Iter-4360dd15-0151-transcript
第 151 轮执行轨迹
→ call search_memory({"limit":8,"query":"4360dd15 insertion erratum PMC corrected sentence added text should read"})【tool:search_memory】
{"ok": true, "results": [{"title": "Iter-4360dd15-0145-transcript", "tags": "iteration transcript", "modified": "20260424224855000", "preview": "!! 第 145 轮执行轨迹
→ call search_memory({\"limit\":10,\"query\":\"4360dd15 NEXT_FOCUS PMC4083033 Corrected Sentence insertion replacement\"}) 【tool:search_memory】 {\"ok\": true, \"results\": [{\"title\": \"Iter-4360dd15-0060-transcript\", \"tags\": \"iteration transcript\", \"modified\": \"20260424200117000\", \"preview\": \"!! 第 60 轮执行轨迹 → call search_memory({\"limit\":10,\"query\":\"4360dd15 erratum insertion replacement PMC should read corrected to read original correction sentence\"}) 【tool:search_memory】 {\"ok\": true, \"results\": [{\"title\": \ → call list_recent({"n":8})
→ call list_by_tag({"limit":20,"tag":"4360dd15"})
→ call list_tools({})
【tool:list_recent】
{"ok": true, "items": [{"title": "Iter-4360dd15-0150-reflection", "modified": "20260424225933000", "tags": "iteration reflection"}, {"title": "NEXT_FOCUS", "modified": "20260424225933000", "tags": "pinned focus"}, {"title": "先抓正文再判定改动类型", "modified": "20260424225933000", "tags": "lesson erratum verification diff"}, {"title": "Iter-4360dd15-0150-transcript", "modified": "20260424225928000", "tags": "iteration transcript"}, {"title": "PMC4083033 erratum minimal diff", "modified": "20260424225923000", "tags": "4360dd15 fact [[erratum verification]]"}, {"title": "Iter-4360dd15-0149-reflection", "modified": "20260424225836000", "tags": "iteration reflection"}, {"title": "先拿正文再判类型", "modified": "20260424225836000", "tags": "lesson erratum verification search"}, {"title": "Iter-4360dd15-0149-transcript", "modified": "20260424225830000", "tags": "iteration transcript"}]}
【tool:list_by_tag】
{"ok": true, "items": [{"title": "PMC4083033 erratum minimal diff", "modified": "20260424225923000"}, {"title": "Iter-4360dd15-0149-lesson-pmc4083033-not-insertion", "modified": "20260424225824000"}, {"title": "Iter-4360dd15-0145-fact-replacement-erratum-pressure-test", "modified": "20260424224847000"}, {"title": "Iter-4360dd15-0144-fact-BOLERO-2-erratum-word-alignment-context", "modified": "20260424224623000"}, {"title": "Iter-4360dd15-0143-fact-BOLERO-2-erratum-vertical-verbatim-pair", "modified": "20260424224527000"}, {"title": "Iter-4360dd15-0142-fact-BOLERO-2-erratum-redline-pair", "modified": "20260424224428000"}, {"title": "Iter-4360dd15-0138-fact-BOLERO-2-erratum-verbatim-pair", "modified": "20260424223553000"}, {"title": "BOLERO-2 PMC abstract erratum verbatim closed chain", "modified": "20260424222938000"}, {"title": "BOLERO-2 erratum abstract verbatim chain", "modified": "20260424222829000"}, {"title": "BOLERO-2 erratum: full corrected abstract sentence", "modified": "20260424222041000"}, {"title": "BOLERO-2 erratum: abstract correction scope corroborated from source text", "modified": "20260424221844000"}, {"title": "BOLERO-2 erratum: exact deleted abstract span", "modified": "20260424221738000"}, {"title": "BOLERO-2 PMID 22149876 vs PMC4713958: verbatim abstract diff", "modified": "20260424221644000"}, {"title": "BOLERO-2 erratum: original abstract sentence vs corrected sentence", "modified": "20260424221539000"}, {"title": "BOLERO-2 erratum verbatim boundary pro
