By Dr. Farshid Pirahansiah — computer vision & embedded edge AI consultant, Berlin, Germany · 12+ years. Updated 2026-09-19.
The New Era of Research Tools
From Passive Chat to Autonomous Research Workflows
Dr. Farshid Pirahansiah
AI & Computer Vision Engineer • pirahansiah.com
The Shift: Old vs New Research Stack
📚 The Old Way
• Manual literature reading, 10,000+ papers/year.
• Copy-paste BibTeX, broken repos, grep-the-whole-repo.
• Passive chatbot that forgets context.
• Write abstract → intro → methods (wrong order).
🤖 The New Era
• Autonomous agents sweep, reproduce, draft.
• Verifiable citation finders, zero hallucinated refs.
• Persistent memory + reusable skills.
• Paper drafted methods → abstract (evidence-first).
Tools now act, not just answer. The researcher directs; the stack executes.
The Modern Research Toolbox
🛠️ Orchestration
• Hermes Agent — terminal + skills + subagents.
• Google Opal [Experiment] — AI app builder (sign-in).
• Agent swarms (kimi.com → fan-out) for parallel sweeps.
🖼️ Insight & Illustration
• LeapSpace (Elsevier) — Deep Research + Trust Cards.
• PaperBanana — text-to-figure diagrams & charts.
• Atlas — query your own library with cited passages.
📑 Citations & KB
• Sourcely / Citely / Paperpal — find & verify refs.
• Scite — support / challenge / mention labels.
• Obsidian — your second brain, agent-editable.
Hermes ties them together: deepdive ≈ Deep Research · factcheck ≈ Trust Cards · cite ≈ citation finders · obsidian ≈ second brain.
Hermes Research Skills Catalog
8 new research skills + 8 existing — literature sweeps, critique, synthesis & citation.
| Skill | Trigger / what it does | Status |
|---|---|---|
deepdive | Deep multi-source investigation; cited synthesis with confidence + disagreement mapping | NEW |
researchgap | Finds gaps, contradictions & open problems in a topic's literature; proposes research questions | NEW |
critic | Rigorous critique of a paper/claim/argument with severity-rated weaknesses + verdict | NEW |
literature-review | Themed survey of a topic with annotated bibliography | NEW |
synthesise | Merges several sources into one attributed synthesis; flags consensus vs open questions | NEW |
factcheck | Verifies claims against sources; labels each supported/contradicted/unverifiable | NEW |
question-storm | Generates diverse, prioritized research questions across levels | NEW |
cite | Formats references in a citation style (APA/MLA/IEEE/BibTeX); finds real sources | NEW |
arxiv | Search arXiv papers by keyword/author/category | existing |
llm-wiki | Build/query interlinked markdown knowledge base | existing |
grounded-citations | Ground answers in cited verifiable sources | existing |
reference-curation | Audit/curate doc reference links | existing |
polymarket | Query Polymarket markets/prices | existing |
competitor-news-monitor | Watch companies for material news | existing |
blogwatcher | Monitor blogs/RSS feeds | existing |
research-paper-writing | Authoring structure for research papers | existing |
LeapSpace & Your Research Profile
Elsevier's research-grade AI workspace (Scopus data) — and the author record it surfaces.
🪐 LeapSpace (Elsevier)
• AI workspace powered by Scopus + Elsevier full-text.
• Deep Research reports: patterns, contradictions, evidence gaps.
• Trust Cards + Claim Radar: sources & contradictions shown.
• Writing Coach, Funding Scout, Author Search, collaborators.
👤 Farshid Pirahansiah — Scopus
• h-index 6 · 12 publications · 73 citations
• Affiliation: Center for AI Technology, Bangi, Malaysia.
• Active years: 2010–2022.
• Topics: camera calibration, robot localization, image segmentation, OCR, license-plate recognition.
• Profile generated by LeapSpace, Sun Sep 06 2026.
Hermes mapping: deepdive/literature-review ≈ Deep Research · grounded-citations/factcheck ≈ Trust Cards/Claim Radar · cite ≈ Author Search.
PaperBanana: Automating Academic Illustration
Text-to-figure AI for researchers — publication-ready diagrams & charts from a description.
