Research Discovery Setup
Help users configure automated discovery that delivers quality papers consistently.
Quick Start: The 5-Minute Setup
Most common scenario: User has a vague research interest and needs help setting up discovery.
Standard Opening
Agent: "Let's get your discovery set up! Three quick questions: 1. What research area interests you? (even if vague - we'll refine it) 2. How much time daily to review papers? (5 mins? 30 mins?) 3. Need cutting-edge research or learning fundamentals? I'll configure everything based on your answers."
After User Answers
Agent: "Perfect! Based on what you said, here's your starter configuration: **Research Focus**: [refined 1-sentence version] **Keywords**: [2-4 core search terms] **Sources**: [1-2 most relevant APIs] **Schedule**: [frequency based on time commitment] **Quality Filter**: [threshold based on volume needs] This should get you ~[X] papers [per day/week] to review. Ready to test it now?"
After Running Test Discovery
Agent: "Test results: [X] papers found Quick scan of titles: ✓ [Y] papers look highly relevant ~ [Z] papers look somewhat relevant ✗ [W] papers look off-topic Is this mix working for you? Too many? Too few? Wrong topic?"
Then: Refine based on feedback (see Refinement Patterns below)
Diagnosis: Where Is The User?
Ask These 3 Questions First
Q1: Do they know what they want to research?
- •✓ Clear idea → Skip to keyword building
- •✗ Vague idea → Question refinement needed
Q2: Have they tried searching yet?
- •✓ Yes, bad results → Diagnose what's wrong (see Troubleshooting)
- •✗ Not yet → Run initial test
Q3: How much time for review?
- •5-10 min/day → ~10-15 papers/day max
- •30 min/week → ~20-30 papers/week batch
- •1+ hour/week → ~50+ papers/week comprehensive
Conversation Patterns
Pattern 1: Vague Idea → Focused Question
User: "I'm interested in AI and finance"
Agent: "Let's narrow that down. Pick ONE direction to start:
- •Using AI to predict stock prices?
- •Using AI to analyze financial news sentiment?
- •Using AI to detect fraud?
- •Something else?
We can always expand later."
User picks one
Agent: "Great! Now let's scope it:
- •What specific data? (news? social media? earnings calls?)
- •What specific outcome? (daily predictions? risk scoring? trading signals?)
- •What timeframe? (real-time? daily? weekly?)
Example refined question: 'Can Twitter sentiment predict daily stock returns?'
Does something like that capture your interest?"
Pattern 2: Bad Results → Diagnosis
Agent: "Let's diagnose the problem. I need:
- •What keywords are you using?
- •Show me 2 papers you WANT
- •Show me 2 papers you're GETTING but don't want"
[User provides]
Agent analyzes and identifies issue:
- •Keywords too broad → Add specific terms
- •Keywords too narrow → Add synonyms, lower threshold
- •Wrong domain → Add negative keywords
- •Wrong timeframe → Add date filter
Agent: "The issue is [specific problem]. Here's the fix: [specific change].
Want me to test this now?"
Pattern 3: Optimization (Already Working)
Agent: "You've been running for [X] days. Let's optimize:
Current results:
- •[Y] papers/day on average
- •You marked [Z]% as relevant
Assessment: [Good/Too many/Too few/Wrong mix]
Recommendations: [1-2 specific tweaks]
Want to try these adjustments?"
Decision Trees
Too Many Papers (>40/day)
Check relevance: ├─ >70% relevant → Just cap max_papers to 25 ├─ 40-70% relevant → Increase threshold +0.1 └─ <40% relevant → Keywords too broad, add specific terms
Too Few Papers (<5/day)
Check specificity: ├─ Keywords very specific → Broaden terms, add synonyms ├─ Keywords normal → Lower threshold -0.1 └─ Field is just slow → Adjust schedule to weekly
Wrong Topic Papers
Check mismatch: ├─ Different domain (crypto vs stocks) → Add negative keywords ├─ Different time period (old papers) → Add date filter: last 2 years ├─ Different methodology → Add method-specific terms └─ Different language → Add language filter
Missing Key Papers
User shows example paper: 1. Look at that paper's title/abstract 2. Extract key terms it uses 3. Add those terms to search 4. Test again
Quick Reference Cards
Card 1: Question Refinement (30 seconds)
Ask 3 questions:
- •"What aspect interests you most?"
- •"Prediction? Analysis? Comparison?"
- •"Any constraints: domain/time/method?"
Result: "[Specific searchable question]"
Card 2: Keyword Building
Question → Keywords (2-step): 1. Extract core nouns from question 2. Add 1 technical synonym if they used plain language Example: Q: "Can Twitter predict stocks?" K: "twitter sentiment stock prediction"
Card 3: Source Selection
Default recommendations:
- •CS/ML/AI → arxiv + semantic_scholar
- •Medical/Bio → pubmed + biorxiv
- •General Science → openalex + crossref
- •Economics/Social → openalex + ssrn
Start with 2 sources max, add more only if missing papers.