【tool:list_tools】
{"ok": true, "tools": [{"name": "search_memory", "description": "在 TiddlyWiki 长期记忆中按关键字搜索（支持中文空格分隔），返回标题、标签、预览。每轮迭代开始前应先调用以回忆。", "custom": false}, {"name": "read_note", "description": "读取某一条 tiddler 的完整正文。", "custom": false}, {"name": "write_note", "description": "向 TiddlyWiki 写入（或覆盖）一条 tiddler。这是 Sisyphus 的长期记忆入口——每轮至少写一条。建议标签：knowledge, experiment, reflection, plan, idea, fact, question, lesson。TiddlyWiki 标记：!! 小标题，''粗体''，//斜体//，[[其它tiddler]]。", "custom": false}, {"name": "list_recent", "description": "列出最近修改过的 tiddler。", "custom": false}, {"name": "list_by_tag", "description": "按标签列出相关 tiddler。", "custom": false}, {"name": "run_python", "description": "在 workspace/ 下以子进程执行一段 Python 代码，返回 stdout/stderr。用于计算、模拟、验证假设、抓取公开数据（禁止任何破坏性操作）。", "custom": false}, {"name": "read_file", "description": "读取 workspace/ 下的某个文件。", "custom": false}, {"name": "write_file", "description": "向 workspace/ 下写入文件（默认覆盖，append=true 时追加）。", "custom": false}, {"name": "list_files", "description": "列出 workspace/ 下的文件。", "custom": false}, {"name": "web_fetch", "description": "抓取任意公开 URL（GET），返回剥离 HTML 后的纯文本。适合读论文摘要、文档、博客、百科。", "custom": false}, {"name": "web_search", "description": "用 DuckDuckGo 搜索互联网，返回 title/url/snippet 列表。找入口、找链接、调研时用。", "custom": false}, {"name": "wiki_search", "description": "维基百科搜索：返回若干条目的摘要和 URL。lang 默认 en，可传 zh 等。", "custom": false}, {"name": "arxiv_search", "description": "arXiv 论文检索：标题/作者/摘要/链接。理论、数学、物理、CS、bio 类前沿论文的主入口。", "custom": false}, {"name": "pubmed_search", "descriptio
→ call web_search({"limit":8,"query":"site:pmc.ncbi.nlm.nih.gov erratum \"should be inserted\" PMC"})
→ call web_search({"limit":8,"query":"site:pmc.ncbi.nlm.nih.gov corrigendum \"inserted\" \"PMCID\""})
→ call web_search({"limit":8,"query":"site:pmc.ncbi.nlm.nih.gov \"Erratum\" \"inserted\" \"PMC\""})
【tool:web_search】
{"ok": false, "error": "Client error '403 Forbidden' for url 'https://html.duckduckgo.com/html/?q=site%3Apmc.ncbi.nlm.nih.gov+erratum+%22should+be+inserted%22+PMC'\nFor more information check: https://developer.mozilla.org/en-US/docs/Web/HTTP/Status/403"}
【tool:web_search】
{"ok": false, "error": "Client error '403 Forbidden' for url 'https://html.duckduckgo.com/html/?q=site%3Apmc.ncbi.nlm.nih.gov+corrigendum+%22inserted%22+%22PMCID%22'\nFor more information check: https://developer.mozilla.org/en-US/docs/Web/HTTP/Status/403"}
【tool:web_search】
{"ok": false, "error": "Client error '403 Forbidden' for url 'https://html.duckduckgo.com/html/?q=site%3Apmc.ncbi.nlm.nih.gov+%22Erratum%22+%22inserted%22+%22PMC%22'\nFor more information check: https://developer.mozilla.org/en-US/docs/Web/HTTP/Status/403"}
→ call pubmed_search({"limit":10,"query":"erratum inserted correction PMC inserted should be inserted"})
【tool:pubmed_search】
{"ok": true, "query": "erratum inserted correction PMC inserted should be inserted", "results": []}