🔧 What it does
• Methodology diagrams — model architectures, algorithm flows, encoders, system pipelines.
• Statistical plots — generates executable Matplotlib code from raw data (no numeric hallucination).
• Aesthetic enhancement — turns hand sketches / whiteboard notes into top-venue art.
• Styles — Transformer, GAN, RAG, Multi-Agent templates; posters & more.
🤖 How it works
• 5-agent closed loop (Planner → Visualizer → …) for faithful, precise, polished figures.
• Planner turns text into structured visual layouts.
• Visualizer renders via Nano-Banana-Pro — exact shapes, connectors, icons.
• Trusted by SNU, Stanford, UC Berkeley, CMU, Tsinghua, SJTU, Yonsei, IIT Madras, Monash, Broad Institute.
Example: prompt "encoder–decoder segmentation pipeline with skip connections" → ready architecture diagram in seconds. Reference: paper-banana.org
Best Reference Finder — AI Citation Tools
Dedicated finders query Crossref / Semantic Scholar — no hallucinated refs like chatbots.
| Tool | Best for | Standout | Styles |
|---|---|---|---|
| Sourcely | Bulk / paragraph | Scans essays, highlights text needing support, summaries | 700+ (BibTeX, RIS) |
| Citely AI | Claim verification | Paste claim → matched to verified DOIs | APA, MLA |
| Grammarly | In-line writing | Flags missing sources in editor, inserts citations | APA, MLA, Chicago |
| Paperpal | MS Word flow | 250M+ articles, search by title/DOI | 10,000+ |
| SciSpace | Partial metadata | Broken URL/author → complete citation | BibTeX, RIS, CSV |
| Writeless | PDF uploads | Filter by min year, inline insertion | APA, MLA, Harvard… |
Beyond find: Scite labels citations support/challenge/mention · Google Scholar (free, manual) · Consensus (Consensus Meter) · manage with Zotero / Mendeley / MyBib. Hermes: cite formats, factcheck verifies, grounded-citations grounds.
How to Write a Paper — Write in This Order
Draft bottom-up: build the evidence first, then frame it. Read top-down.
- 1 · Methods — Lock the protocol, setup, datasets & metrics. The foundation everything cites.
- 2 · Results — Report what happened, raw: numbers, curves, observed behaviour.
- 3 · Figures — Build the visuals: plots, diagrams, architecture art. One idea each.
- 4 · Tables — Assemble comparison/benchmark tables; numbers must match figures.
- 5 · Discussion — Interpret: why it works, limits, implications, relation to prior work.
- 6 · Introduction — Open with the gap & motivation; now you know what you proved.
- 7 · Abstract — Written last: the 200-word distillation of the finished paper.
Hermes: researchgap scopes the gap · critic stress-tests claims · cite formats refs · research-paper-writing structures the draft.
Agent Swarms: Parallel Research at Scale
One orchestrator fans out to many specialized workers, then merges results.
🐝 How a swarm runs
• Orchestrator splits the task into independent sub-goals.
• Swarm = N parallel subagents, each with its own context & tools.
• Merge: results aggregated, deduplicated, cross-checked.
• Hermes: delegate_task spawns concurrent workers (no shared context bloat).
🌊 Example: kimi.com → swarm
1. kimi.com receives the research question (e.g. "compare 2025 VLM agents").
2. → swarm: fans out to subagents — ArXiv sweep, benchmark mining, repo cloning.
3. → …: each worker returns findings; orchestrator synthesizes one report + BibTeX.
• Same pattern in Hermes: 3 delegate_task calls → one literature matrix.
Why: 10× speedup vs serial search, isolated failures, no single context overflow. Pair with synthesise + critic.
Academic Peer-Review Loop
From submission to camera-ready — and how Hermes shortens each cycle.
📤 Submit
• Format to venue template (IEEE/ACM).
• grounded-citations checks every claim links to a real source.
• cite exports clean BibTeX/references.
🔍 Review
• Editors assign 2–3 anonymous reviewers.
• critic pre-empts weaknesses before submission.
• factcheck flags unsupported claims.