Card 4: Threshold Settings
Default: 0.7 (works for 80% of cases) Adjustments: - User wants only best papers → 0.8 - User wants comprehensive coverage → 0.65 - Getting <5 papers/day → Lower by 0.05 - Getting >40 papers/day → Raise by 0.05
Card 5: Schedule Guide
Based on user's available time: - 10 min/day → Daily, 10-15 papers, threshold 0.75 - 30 min/3x week → Every other day, 20-30 papers, threshold 0.7 - 1 hour/week → Weekly, 50 papers, threshold 0.65
Refinement Patterns
Refinement 1: Too Much Noise
Symptom: <50% of papers are relevant
Diagnosis: Filter is too permissive OR keywords too broad
Fix:
Option A: Increase threshold (0.7 → 0.75 or 0.8) Option B: Add specific terms to keywords Option C: Remove noisy source if one is producing junk Recommendation: Try A first (fastest), then B if needed
Refinement 2: Too Little Coverage
Symptom: <10 papers/day in active field
Diagnosis: Filter too strict OR keywords too narrow
Fix:
Option A: Lower threshold (0.7 → 0.65) Option B: Add synonym terms to keywords Option C: Add another relevant source Recommendation: Try B first (maintains quality), then A
Refinement 3: Wrong Time Period
Symptom: Getting papers from 2015-2019, user wants recent
Fix:
Add date filter: published_after="2022-01-01" Or for cutting-edge: published_after="2024-01-01"
Refinement 4: Domain Mismatch
Symptom: Getting crypto papers when researching stocks
Fix:
Add negative keywords: exclude_terms = ["cryptocurrency", "bitcoin", "crypto", "blockchain"]
Troubleshooting Quick Reference
| Problem | Instant Fix |
|---|---|
| Zero results | Lower threshold to 0.6, broader keywords |
| 100+ results/day | Raise threshold to 0.8, add specific terms |
| All old papers (>3 years) | Add date filter: last 2 years |
| Papers in wrong language | Add language filter: English |
| Wrong scientific domain | Add negative keywords for that domain |
| Too many duplicates | Normal - Thoth auto-deduplicates by DOI/title |
| Missing recent papers | Add arxiv source (most current) |
| Missing published papers | Add openalex or crossref |
Advanced Scenarios
Scenario: Comprehensive Literature Review
User: "I'm writing a survey paper, need EVERYTHING"
Agent: "Comprehensive strategy:
- •Sources: ALL available (arxiv, semantic_scholar, openalex, crossref)
- •Threshold: 0.65 (permissive)
- •Schedule: Daily for 2 weeks
- •Max: 50 papers/day
You'll get 400-700 papers total. This is the 'fire hose' approach. After 2 weeks, we'll refine based on what you found.
Ready for high volume?"
Scenario: Staying Current (Minimal Time)
User: "Just want to stay current, very busy"
Agent: "Time-efficient strategy:
- •Sources: arxiv only (most current for your field)
- •Threshold: 0.8 (very strict - only best)
- •Schedule: Weekly on Monday
- •Max: 10 papers/week
One 15-minute review session per week. You'll catch major advances without daily commitment.
Sound good?"
Scenario: Learning New Field
User: "I'm new to this field, need foundational papers"
Agent: "Learning strategy:
- •Sources: openalex + semantic_scholar (broader coverage)
- •Threshold: 0.7 (balanced)
- •Date filter: 2019-present (recent but not bleeding edge)
- •Max: 20 papers/week
Mix of recent reviews and important papers. Good for building understanding.
Ready to start?"
Source-Specific Notes
ArXiv
- •Best for: CS, Physics, Math, Stats preprints
- •Freshness: Papers within days of submission
- •Peer review: Minimal (pre-publication)
- •When to use: Need cutting-edge, active research areas
Semantic Scholar
- •Best for: AI-powered semantic search
- •Freshness: Mix of preprints and published
- •Coverage: Broad, finds related papers well
- •When to use: Want discovery of unexpected connections
PubMed
- •Best for: Medical, biomedical sciences
- •Freshness: Published papers (peer-reviewed)
- •Coverage: Comprehensive for medicine
- •When to use: Medical/bio research only
OpenAlex
- •Best for: General academic research
- •Freshness: Mix of everything
- •Coverage: Most comprehensive (200M+ papers)
- •When to use: Want broad coverage across fields
Crossref
- •Best for: DOI metadata
- •Freshness: Published papers only
- •Coverage: Journal articles, conferences
- •When to use: Need published/citable papers
Testing and Validation
After Initial Setup
Agent: "I've configured your discovery. Before scheduling it, let's test: [Run discovery once] Got [X] papers. Let's review together: 1. Look at top 5 titles - relevant? 2. Any obvious misses or noise? 3. Is [X] papers manageable for you? Based on your feedback, we'll adjust before going live."
Weekly Check-In Pattern
Agent: "You've been running for a week. Quick review: **Volume**: [X] papers/day average **Your feedback**: [Y]% marked as relevant [If >70% relevant]: "This is working well! Any tweaks needed?" [If <50% relevant]: "We need to refine. The issue is likely [diagnosis]"
Summary: The Agent's Mental Model
- •Start simple: 2 sources, 0.7 threshold, reasonable schedule
- •Test immediately: Run discovery once to validate
- •Analyze results: Look at actual papers with user
- •Refine based on evidence: Adjust what's broken
- •Iterate: Test again after changes
- •Deploy when good: Set schedule and let it run
The goal: Get user from "vague idea" to "working discovery" in one conversation, with working system at the end.
Success metric: User gets relevant papers they can actually review consistently.