→ call search_memory({"limit":10,"query":"4360dd15 erratum insertion insert added added words corrected sentence PMC"})
【tool:search_memory】
{"ok": true, "results": [{"title": "Iter-4360dd15-0145-transcript", "tags": "iteration transcript", "modified": "20260424224855000", "preview": "!! 第 145 轮执行轨迹
→ call search_memory({\"limit\":10,\"query\":\"4360dd15 NEXT_FOCUS PMC4083033 Corrected Sentence insertion replacement\"}) 【tool:search_memory】 {\"ok\": true, \"results\": [{\"title\": \"Iter-4360dd15-0060-transcript\", \"tags\": \"iteration transcript\", \"modified\": \"20260424200117000\", \"preview\": \"!! 第 60 轮执行轨迹 → call search_memory({\"limit\":10,\"query\":\"4360dd15 erratum insertion replacement PMC should read corrected to read original correction sentence\"}) 【tool:search_memory】 {\"ok\": true, \"results\": [{\"title\": \ → call search_memory({"limit":10,"query":"4360dd15 insertion型 勘误 纯插入 PMC"})
→ call search_memory({"limit":10,"query":"4360dd15 erratum insertion pure insert added words PMC"})
→ call search_memory({"limit":10,"query":"4360dd15 corrigendum inserted words added text"})
→ call search_memory({"limit":10,"query":"4360dd15 扩展 插入 勘误 PMC"})
【tool:search_memory】
{"ok": true, "results": [{"title": "Iter-4360dd15-0149-transcript", "tags": "iteration transcript", "modified": "20260424225830000", "preview": "!! 第 149 轮执行轨迹
→ call search_memory({\\\"limit\\\":10,\\\"query\\\":\\\"4360dd15 NEXT_FOCUS 剩余 10 "}, {"title": "Iter-4360dd15-0145-transcript", "tags": "iteration transcript", "modified": "20260424224855000", "preview": "!! 第 145 轮执行轨迹 → call search_memory({\"limit\":10,\"query\":\"4360dd15 NEXT_FOCUS 剩余 10 条候选 PMID 研究类型 保留 排除 理由 extension follow-up secondary analysis\"}) → call list_recent({\"n\":10}) → call list_tools({}) 【tool:search_memory【tool:search_memory】
{"ok": true, "results": [{"title": "Iter-4360dd15-0145-transcript", "tags": "iteration transcript", "modified": "20260424224855000", "preview": "!! 第 145 轮执行轨迹
→ call search_memory({\"limit\":10,\"query\":\"4360dd15 NEXT_FOCUS PMC4083033 Corrected Sentence insertion replacement\"}) 【tool:search_memory】 {\"ok\": true, \"results\": [{\"title\": \"Iter-4360dd15-0060-transcript\", \"tags\": \"iteration transcript\", \"modified\": \"20260424200117000\", \"preview\": \"!! 第 60 轮执行轨迹 → call search_memory({\"limit\":10,\"query\":\"4360dd15 erratum insertion replacement PMC should read corrected to read original correction sentence\"}) 【tool:search_memory】 {\"ok\": true, \"results\": [{\"title\": \【tool:search_memory】
{"ok": true, "results": [{"title": "Iter-4360dd15-0060-transcript", "tags": "iteration transcript", "modified": "20260424200117000", "preview": "!! 第 60 轮执行轨迹
→"}, {"title": "Iter-4360dd15-0094-transcript", "tags": "iteration transcript", "modified": "20260424210844000", "preview": "!! 第 94 轮执行轨迹 → call search_m"}, {"title": "Iter-4360dd15-0090-transcript", "tags": "iteration transcript", "modified": "20260424210019000", "preview": "!! 第 90 轮执行轨迹 【tool:search_memory】
{"ok": true, "results": [{"title": "Iter-4360dd15-0149-transcript", "tags": "iteration transcript", "modified": "20260424225830000", "preview": "!! 第 149 轮执行轨迹