✏️ Revise
• Address each point (accept / rebut).
• deepdive gathers new evidence for gaps.
• synthesise merges reviewer feedback.
Loop repeats per round (R1 → R2 → …) until accept; then camera-ready + research-paper-writing polish. Average: 2–4 months per round.
Second Brain: Obsidian × Hermes
Turn your notes into a queryable, agent-editable knowledge base.
🧠 Connect Obsidian
• Vault = plain markdown; Hermes reads/writes via the obsidian skill.
• Path from OBSIDIAN_VAULT_PATH or ~/Documents/Obsidian Vault.
• Use [[wikilinks]] + YAML frontmatter (tags, aliases) for structure.
• Two-way sync: edit in Obsidian, Hermes sees it next turn.
🔌 Hermes skills for your vault
• obsidian — search, read, create, edit notes & wikilinks.
• llm-wiki — build interlinked markdown KB.
• synthesise — merge notes into one.
• cite — attach BibTeX to literature notes.
• factcheck / grounded-citations — verify before saving.
Flow: capture → Hermes tags & links → query with search_files → surface in deepdive / literature-review. Your second brain, always current.
Google Opal Experiment
Google's experimental AI app platform — verified facts only; function not yet documented publicly.
🔎 What is confirmed
• Official Google product labelled "Opal [Experiment]".
• Web app (opal.google) loading in a sandboxed iframe.
• Requires Google sign-in (OAuth) to use.
• Requests camera & microphone permissions.
❓ Not yet public
• Exact purpose / feature set is not in the page source.
• Positioned in Google's "experiments" track (like Labs).
• Likely an AI app-/agent-building surface — unconfirmed.
• Check opal.google after sign-in for live capability.
Hermes angle: if Opal is an app/agent builder, it parallels skill_manage (custom skills) & delegate_task (subagents) — but treat as speculation until docs ship.
The New Research Stack
✔ Act, don't just answer: agents sweep, reproduce, draft & verify.
✔ Verifiable by default: citation finders & Trust Cards kill hallucinated refs.
✔ Evidence-first writing: methods → results → figures → tables → discussion → intro → abstract.
✔ Parallel & persistent: swarms via delegate_task, memory + Obsidian second brain.
Explore the tooling & code: pirahansiah.com
Validated Skills Library installed & scanned
All installed via hermes skills install, security-scanned, and verified (valid SKILL.md, enabled).
Web & Research
agent-reach · youtube-full · defuddle · resemble-detect
Build & Engineering
using-agent-skills · setup-matt-pocock-skills · make-interfaces-feel-better · humanizer
Agents & Ops
browser-harness · i-have-adhd · loopy · loop-library · skillclaw
Command Cheat Sheet DESK · CLI · MSG · SHELL
Everyday commands — Desktop, CLI chat, messaging, shell. (Verified vs current Hermes source, Sep 2026.)
Sessions & Context
/new · /resume · /sessions · /title · /branch · /compress · /context · /status
Control Work
/queue · /steer · /bg · /btw · /agents · /stop
Goals, Loops & Plans
/goal · /subgoal · /heartbeat · /loop · /plan · /review · /refine
Models & Behavior
/model · /moa · /personality · /reasoning · /fast · /approvals · /yolo · /busy · /voice
Skills, Memory & Tools
/skills · /learn · /memory · /init · /tools · /browser
Automation & Coord
/cron · /suggestions · /blueprint · /kanban
Inspect, Recover & Fix
/retry · /undo · /save · /diff · /rollback · /usage · /debug · /help
Messaging / Gateway
/sethome · /topic · /commands · /approve · /deny · /pause · /platform · /restart
Terminal Essentials
hermes / hermes chat · -z "prompt" · model · status · doctor · gateway status · --safe-mode · update
Thank You & Discussion
The New Era of Research Tools
All Presentations • GitHub Repositories
Source: Pirahansiah, F. “The New Era of Research Tools”. pirahansiah.com, updated 2026-09-19. Canonical URL https://pirahansiah.com/farshid/content/presentation-research-tools/ · markdown source presentation-research-tools.md · how to cite, quote and link this site.