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| author | sillylaird <sillyfanboy@gmail.com> | 2026-09-03 00:33:59 +0000 |
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| committer | sillylaird <sillyfanboy@gmail.com> | 2026-09-03 00:33:59 +0000 |
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diff --git a/.agents/skills/ml-paper-writing/references/citation-workflow.md b/.agents/skills/ml-paper-writing/references/citation-workflow.md new file mode 100644 index 0000000..b7ec90b --- /dev/null +++ b/.agents/skills/ml-paper-writing/references/citation-workflow.md @@ -0,0 +1,562 @@ +# Citation Management & Hallucination Prevention + +This reference provides a complete workflow for managing citations programmatically, preventing AI-generated citation hallucinations, and maintaining clean bibliographies. + +--- + +## Contents + +- [Why Citation Verification Matters](#why-citation-verification-matters) +- [Citation APIs Overview](#citation-apis-overview) +- [Verified Citation Workflow](#verified-citation-workflow) +- [Python Implementation](#python-implementation) +- [BibTeX Management](#bibtex-management) +- [Common Citation Formats](#common-citation-formats) +- [Troubleshooting](#troubleshooting) + +--- + +## Why Citation Verification Matters + +### The Hallucination Problem + +Research has documented significant issues with AI-generated citations: +- **~40% error rate** in AI-generated citations (Enago Academy research) +- NeurIPS 2025 found **100+ hallucinated citations** slipped through review +- Common errors include: + - Fabricated paper titles with real author names + - Wrong publication venues or years + - Non-existent papers with plausible metadata + - Incorrect DOIs or arXiv IDs + +### Consequences + +- Desk rejection at some venues +- Loss of credibility with reviewers +- Potential retraction if published +- Wasted time chasing non-existent sources + +### Solution + +**Never generate citations from memory—always verify programmatically.** + +--- + +## Citation APIs Overview + +### Primary APIs + +| API | Coverage | Rate Limits | Best For | +|-----|----------|-------------|----------| +| **Semantic Scholar** | 214M papers | 1 RPS (free key) | ML/AI papers, citation graphs | +| **CrossRef** | 140M+ DOIs | Polite pool with mailto | DOI lookup, BibTeX retrieval | +| **arXiv** | Preprints | 3-second delays | ML preprints, PDF access | +| **OpenAlex** | 240M+ works | 100K/day, 10 RPS | Open alternative to MAG | + +### API Selection Guide + +``` +Need ML paper search? → Semantic Scholar +Have DOI, need BibTeX? → CrossRef content negotiation +Looking for preprint? → arXiv API +Need open data, bulk access? → OpenAlex +``` + +### No Official Google Scholar API + +Google Scholar has no official API. Scraping violates ToS. Use SerpApi ($75-275/month) only if Semantic Scholar coverage is insufficient. + +--- + +## Verified Citation Workflow + +### 5-Step Process + +``` +1. SEARCH → Query Semantic Scholar with specific keywords + ↓ +2. VERIFY → Confirm paper exists in 2+ sources + ↓ +3. RETRIEVE → Get BibTeX via DOI content negotiation + ↓ +4. VALIDATE → Confirm the claim appears in source + ↓ +5. ADD → Add verified entry to .bib file +``` + +### Step 1: Search + +Use Semantic Scholar for ML/AI papers: + +```python +from semanticscholar import SemanticScholar + +sch = SemanticScholar() +results = sch.search_paper("transformer attention mechanism", limit=10) + +for paper in results: + print(f"Title: {paper.title}") + print(f"Year: {paper.year}") + print(f"DOI: {paper.externalIds.get('DOI', 'N/A')}") + print(f"arXiv: {paper.externalIds.get('ArXiv', 'N/A')}") + print(f"Citation count: {paper.citationCount}") + print("---") +``` + +### Step 