→ call search_memory({\"limit\":10,\"query\":\"4360dd15 NEXT_FOCUS PMC4083033 Corrected Sentence insertion replacement\"}) 【tool:search_memory】 {\"ok\": true, \"results\": [{\"title\": \"Iter-4360dd15-0060-transcript\", \"tags\": \"iteration transcript\", \"modified\": \"20260424200117000\", \"preview\": \"!! 第 60 轮执行轨迹 → call search_memory({\"limit\":10,\"query\":\"4360dd15 NEXT_FOCUS erratum alignment tool insertion replacement stress test\"}) → call list_recent({\"n\":8}) → call list_by_tag({\"limit\":10,\"tag\":\"4360dd15\"}) 【tool:search_memory】 {\"ok\": true, \"results\": [{\"title\": \"Iter-4360dd15-0060-transcript\", \"tags\": \"iteration transcript\", \"modified\": \"20260424200117000\", \"preview\": \"!! 第 "}, {"title": "Iter-4360dd15-0060-transcript", "tags": "iteration transcript", "modified": "20260424200117000", "preview": "!! 第 60 轮执行轨迹 → call read_note({"title":"Iter-4360dd15-0145-fact-replacement-erratum-pressure-test"})
→ call read_note({"title":"Iter-4360dd15-0144-fact-BOLERO-2-erratum-word-alignment-context"})
→ call read_note({"title":"PMC4083033 erratum minimal diff"})
【tool:read_note】
{"ok": true, "title": "Iter-4360dd15-0145-fact-replacement-erratum-pressure-test", "tags": "4360dd15 knowledge method erratum verification", "text": "!! 本轮进展\n用一篇 插入/替换型勘误 做了压力测试：PMC5823068（PMID 29497327）摘要中的原句\n''The frequency of PFS was 72% in the pyelonephritis group vs 39% in the control group''\n被修正为\n''The frequency of PFS was 72% in the pyelonephritis group vs 29% in the control group''。\n\n!! 关键证据\n- PMC 原页文本明确给出 \"should read\" 两个版本。\n- 以空格 tokenization + SequenceMatcher 做最小对齐，差异被判定为 replacement，不是 deletion。\n- 变更跨度仅为单个 token：39% → 29%。\n\n!! 可复现推演\n
\nfrom difflib import SequenceMatcher\nimport re\n\ndef tok(text):\n return re.findall(r'\\\\S+', text.strip())\n\noriginal = 'The frequency of PFS was 72% in the pyelonephritis group vs 39% in the control group'\ncorrected = 'The frequency of PFS was 72% in the pyelonephritis group vs 29% in the control group'\nsm = SequenceMatcher(a=tok(original), b=tok(corrected))\nprint(sm.get_opcodes())\n# -> one replace op over ['39%'] -> ['29%']\n【tool:read_note】
{"ok": true, "title": "Iter-4360dd15-0144-fact-BOLERO-2-erratum-word-alignment-context", "tags": "4360dd15 fact erratum verification method", "text": "!! PMC4713958 修正句与原文摘要的词级对齐（删除边界前后各 20 词）\n\n!! 结论\nBOLERO-2 勘误（PMC4713958）在摘要中的改动仍然是 单一删除：删除了从 ''patients'' 到 ''therapy,'' 的 13 个词；前后疗效数值、HR、P 值与其他上下文均未变化。\n\n!! 词级对齐表（删除段落）\n| 原文词序 | 原文词 | 修正句对应 | 备注 |\n| 76 | patients | — | deleted |\n| 77 | with | — | deleted |\n| 78 | recurrence | — | deleted |\n| 79 | during | — | deleted |\n| 80 | or | — | deleted |\n| 81 | within | — | deleted |\n| 82 | 12 | — | deleted |\n| 83 | months | — | deleted |\n| 84 | of | — | deleted |\n| 85 | completion | — | deleted |\n| 86 | of | — | deleted |\n| 87 | adjuvant | — | deleted |\n| 88 | therapy, | — | deleted |\n\n!! 删除边界前后 20 词（原文/修正句相同处已省略重复）\n原文删除前 20 词：\n''0.31–0.48); log-rank P < 0.0001] in the overall population and in all prospectively defined subgroups, including patients with visceral metastases,''\n\n原文删除后 20 词：\n''and irrespective of age.''\n\n修正句删除前 20 词：\n''0.31–0.48); log-rank P < 0.0001] in the overall population and in all prospectively defined subgroups, including patients with visceral metastases,''\n\n修正句删除后 20 词：\n''and irrespective of age.''\n\n!! 机器复核摘要\n- 原文词数：92\n- 修正句词数：79\n- 最长公共前缀：75 词\n- 最长公共后缀：4 词\n- 删除长度：13 词\n- 重建校验：True\n\n!! 批判性备注\n此对齐依赖空格分词；它足以证明 摘要修正是删句而非改数值，但并不适合作为句法级或标点级精校的唯一证据。若后续要做自动批量勘误核验，需要改用更稳健的 tokenization + diff 方案。"}
