569 100644 --- a/_sass/minimal-mistakes/_navigation.scss +++ b/_sass/minimal-mistakes/_navigation.scss @@ -513,7 +513,7 @@ .nav__title { color: #fff; font-size: $type-size-6; - background: $primary-color; + background: $toc-color; border-start-start-radius: $border-radius; border-start-end-radius: $border-radius; } diff --git a/_sass/minimal-mistakes/_page.scss b/_sass/minimal-mistakes/_page.scss index e33888400eed..9038e5a2cdad 100644 --- a/_sass/minimal-mistakes/_page.scss +++ b/_sass/minimal-mistakes/_page.scss @@ -36,12 +36,12 @@ body { .page { @include breakpoint($large) { float: inline-end; - width: calc(100% - #{$right-sidebar-width-narrow}); + width: calc(100%); padding-inline-end: $right-sidebar-width-narrow; } @include breakpoint($x-large) { - width: calc(100% - #{$right-sidebar-width}); + width: calc(100%); padding-inline-end: $right-sidebar-width; } diff --git a/_sass/minimal-mistakes/_variables.scss b/_sass/minimal-mistakes/_variables.scss index 989d034c8ea1..98dbaf781fca 100644 --- a/_sass/minimal-mistakes/_variables.scss +++ b/_sass/minimal-mistakes/_variables.scss @@ -174,3 +174,5 @@ $navicon-width: 1.5rem !default; $navicon-height: 0.25rem !default; $global-transition: all 0.2s ease-in-out !default; $intro-transition: intro 0.3s both !default; + +$toc-color: #20262e !default; \ No newline at end of file diff --git a/_sass/minimal-mistakes/skins/_contrast.scss b/_sass/minimal-mistakes/skins/_contrast.scss index 38283b8f6fe4..19f8b6b15d50 100644 --- a/_sass/minimal-mistakes/skins/_contrast.scss +++ b/_sass/minimal-mistakes/skins/_contrast.scss @@ -5,10 +5,10 @@ /* Colors */ $text-color: #000 !default; $muted-text-color: $text-color !default; -$primary-color: #ff0000 !default; +$primary-color: #20262e !default; $border-color: mix(#fff, $text-color, 75%) !default; $footer-background-color: #000 !default; -$link-color: #0000ff !default; +$link-color: #6161d9 !default; $masthead-link-color: $text-color !default; $masthead-link-color-hover: $text-color !default; $navicon-link-color-hover: mix(#fff, $text-color, 80%) !default; From 503c9ad0fee1b123ae04c9ed2a8ba425d3dc9903 Mon Sep 17 00:00:00 2001 From: choisunmi00 Date: Thu, 21 Nov 2024 11:59:14 +0900 Subject: [PATCH 15/62] modify css --- _sass/minimal-mistakes/_variables.scss | 4 ++-- _sass/minimal-mistakes/skins/_contrast.scss | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/_sass/minimal-mistakes/_variables.scss b/_sass/minimal-mistakes/_variables.scss index 98dbaf781fca..34931dbc6be9 100644 --- a/_sass/minimal-mistakes/_variables.scss +++ b/_sass/minimal-mistakes/_variables.scss @@ -41,7 +41,7 @@ $type-size-1: 2.441em !default; // ~39.056px $type-size-2: 1.953em !default; // ~31.248px $type-size-3: 1.563em !default; // ~25.008px $type-size-4: 1.25em !default; // ~20px -$type-size-5: 1em !default; // ~16px +$type-size-5: 0.75em !default; // ~16px $type-size-6: 0.75em !default; // ~12px $type-size-7: 0.6875em !default; // ~11px $type-size-8: 0.625em !default; // ~10px @@ -175,4 +175,4 @@ $navicon-height: 0.25rem !default; $global-transition: all 0.2s ease-in-out !default; $intro-transition: intro 0.3s both !default; -$toc-color: #20262e !default; \ No newline at end of file +$toc-color: #4f4f67 !default; \ No newline at end of file diff --git a/_sass/minimal-mistakes/skins/_contrast.scss b/_sass/minimal-mistakes/skins/_contrast.scss index 19f8b6b15d50..3e1cfd3f14a3 100644 --- a/_sass/minimal-mistakes/skins/_contrast.scss +++ b/_sass/minimal-mistakes/skins/_contrast.scss @@ -5,10 +5,10 @@ /* Colors */ $text-color: #000 !default; $muted-text-color: $text-color !default; -$primary-color: #20262e !default; +$primary-color: #4f4f67 !default; $border-color: mix(#fff, $text-color, 75%) !default; $footer-background-color: #000 !default; -$link-color: #6161d9 !default; +$link-color: #a3a3e3 !default; $masthead-link-color: $text-color !default; $masthead-link-color-hover: $text-color !default; $navicon-link-color-hover: mix(#fff, $text-color, 80%) !default; From a6faed1ae831a6a54a0d3c5ecaca76cf070bfcb8 Mon Sep 17 00:00:00 2001 From: choisunmi00 Date: Thu, 21 Nov 2024 12:08:07 +0900 Subject: [PATCH 16/62] change color --- _sass/minimal-mistakes/_variables.scss | 4 ++-- _sass/minimal-mistakes/skins/_contrast.scss | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/_sass/minimal-mistakes/_variables.scss b/_sass/minimal-mistakes/_variables.scss index 34931dbc6be9..1954e523f256 100644 --- a/_sass/minimal-mistakes/_variables.scss +++ b/_sass/minimal-mistakes/_variables.scss @@ -41,7 +41,7 @@ $type-size-1: 2.441em !default; // ~39.056px $type-size-2: 1.953em !default; // ~31.248px $type-size-3: 1.563em !default; // ~25.008px $type-size-4: 1.25em !default; // ~20px -$type-size-5: 0.75em !default; // ~16px +$type-size-5: 1em !default; // ~16px $type-size-6: 0.75em !default; // ~12px $type-size-7: 0.6875em !default; // ~11px $type-size-8: 0.625em !default; // ~10px @@ -175,4 +175,4 @@ $navicon-height: 0.25rem !default; $global-transition: all 0.2s ease-in-out !default; $intro-transition: intro 0.3s both !default; -$toc-color: #4f4f67 !default; \ No newline at end of file +$toc-color: #1d2228 !default; \ No newline at end of file diff --git a/_sass/minimal-mistakes/skins/_contrast.scss b/_sass/minimal-mistakes/skins/_contrast.scss index 3e1cfd3f14a3..128c58b6d489 100644 --- a/_sass/minimal-mistakes/skins/_contrast.scss +++ b/_sass/minimal-mistakes/skins/_contrast.scss @@ -5,10 +5,10 @@ /* Colors */ $text-color: #000 !default; $muted-text-color: $text-color !default; -$primary-color: #4f4f67 !default; +$primary-color: #2a62ad !default; $border-color: mix(#fff, $text-color, 75%) !default; $footer-background-color: #000 !default; -$link-color: #a3a3e3 !default; +$link-color: #2a62ad !default; $masthead-link-color: $text-color !default; $masthead-link-color-hover: $text-color !default; $navicon-link-color-hover: mix(#fff, $text-color, 80%) !default; From 062c3ec06e253118c4dd37a7eaf30455f45c4a88 Mon Sep 17 00:00:00 2001 From: choisunmi00 Date: Thu, 21 Nov 2024 13:58:34 +0900 Subject: [PATCH 17/62] Update _config.yml --- _config.