AI for Researchers · Visual Deck

Session 1: AI Foundations for Researchers

How large language models work, where they fail, and how to tell the difference

{{Presenter Name}}

Landscape as of August 2026

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2-Minute Orientation

Seven Sessions, One Arc


flowchart LR
  s1(["1 · Foundations
today"]):::today --> s2(["2 · Literature
discovery"]):::next s2 --> s3(["3 · Reading
& notes"]):::rest s3 --> s4(["4 · Writing
& integrity"]):::rest s4 --> s5(["5 · Data
& code"]):::rest s5 --> s6(["6 · Multi-
disciplinary"]):::rest s6 --> s7(["7 · Discipline
deep-dives"]):::rest classDef today fill:#ab7d22,stroke:#d9b36c,color:#14132b,font-size:19px classDef next fill:#23204c,stroke:#d9b36c,color:#eceaf8,font-size:19px classDef rest fill:#23204c,stroke:#8f8cb8,color:#b9b7d6,font-size:19px

~20 min foundation · ~25 min live demo · ~15 min Q&A — every session.
Today builds the two artefacts the whole series reuses: the capability/failure map and the 2026 tool taxonomy.

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Learning Objectives

By the End of This Session…


1Explain the machine — tokens, the context window, structural hallucinationnot a bug to be patched: a property to be managed
2Explain extended thinking, now that it is on by defaultand what it still does not fix
3Classify any AI tool in the 2026 landscapegeneral chatbot · research-specific tool · deep-research agent

Objectives 4–6 next · full verbatim wording in the reference deck and curriculum

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Learning Objectives

…And You Will Also Be Able To


4Judge any research task with the capability/failure mapsafe · unreliable · dangerous
5Turn a weak prompt into a strong one with CRITcontext · role · instructions · task — then iterate
6Catch a fabricated citation with a verification methoddemonstrated live in today's demo

Full verbatim wording in the reference deck and curriculum

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Section 01

Inside the Box

What the machine is actually doing when it answers your research question — and why that explains almost every failure you will meet.

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Literacy Foundation

Start Where You Already Are


80% vs 25%reach for a general chatbot vs an AI research assistant [16]
74%call inaccuracy a major barrier — the top concern in every survey [15] [17]

Wiley ExplanAItions, fielded Aug 2025 (latest wave; vendor self-reported) [16] · peer-reviewed corroboration [15]

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Literacy Foundation

It Predicts the Next Token. That Is the Whole Trick.


flowchart LR
  P["“The study was published by …”
your prompt, as tokens"]:::prompt --> M(["statistical patterns"]):::model M -- "p = .41" --> A["Smith ▊"]:::top M -- "p = .22" --> B["Gorman ▊"]:::mid M -- "p = .04 · long tail…" --> C["Nguyen ▊"]:::low classDef prompt fill:#23204c,stroke:#8f8cb8,color:#eceaf8,font-size:19px classDef model fill:#1c1a3f,stroke:#d9b36c,color:#d9b36c,font-size:19px classDef top fill:#23204c,stroke:#d9b36c,color:#d9b36c,font-size:20px classDef mid fill:#23204c,stroke:#8f8cb8,color:#b9b7d6,font-size:20px classDef low fill:#23204c,stroke:#55527e,color:#8f8cb8,font-size:20px
no database of facts — nothing is looked up
fluency and truth are separate properties; the model optimises fluency
a real citation and a fabricated one exit the identical process [4]
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Literacy Foundation

Tokens: What the Model Actually Reads


"Comparative genomics of penguins" —

Comparative␣genomics␣of␣penguins = 5 tokens
≈ ¾ word1 token ≈ 4 characters; 100 tokens ≈ 75 words [1]
≈ 20,000tokens in "my 40-page PDF" — everything is counted and priced in tokens, never pages
~30%more tokens for the same text on a newer tokenizer [2]
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Literacy Foundation

The Context Window: Working Memory, Not the World


the window — frontier models advertise 1,000,000 tokens [2] [3]
your prompt
your files
hidden "thinking"
on by default [2] [10]
its own output so far

outside the window: your other chats · yesterday's upload · the rest of the literature —
it exists only if the product deliberately re-injects it (saved memory, project files)

separate limit: reliable knowledge can end months before today's date [2] [3]

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Literacy Foundation

A Big Window Is Not Perfect Recall


Put what matters at the top or bottom — and five well-chosen papers beat fifty dumped in. Measured on the 2023-era cohort [9]; no current-generation replication, so assume it still applies.

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Literacy Foundation

Why Hallucination Is Structural


flowchart TB
  M(("statistical patterns
of plausible text")):::model --> R["Gorman et al. (2014)
real"]:::real M --> F["Sørensen et al. (2019)
invented — same font, same confidence"]:::fake classDef model fill:#23204c,stroke:#8f8cb8,color:#eceaf8,font-size:19px classDef real fill:#1c1a3f,stroke:#2fae74,color:#7fd6a4,font-size:19px classDef fake fill:#1c1a3f,stroke:#c14b58,color:#ef9a9a,font-size:19px
+11% / +6%Opus 5 card: "accuracy is 11% higher than Opus 4.8, but its rate of hallucinations is also 6% higher" — vendors document the tradeoff themselves [27]
−27.7 ptscitation accuracy, popular → recent papers: the rarer the fact, the worse it gets [7]

Confident, well-formed and wrong is the expected failure mode — not an anomaly [4]

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Literacy Foundation

And Why It Persists: We Grade It In


how most benchmarks score an uncertain model [4]

"I don't know"0 points
a confident guesssometimes 1

models are "optimized to be good test-takers" — guessing raises the score

What you can do today: give the model explicit permission to abstain, in your prompt [4]