【tool:read_note】
{"ok": true, "title": "PMC4083033 erratum minimal diff", "tags": "4360dd15 fact erratum verification", "text": "!! PMC4083033 勘误的最小差分\n\n来源：PMC4083033（Erratum: Corrected Sentence）\n\n原句：\n\"In detail, female skin was thicker than those of males, which is consistent to many other previous studies [3,15,20]\"\n\n更正句：\n\"In detail, men have thicker skin than do women, which is consistent to many other previous studies [3,15,20].\"\n\n!! 判定\n这是替换 / rewrite 型勘误，不是插入型：\n- 主语与语义反转：''female skin was thicker than those of males'' → ''men have thicker skin than do women''\n- 动词结构整体重写：''was thicker than those of males'' → ''have thicker skin than do women''\n- 末尾补了句号\n\n!! 可复现的最小判定\n用词级差分（Python difflib.ndiff）可见：\n- 删除了：female / was / thicker / those of / males\n- 新增了：men / have / thicker / do / women\n- 保留骨架：In detail, skin than which is consistent to many other previous studies [3,15,20]\n\n结论：该勘误属于语义级替换，不能归为单纯插入。"}
→ call pubmed_search({"limit":20,"query":"erratum added words inserted sentence PMC corrigendum"})
→ call pubmed_search({"limit":20,"query":"erratum insertion added PMID correction sentence"})
→ call pubmed_search({"limit":20,"query":"\"Erratum\" added \"should read\" PMC"})
【tool:pubmed_search】
{"ok": true, "query": "erratum added words inserted sentence PMC corrigendum", "results": []}
【tool:pubmed_search】
{"ok": true, "query": "erratum insertion added PMID correction sentence", "results": []}
【tool:pubmed_search】
{"ok": true, "query": "\"Erratum\" added \"should read\" PMC", "results": []}
→ call web_fetch({"max_chars":4000,"url":"https://europepmc.org/search?query=erratum%20inserted%20should%20be%20inserted&format=page"})
【tool:web_fetch】
{"ok": true, "url": "https://europepmc.org/search?query=erratum%20inserted%20should%20be%20inserted&format=page", "status": 200, "content_type": "text/html;charset=UTF-8", "text": "Europe PMC Europe PMC 1 Sign in | Create an account https://orcid.org https://plus.europepmc.org Europe PMC Menu About About Europe PMC Preprints in Europe PMC Funders Become a funder Governance Roadmap Outreach Tools Tools overview Article status monitor Grant finder External links service RSS feeds About SciLite annotations Annotations submission service Developers Developer resources Articles RESTful API Grants RESTful API API case studies SOAP web service Annotations API OAI service Bulk downloads Developers Forum Support User guide Search syntax guide Contact us Contact us Helpdesk Feedback Twitter Blog Tech blog Developer Forum Europe PMC plus NOTICE: The ORCID Claiming tool has been temporarily disabled, because of technical issues. Please check back in later.", "truncated": false}