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/_config.yml b/_config.yml index 801b13ff3fb9..30b8ee99b9de 100644 --- a/_config.yml +++ b/_config.yml @@ -326,7 +326,7 @@ defaults: show_date: true toc: true toc_sticky: true - toc_icon: "" + toc_icon: "fa-regular fa-circle" toc_label: Contents toc_depth: 1 From 3a655d5ee55fd68ca3c8b51c78745a219fe864f2 Mon Sep 17 00:00:00 2001 From: choisunmi00 Date: Thu, 21 Nov 2024 14:26:49 +0900 Subject: [PATCH 18/62] modify font --- _config.yml | 4 ++-- _sass/minimal-mistakes/_variables.scss | 2 +- docs/_docs/16-stylesheets.md | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/_config.yml b/_config.yml index 30b8ee99b9de..bdb37d5ad04b 100644 --- a/_config.yml +++ b/_config.yml @@ -326,8 +326,8 @@ defaults: show_date: true toc: true toc_sticky: true - toc_icon: "fa-regular fa-circle" + toc_icon: "fa-solid fa-bars" toc_label: Contents - toc_depth: 1 + toc_h_max: 2 date_format: "%Y-%m-%d" diff --git a/_sass/minimal-mistakes/_variables.scss b/_sass/minimal-mistakes/_variables.scss index 1954e523f256..2dda2a59dd16 100644 --- a/_sass/minimal-mistakes/_variables.scss +++ b/_sass/minimal-mistakes/_variables.scss @@ -41,7 +41,7 @@ $type-size-1: 2.441em !default; // ~39.056px $type-size-2: 1.953em !default; // ~31.248px $type-size-3: 1.563em !default; // ~25.008px $type-size-4: 1.25em !default; // ~20px -$type-size-5: 1em !default; // ~16px +$type-size-5: 0.75em !default; // ~16px (1em) $type-size-6: 0.75em !default; // ~12px $type-size-7: 0.6875em !default; // ~11px $type-size-8: 0.625em !default; // ~10px diff --git a/docs/_docs/16-stylesheets.md b/docs/_docs/16-stylesheets.md index c8acf05146d5..9605fed257e8 100644 --- a/docs/_docs/16-stylesheets.md +++ b/docs/_docs/16-stylesheets.md @@ -139,7 +139,7 @@ $type-size-1 : 2.441em; // ~39.056px $type-size-2 : 1.953em; // ~31.248px $type-size-3 : 1.563em; // ~25.008px $type-size-4 : 1.25em; // ~20px -$type-size-5 : 1em; // ~16px +$type-size-5 : 0.75em; // ~16px (1em) $type-size-6 : 0.75em; // ~12px $type-size-7 : 0.6875em; // ~11px $type-size-8 : 0.625em; // ~10px From 2eb51c1943f4ec05d6e83a346bbd839bf6dfe12e Mon Sep 17 00:00:00 2001 From: choisunmi00 Date: Thu, 21 Nov 2024 14:34:49 +0900 Subject: [PATCH 19/62] modify font --- _config.yml | 2 ++ _sass/minimal-mistakes/_notices.scss | 2 +- _sass/minimal-mistakes/_variables.scss | 2 +- docs/_docs/16-stylesheets.md | 2 +- 4 files changed, 5 insertions(+), 3 deletions(-) diff --git a/_config.yml b/_config.yml index bdb37d5ad04b..d77cf3463675 100644 --- a/_config.yml +++ b/_config.yml @@ -325,9 +325,11 @@ defaults: related: true show_date: true toc: true + toc_depth: 2 toc_sticky: true toc_icon: "fa-solid fa-bars" toc_label: Contents + toc_h_min: 1 toc_h_max: 2 date_format: "%Y-%m-%d" diff --git a/_sass/minimal-mistakes/_notices.scss b/_sass/minimal-mistakes/_notices.scss index 6b4e40128803..08975559830a 100644 --- a/_sass/minimal-mistakes/_notices.scss +++ b/_sass/minimal-mistakes/_notices.scss @@ -30,7 +30,7 @@ @at-root .page__content #{&} h4 { /* using at-root to override .page-content h4 font size*/ margin-bottom: 0; - font-size: 1em; + font-size: 0.75em; } p { diff --git a/_sass/minimal-mistakes/_variables.scss b/_sass/minimal-mistakes/_variables.scss index 2dda2a59dd16..1954e523f256 100644 --- a/_sass/minimal-mistakes/_variables.scss +++ b/_sass/minimal-mistakes/_variables.scss @@ -41,7 +41,7 @@ $type-size-1: 2.441em !default; // ~39.056px $type-size-2: 1.953em !default; // ~31.248px $type-size-3: 1.563em !default; // ~25.008px $type-size-4: 1.25em !default; // ~20px -$type-size-5: 0.75em !default; // ~16px (1em) +$type-size-5: 1em !default; // ~16px $type-size-6: 0.75em !default; // ~12px $type-size-7: 0.6875em !default; // ~11px $type-size-8: 0.625em !default; // ~10px diff --git a/docs/_docs/16-stylesheets.md b/docs/_docs/16-stylesheets.md index 9605fed257e8..c8acf05146d5 100644 --- a/docs/_docs/16-stylesheets.md +++ b/docs/_docs/16-stylesheets.md @@ -139,7 +139,7 @@ $type-size-1 : 2.441em; // ~39.056px $type-size-2 : 1.953em; // ~31.248px $type-size-3 : 1.563em; // ~25.008px $type-size-4 : 1.25em; // ~20px -$type-size-5 : 0.75em; // ~16px (1em) +$type-size-5 : 1em; // ~16px $type-size-6 : 0.75em; // ~12px $type-size-7 : 0.6875em; // ~11px $type-size-8 : 0.625em; // ~10px From 2afbd6535f019da41b61d36ffa64f34a6b79af06 Mon Sep 17 00:00:00 2001 From: choisunmi00 Date: Thu, 21 Nov 2024 14:50:43 +0900 Subject: [PATCH 20/62] modify _page.scss --- _config.yml | 3 --- _includes/toc.html | 2 +- _sass/minimal-mistakes/_notices.scss | 2 +- _sass/minimal-mistakes/_page.scss | 2 +- assets/css/main.scss | 8 ++++---- 5 files changed, 7 insertions(+), 10 deletions(-) diff --git a/_config.yml b/_config.yml index d77cf3463675..8d27db0f41ee 100644 --- a/_config.yml +++ b/_config.yml @@ -325,11 +325,8 @@ defaults: related: true show_date: true toc: true - toc_depth: 2 toc_sticky: true toc_icon: "fa-solid fa-bars" toc_label: Contents - toc_h_min: 1 - toc_h_max: 2 date_format: "%Y-%m-%d" diff --git a/_includes/toc.html b/_includes/toc.html index bc90d08a994b..66af9bfbaff9 100644 --- a/_includes/toc.html +++ b/_includes/toc.html @@ -74,7 +74,7 @@ {% assign baseURL = include.base_url | default: include.baseurl | default: '' %} {% assign skipNoIDs = include.skip_no_ids | default: include.skipNoIDs | default: false %} {% assign minHeader = include.h_min | default: 1 %} - {% assign maxHeader = include.h_max | default: 6 %} + {% assign maxHeader = include.h_max | default: 2 %} {% assign nodes = include.html | strip | split: ' Date: Thu, 21 Nov 2024 14:55:10 +0900 Subject: [PATCH 21/62] Update main.scss --- assets/css/main.scss | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/assets/css/main.scss b/assets/css/main.scss index 8fcee37b3172..1f0ead318516 100644 --- a/assets/css/main.scss +++ b/assets/css/main.scss @@ -1,7 +1,7 @@ -// --- -// # Only the main Sass file needs front matter (the dashes are enough) -// search: false -// --- +--- +# Only the main Sass file needs front matter (the dashes are enough) +search: false +--- @charset "utf-8"; From 42d82a17a55b2642e00b9e7e7af042165b2bb7d0 Mon Sep 17 00:00:00 2001 From: choisunmi00 Date: Thu, 21 Nov 2024 15:06:04 +0900 Subject: [PATCH 22/62] modify --- _config.yml | 2 +- _sass/minimal-mistakes/_page.scss | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/_config.yml b/_config.yml index 8d27db0f41ee..749eb964d010 100644 --- a/_config.yml +++ b/_config.yml @@ -319,7 +319,7 @@ defaults: values: layout: single author_profile: true - read_time: true + read_time: # true comments: # true share: true related: true diff --git a/_sass/minimal-mistakes/_page.scss b/_sass/minimal-mistakes/_page.scss index 6db1ebf560de..9038e5a2cdad 100644 --- a/_sass/minimal-mistakes/_page.scss +++ b/_sass/minimal-mistakes/_page.scss @@ -109,7 +109,7 @@ body { p, li, dl { - font-size: 0.75em; + font-size: 1em; } /* paragraph indents */ From 2f16de69f1ba6ee289e3866fc955533a950d08d4 Mon Sep 17 00:00:00 2001 From: choisunmi00 Date: Thu, 21 Nov 2024 15:34:37 +0900 Subject: [PATCH 23/62] modify details --- _includes/head.html | 4 ++-- _includes/page__date.html | 4 ++-- _includes/page__related.html | 4 ++-- _sass/minimal-mistakes.scss | 2 +- _sass/minimal-mistakes/_page.scss | 18 ++++++++++++++---- _sass/minimal-mistakes/_variables.scss | 2 +- docs/_config.yml | 2 +- test/_config.yml | 2 +- 8 files changed, 24 insertions(+), 14 deletions(-) diff --git a/_includes/head.html b/_includes/head.html index c214bea57cc9..ab5697e3762f 100644 --- a/_includes/head.html +++ b/_includes/head.html @@ -2,9 +2,9 @@ {% include seo.html %} -{% unless site.atom_feed.hide %} + {%- comment %} https://docs.google.com/presentation/d/1rmxwWa9P6_xHqonmh5ONXRS-jPc5XKbnv99Rjkhe04s/present {% endcomment -%} diff --git a/_includes/page__date.html b/_includes/page__date.html index ec02005f1307..ed96d500128a 100644 --- a/_includes/page__date.html +++ b/_includes/page__date.html @@ -1,6 +1,6 @@ {% assign date_format = site.date_format | default: "%B %-d, %Y" %} {% if page.last_modified_at %} -

{{ site.data.ui-text[site.locale].date_label | default: "Updated:" }}

+

{{ site.data.ui-text[site.locale].date_label | default: "Updated:" }}

{% elsif page.date %} -

{{ site.data.ui-text[site.locale].date_label | default: "Updated:" }}

+

{{ site.data.ui-text[site.locale].date_label | default: "Updated:" }}

{% endif %} \ No newline at end of file diff --git a/_includes/page__related.html b/_includes/page__related.html index 9777865eeefd..3bfe2e364b38 100644 --- a/_includes/page__related.html +++ b/_includes/page__related.html @@ -1,4 +1,4 @@ -{% assign posts = include.posts | where_exp: "post", "post.hidden != true" %} + diff --git a/_sass/minimal-mistakes.scss b/_sass/minimal-mistakes.scss index 5be40467d81b..c1890825a725 100644 --- a/_sass/minimal-mistakes.scss +++ b/_sass/minimal-mistakes.scss @@ -37,4 +37,4 @@ @import "minimal-mistakes/print"; /* google fonts */ -@import url('https://fonts.googleapis.com/css2?family=Nanum+Myeongjo&display=swap'); \ No newline at end of file +@import url('https://fonts.googleapis.com/css2?family=Noto+Serif+KR:wght@200..900&display=swap'); \ No newline at end of file diff --git a/_sass/minimal-mistakes/_page.scss b/_sass/minimal-mistakes/_page.scss index 9038e5a2cdad..ac7b034f39cb 100644 --- a/_sass/minimal-mistakes/_page.scss +++ b/_sass/minimal-mistakes/_page.scss @@ -109,7 +109,7 @@ body { p, li, dl { - font-size: 1em; + font-size: 0.8em; } /* paragraph indents */ @@ -332,14 +332,24 @@ body { } } +// .page__taxonomy-item { +// display: inline-block; +// margin-inline-end: 5px; +// margin-bottom: 8px; +// padding: 5px 10px; +// text-decoration: none; +// border: 1px solid mix(#000, $border-color, 25%); +// border-radius: $border-radius; .page__taxonomy-item { display: inline-block; margin-inline-end: 5px; margin-bottom: 8px; - padding: 5px 10px; + padding: 2px 10px; /* 세로 폭 줄이기: 기존 5px에서 2px로 */ text-decoration: none; - border: 1px solid mix(#000, $border-color, 25%); - border-radius: $border-radius; + border: none; /* 테두리 제거 */ + background-color: #d4e0ef; /* 배경색을 옅은 회색으로 */ + border-radius: $border-radius; /* 모서리 둥글기는 유지 (필요 시 수정 가능) */ +} &:hover { text-decoration: none; diff --git a/_sass/minimal-mistakes/_variables.scss b/_sass/minimal-mistakes/_variables.scss index 1954e523f256..61e2bbdb7b59 100644 --- a/_sass/minimal-mistakes/_variables.scss +++ b/_sass/minimal-mistakes/_variables.scss @@ -17,7 +17,7 @@ $indent-var: 1.3em !default; /* system typefaces */ $serif: Georgia, Times, serif !default; -$sans-serif: -apple-system, BlinkMacSystemFont, "Nanum Myeongjo", "Roboto", "Segoe UI", +$sans-serif: -apple-system, BlinkMacSystemFont, "Noto Serif KR", "Roboto", "Segoe UI", "Helvetica Neue", "Lucida Grande", Arial, sans-serif !default; $monospace: Monaco, Consolas, "Lucida Console", monospace !default; diff --git a/docs/_config.yml b/docs/_config.yml index 2266a9047012..4c4554ab1085 100644 --- a/docs/_config.yml +++ b/docs/_config.yml @@ -211,7 +211,7 @@ defaults: values: layout: single author_profile: true - read_time: true + read_time: false comments: true share: true related: true diff --git a/test/_config.yml b/test/_config.yml index 9656a3764878..f362cce76905 100644 --- a/test/_config.yml +++ b/test/_config.yml @@ -272,7 +272,7 @@ defaults: values: layout: single author_profile: true - read_time: true + read_time: false share: true related: true # _pages From 7770c65ea4a19213895d9690ed8dd5d372a3d44e Mon Sep 17 00:00:00 2001 From: choisunmi00 Date: Thu, 21 Nov 2024 15:35:38 +0900 Subject: [PATCH 24/62] Update _page.scss --- _sass/minimal-mistakes/_page.scss | 1 - 1 file changed, 1 deletion(-) diff --git a/_sass/minimal-mistakes/_page.scss b/_sass/minimal-mistakes/_page.scss index ac7b034f39cb..2df370c55e2e 100644 --- a/_sass/minimal-mistakes/_page.scss +++ b/_sass/minimal-mistakes/_page.scss @@ -349,7 +349,6 @@ body { border: none; /* 테두리 제거 */ background-color: #d4e0ef; /* 배경색을 옅은 회색으로 */ border-radius: $border-radius; /* 모서리 둥글기는 유지 (필요 시 수정 가능) */ -} &:hover { text-decoration: none; From 17da6f44beb500c94cdf495a6efcec231e7c1578 Mon Sep 17 00:00:00 2001 From: choisunmi00 Date: Thu, 21 Nov 2024 15:48:15 +0900 Subject: [PATCH 25/62] modify --- _includes/page__meta.html | 2 +- _includes/social-share.html | 4 +-- _sass/minimal-mistakes/_page.scss | 54 +++++++++++++------------------ 3 files changed, 26 insertions(+), 34 deletions(-) diff --git a/_includes/page__meta.html b/_includes/page__meta.html index 3d228c921205..e356dc04e744 100644 --- a/_includes/page__meta.html +++ b/_includes/page__meta.html @@ -4,7 +4,7 @@ {% if document.show_date and document.date %} {% assign date = document.date %} - + {% assign date_format = site.date_format | default: "%B %-d, %Y" %} diff --git a/_includes/social-share.html b/_includes/social-share.html index 847baa32d5da..4be520105b6c 100644 --- a/_includes/social-share.html +++ b/_includes/social-share.html @@ -1,4 +1,4 @@ -