2: Verify Existence + +Confirm paper exists in at least two sources: + +```python +import requests + +def verify_paper(doi=None, arxiv_id=None, title=None): + """Verify paper exists in multiple sources.""" + sources_found = [] + + # Check Semantic Scholar + sch = SemanticScholar() + if doi: + paper = sch.get_paper(f"DOI:{doi}") + if paper: + sources_found.append("Semantic Scholar") + + # Check CrossRef (via DOI) + if doi: + resp = requests.get(f"https://api.crossref.org/works/{doi}") + if resp.status_code == 200: + sources_found.append("CrossRef") + + # Check arXiv + if arxiv_id: + resp = requests.get( + f"http://export.arxiv.org/api/query?id_list={arxiv_id}" + ) + if "<entry>" in resp.text: + sources_found.append("arXiv") + + return len(sources_found) >= 2, sources_found +``` + +### Step 3: Retrieve BibTeX + +Use DOI content negotiation for guaranteed accuracy: + +```python +import requests + +def doi_to_bibtex(doi: str) -> str: + """Get verified BibTeX from DOI via CrossRef content negotiation.""" + response = requests.get( + f"https://doi.org/{doi}", + headers={"Accept": "application/x-bibtex"}, + allow_redirects=True + ) + response.raise_for_status() + return response.text + +# Example: "Attention Is All You Need" +bibtex = doi_to_bibtex("10.48550/arXiv.1706.03762") +print(bibtex) +``` + +### Step 4: Validate Claims + +Before citing a paper for a specific claim, verify the claim exists: + +```python +def get_paper_abstract(doi): + """Get abstract to verify claims.""" + sch = SemanticScholar() + paper = sch.get_paper(f"DOI:{doi}") + return paper.abstract if paper else None + +# Verify claim appears in abstract +abstract = get_paper_abstract("10.48550/arXiv.1706.03762") +claim = "attention mechanism" +if claim.lower() in abstract.lower(): + print("Claim appears in paper") +``` + +### Step 5: Add to Bibliography + +Add verified entry to your .bib file with consistent key format: + +```python +def generate_citation_key(bibtex: str) -> str: + """Generate consistent citation key: author_year_firstword.""" + import re + + # Extract author + author_match = re.search(r'author\s*=\s*\{([^}]+)\}', bibtex, re.I) + if author_match: + first_author = author_match.group(1).split(',')[0].split()[-1] + else: + first_author = "unknown" + + # Extract year + year_match = re.search(r'year\s*=\s*\{?(\d{4})\}?', bibtex, re.I) + year = year_match.group(1) if year_match else "0000" + + # Extract title first word + title_match = re.search(r'title\s*=\s*\{([^}]+)\}', bibtex, re.I) + if title_match: + first_word = title_match.group(1).split()[0].lower() + first_word = re.sub(r'[^a-z]', '', first_word) + else: + first_word = "paper" + + return f"{first_author.lower()}_{year}_{first_word}" +``` + +--- + +## Python Implementation + +### Complete Citation Manager Class + +```python +""" +Citation Manager - Verified citation workflow for ML papers. +""" + +import requests +import time +from typing import Optional, List, Dict, Tuple +from dataclasses import dataclass + +try: + from semanticscholar import SemanticScholar +except ImportError: + print("Install: pip install semanticscholar") + SemanticScholar = None + +@dataclass +class Paper: + title: str + authors: List[str] + year: int + doi: Optional[str] + arxiv_id: Optional[str] + venue: Optional[str] + citation_count: int + abstract: Optional[str] + +class CitationManager: + """Manage citations with verification.""" + + def __init__(self, api_key: Optional[str] = None): + self.sch = SemanticScholar(api_key=api_key) if SemanticScholar else None + self.verified_papers: Dict[str, Paper] = {} + + def search(self, query: str, limit: int = 10) -> List[Paper]: + """Search for papers using Semantic Scholar.""" + if not