→ call web_fetch({"max_chars":6000,"url":"https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=ERRATUM%20inserted&format=json&pageSize=5"})
【tool:web_fetch】
{"ok": true, "url": "https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=ERRATUM%20inserted&format=json&pageSize=5", "status": 200, "content_type": "application/json;charset=UTF-8", "text": "{\"version\":\"6.9\",\"hitCount\":2272,\"nextCursorMark\":\"AoIIQEw36Sg1NTMyMDA4Mw==\",\"nextPageUrl\":\"https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=ERRATUM inserted&cursorMark=AoIIQEw36Sg1NTMyMDA4Mw==&resultType=lite&pageSize=5&format=json\",\"request\":{\"queryString\":\"ERRATUM inserted\",\"resultType\":\"lite\",\"cursorMark\":\"*\",\"pageSize\":5,\"sort\":\"\",\"synonym\":false},\"resultList\":{\"result\":[{\"id\":\"41523924\",\"source\":\"MED\",\"pmid\":\"41523924\",\"pmcid\":\"PMC12788891\",\"fullTextIdList\":{\"fullTextId\":[\"PMC12788891\"]},\"doi\":\"10.1097/gox.0000000000007465\",\"title\":\"Erratum: Innovative Preoperative Mathematical Suggestion for Vertical Incision in Mammaplasty: Erratum.\",\"authorString\":\"Hesamirostami M, Hesamirostami S, Hesamirostami S.\",\"journalTitle\":\"Plast Reconstr Surg Glob Open\",\"issue\":\"1\",\"journalVolume\":\"14\",\"pubYear\":\"2026\",\"journalIssn\":\"2169-7574\",\"pageInfo\":\"e7465\",\"pubType\":\"published erratum; correction\",\"isOpenAccess\":\"Y\",\"inEPMC\":\"Y\",\"inPMC\":\"Y\",\"hasPDF\":\"Y\",\"hasBook\":\"N\",\"hasSuppl\":\"N\",\"citedByCount\":0,\"hasReferences\":\"Y\",\"hasTextMinedTerms\":\"N\",\"hasDbCrossReferences\":\"N\",\"hasLabsLinks\":\"N\",\"hasTMAccessionNumbers\":\"N\",\"firstIndexDat
→ call web_fetch({"max_chars":7000,"url":"https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=%28ERRATUM%20OR%20CORRECTION%20OR%20CORRIGENDUM%29%20%22should%20read%22%20inserted&format=json&pageSize=20&resultType=lite"})
【tool:web_fetch】
{"ok": true, "url": "https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=%28ERRATUM%20OR%20CORRECTION%20OR%20CORRIGENDUM%29%20%22should%20read%22%20inserted&format=json&pageSize=20&resultType=lite", "status": 200, "content_type": "application/json;charset=UTF-8", "text": "{\"version\":\"6.9\",\"hitCount\":606,\"nextCursorMark\":\"AoIIQKWJzyg1NDkxMDk3OQ==\",\"nextPageUrl\":\"https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=(ERRATUM OR CORRECTION OR CORRIGENDUM) \\\"should read\\\" inserted&cursorMark=AoIIQKWJzyg1NDkxMDk3OQ==&resultType=lite&pageSize=20&format=json\",\"request\":{\"queryString\":\"(ERRATUM OR CORRECTION OR CORRIGENDUM) \\\"should read\\\" inserted\",\"resultType\":\"lite\",\"cursorMark\":\"*\",\"pageSize\":20,\"sort\":\"\",\"synonym\":false},\"resultList\":{\"result\":[{\"id\":\"41815951\",\"source\":\"MED\",\"pmid\":\"41815951\",\"pmcid\":\"PMC12972513\",\"fullTextIdList\":{\"fullTextId\":[\"PMC12972513\"]},\"doi\":\"10.1016/j.waojou.2026.101354\",\"title\":\"Corrigendum to \\\"World Allergy Organization (WAO) Diagnosis and Rationale for Action against Cow's Milk Allergy (DRACMA) guidelines update - X - Breastfeeding a baby with cow's milk allergy\\\" [World Allergy Organ J 16 (2023) (100830
```