self.sch: + raise RuntimeError("Semantic Scholar not available") + + results = self.sch.search_paper(query, limit=limit) + papers = [] + + for r in results: + paper = Paper( + title=r.title, + authors=[a.name for a in (r.authors or [])], + year=r.year or 0, + doi=r.externalIds.get('DOI') if r.externalIds else None, + arxiv_id=r.externalIds.get('ArXiv') if r.externalIds else None, + venue=r.venue, + citation_count=r.citationCount or 0, + abstract=r.abstract + ) + papers.append(paper) + + return papers + + def verify(self, paper: Paper) -> Tuple[bool, List[str]]: + """Verify paper exists in multiple sources.""" + sources = [] + + # Already found in Semantic Scholar via search + sources.append("Semantic Scholar") + + # Check CrossRef if DOI available + if paper.doi: + try: + resp = requests.get( + f"https://api.crossref.org/works/{paper.doi}", + timeout=10 + ) + if resp.status_code == 200: + sources.append("CrossRef") + except: + pass + + # Check arXiv if ID available + if paper.arxiv_id: + try: + resp = requests.get( + f"http://export.arxiv.org/api/query?id_list={paper.arxiv_id}", + timeout=10 + ) + if "<entry>" in resp.text and "<title>" in resp.text: + sources.append("arXiv") + except: + pass + + return len(sources) >= 2, sources + + def get_bibtex(self, paper: Paper) -> Optional[str]: + """Get BibTeX for verified paper.""" + if paper.doi: + try: + resp = requests.get( + f"https://doi.org/{paper.doi}", + headers={"Accept": "application/x-bibtex"}, + timeout=10, + allow_redirects=True + ) + if resp.status_code == 200: + return resp.text + except: + pass + + # Fallback: generate from paper data + return self._generate_bibtex(paper) + + def _generate_bibtex(self, paper: Paper) -> str: + """Generate BibTeX from paper metadata.""" + # Generate citation key + first_author = paper.authors[0].split()[-1] if paper.authors else "unknown" + first_word = paper.title.split()[0].lower().replace(',', '').replace(':', '') + key = f"{first_author.lower()}_{paper.year}_{first_word}" + + # Format authors + authors = " and ".join(paper.authors) if paper.authors else "Unknown" + + bibtex = f"""@article{{{key}, + title = {{{paper.title}}}, + author = {{{authors}}}, + year = {{{paper.year}}}, + {'doi = {' + paper.doi + '},' if paper.doi else ''} + {'eprint = {' + paper.arxiv_id + '},' if paper.arxiv_id else ''} + {'journal = {' + paper.venue + '},' if paper.venue else ''} +}}""" + return bibtex + + def cite(self, query: str) -> Optional[str]: + """Full workflow: search, verify, return BibTeX.""" + # Search + papers = self.search(query, limit=5) + if not papers: + return None + + # Take top result + paper = papers[0] + + # Verify + verified, sources = self.verify(paper) + if not verified: + print(f"Warning: Could only verify in {sources}") + + # Get BibTeX + bibtex = self.get_bibtex(paper) + + # Cache + if bibtex: + self.verified_papers[paper.title] = paper + + return bibtex + + +# Usage example +if __name__ == "__main__": + cm = CitationManager() + + # Search and cite + bibtex = cm.cite("attention is all you need transformer") + if bibtex: + print(bibtex) +``` + +### Quick Functions + +```python +def quick_cite(query: str) -> str: + """One-liner citation.""" + cm = CitationManager() + return cm.cite(query) + +def batch_cite(queries: List[str], output_file: str = "references.bib"): + """Cite multiple papers and save to file.""" + cm = CitationManager() + bibtex_entries = [] + + for query in queries: + print(f"Processing: {query}") + bibtex = cm.cite(query) + if bibtex: + bibtex_entries.append(bibtex) + time.sleep(1) # Rate limiting + + with open(output_file, 'w') as f: + f.write("\n\n".join(bibtex_entries)) + + print(f"Saved {len(bibtex_entries)} citations to {output_file}") +``` + +--- + +## BibTeX Management + +### BibTeX vs BibLaTeX + +| Feature | BibTeX | BibLaTeX | +|---------|--------|----------| +| Unicode support | Limited | Full | +| Entry types | Standard | Extended (@online, @dataset) | +| Customization | Limited | Highly flexible | +| Backend | bibtex | Biber (recommended) | + +**Recommendation**: Use BibLaTeX with Biber for new papers. + +### LaTeX Setup + +```latex +% In preamble +\usepackage[ + backend=biber, + style=numeric, + sorting=none +]{biblatex} +\addbibresource{references.bib} + +% In document +\cite{vaswani_2017_attention} + +% At end +\printbibliography +``` + +### Citation Commands + +```latex +\cite{key} % Numeric: [1] +\citep{key} % Parenthetical: (Author, 2020) +\citet{key} % Textual: Author (2020) +\citeauthor{key} % Just author name +\citeyear{key} % Just year +``` + +### Consistent Citation Keys + +Use format: `author_year_firstword` + +``` +vaswani_2017_attention +devlin_2019_bert +brown_2020_language +``` + +--- + +## Common Citation Formats + +### Conference Paper + +```bibtex +@inproceedings{vaswani_2017_attention, + title = {Attention Is All You Need}, + author = {Vaswani, Ashish and Shazeer, Noam and Parmar, Niki and + Uszkoreit, Jakob and Jones, Llion and Gomez, Aidan N and + Kaiser, Lukasz and Polosukhin, Illia}, + booktitle = {Advances in Neural Information Processing Systems}, + volume = {30}, + year = {2017}, + publisher = {Curran Associates, Inc.} +} +``` + +### Journal Article + +```bibtex +@article{hochreiter_1997_long, + title = {Long Short-Term Memory}, + author = {Hochreiter, Sepp and Schmidhuber, J{\"u}rgen}, + journal = {Neural Computation}, + volume = {9}, + number = {8}, + pages = {1735--1780}, + year = {1997}, + publisher = {MIT Press} +} +``` + +### arXiv Preprint + +```bibtex +@misc{brown_2020_language, + title = {Language Models are Few-Shot Learners}, + author = {Brown, Tom and Mann, Benjamin and Ryder, Nick and others}, + year = {2020}, + eprint = {2005.14165}, + archiveprefix = {arXiv}, + primaryclass = {cs.CL} +} +``` + +--- + +## Troubleshooting + +### Common Issues + +**Issue: Semantic Scholar returns no results** +- Try more specific keywords +- Check spelling of author names +- Use quotation marks for exact phrases + +**Issue: DOI doesn't resolve to BibTeX** +- DOI may be registered but not linked to CrossRef +- Try arXiv ID instead if available +- Generate BibTeX from metadata manually + +**Issue: Rate limiting errors** +- Add delays between requests (1-3 seconds) +- Use API key if available +- Cache results to avoid repeat queries + +**Issue: Encoding problems in BibTeX** +- Use proper LaTeX escaping: `{\"u}` for ü +- Ensure file is UTF-8 encoded +- Use BibLaTeX with Biber for better Unicode + +### Verification Checklist + +Before adding a citation: + +- [ ] Paper found in at least 2 sources +- [ ] DOI or arXiv ID verified +- [ ] BibTeX retrieved (not generated from memory) +- [ ] Entry type correct (@inproceedings vs @article) +- [ ] Author names complete and correctly formatted +- [ ] Year and venue verified +- [ ] Citation key follows consistent format + +--- + +## Additional Resources + +**APIs:** +- Semantic Scholar: https://api.semanticscholar.org/api-docs/ +- CrossRef: https://www.crossref.org/documentation/retrieve-metadata/rest-api/ +- arXiv: https://info.arxiv.org/help/api/basics.html +- OpenAlex: https://docs.openalex.org/ + +**Python Libraries:** +- `semanticscholar`: https://pypi.org/project/semanticscholar/ +- `arxiv`: https://pypi.org/project/arxiv/ +- `habanero` (CrossRef): https://github.com/sckott/habanero + +**Verification Tools:** +- Citely: https://citely.ai/citation-checker +- ReciteWorks: https://reciteworks.com/ |