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Literacy Foundation

Hallucination, Measured: The Citation Case


50.9%of frontier-model BibTeX entries fully correct — with web search on (2026) [7]
3–13%of deep-research agents' citation URLs hallucinated; 5–18% non-resolving [8]
~146,932hallucinated citations estimated in the 2025 literature, from an audit of 111M references [6]
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Literacy Foundation

Extended Thinking: A Dial, Not a Model Choice


flowchart LR
  P["your prompt"]:::io --> T["hidden thinking tokens
─ effort dial: minimal ⟶ max ─"]:::think --> A["answer"]:::hot classDef io fill:#23204c,stroke:#8f8cb8,color:#eceaf8,font-size:20px classDef think fill:#1c1a3f,stroke:#8f8cb8,color:#b9b7d6,stroke-dasharray:6 6,font-size:20px classDef hot fill:#23204c,stroke:#d9b36c,color:#d9b36c,font-size:20px
collapsedthe standard-vs-reasoning split is gone — thinking is spent by default [2] [10]; Fable 5: "Adaptive thinking is always on" [2]
a dial nowChatGPT gives Plus/Pro an effort slider; Gemini exposes minimal→high [29] [3] · ancestor: chain-of-thought prompting, 2022 [12]
cost unchangedthinking tokens are billed as output and eat your context window [10]
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Literacy Foundation

What Extended Thinking Still Does Not Fix


still trueA careful wrong answer is still wrongthe statistical origin of hallucination is untouched [4] [27]
still trueYou cannot audit the thinkingraw chains of thought are hidden or summarised [2]; models "often deny intending to use" hints they used [11]
still trueThinking is not groundingnothing was retrieved unless a tool actually retrieved it

Raise the dial for hard multi-step work; verify facts exactly as before.

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Section 02

The Capability/Failure Map

One table you can hold in your head: which research tasks are safe to hand to AI, which are unreliable, and which are simply dangerous.

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Series Artefact

The Capability/Failure Map for Research Tasks


Safedraft with it, still read it
polish & translate your own text · brainstorm search terms · explain what you can check
Read every line. Disclose where required [25]
Unreliableneeds checking, every time
summarise a paper · first-pass screening · extraction tables · analysis code
Spot-check the source. Never the only pass [18]
Dangerousdo not delegate
references from memory · AI synthesis as evidence · uploading confidential material
Use a database instead. Funders ban AI peer review [26]

"Safe" means safe to draft with — never safe to skip reading. Fabrication is structural; vendors document it in their own cards [5] [7] [27]

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Series Artefact

Using the Map: Three Rules


Rule 1Could you catch the error?if you could not spot it, the task is not in the Safe zone
Rule 2Rarity moves tasks rightwardthe more specific and recent the fact, the worse the accuracy [7]
Rule 3Grounding changes the zone, not the obligationretrieval cuts fabrication but does not remove it [7] [8]
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Section 03

The 2026 Tool Landscape

Three tiers, one question: before you type anything, know which kind of tool you have just opened.

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Series Artefact

The 2026 Tool Landscape Taxonomy


Tier 1 · General chatbots
an LLM in a chat box; leans on memory even when search runs [7] — worst thing to ask for: citations [5]
ChatGPT (GPT-5.6) · Claude (Fable 5 / Opus 5) · Gemini (3.1 Pro / 3.7 Flash) · Kimi (K3)
Tier 2 · Research-specific
retrieval over a scholarly corpus first, generation second [19]; bounded by corpus coverage
Elicit · Consensus · Semantic Scholar · SCiNiTO · Scite · Gemini Notebook
Tier 3 · Deep-research agents
plans, browses, iterates, returns a long cited report [23]; more citations, higher URL-hallucination rate [8]
ChatGPT deep research · Gemini Deep Research

One caveat: Tier-2 tools such as Consensus and Scite now ship MCP servers, so a Tier-1 chatbot can call them directly [30] [31] — read the tiers as what you are reaching for, not walls. Examples illustrative, not endorsements.

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Series Artefact

The Difference That Matters: Which Comes First?


Tier 1 — generate first

flowchart LR
  G["GENERATE"]:::hot --> S["search
(bolted on, maybe)"]:::ghost classDef hot fill:#23204c,stroke:#d9b36c,color:#d9b36c,font-size:20px classDef ghost fill:#1c1a3f,stroke:#55527e,color:#8f8cb8,stroke-dasharray:6 6,font-size:19px

leans on memory even when search runs [7] · its library ends at the knowledge cutoff [2] [3] · excellent at language, structure, brainstorming

Tier 2 — retrieve first

flowchart LR
  S2["SEARCH
scholarly corpus"]:::safe --> G2["generate"]:::norm classDef safe fill:#1c1a3f,stroke:#2fae74,color:#7fd6a4,font-size:20px classDef norm fill:#23204c,stroke:#8f8cb8,color:#eceaf8,font-size:20px

"We only use AI after we search the scientific literature" [19] · built on Semantic Scholar, OpenAlex [19] [21] · still summarises — still flattens nuance (Session 3)

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Series Artefact

Tier 3: Deep-Research Agents


flowchart LR
  P["plan"]:::n --> S["search"]:::n --> R["read"]:::n --> I["iterate…"]:::n
  I --> S
  I --> REP["cited report
minutes, not seconds"]:::hot classDef n fill:#23204c,stroke:#8f8cb8,color:#eceaf8,font-size:19px classDef hot fill:#1c1a3f,stroke:#d9b36c,color:#d9b36c,font-size:19px

More citations per query — and worse odds each [8]. Some let you edit the plan before it runs [23]. Treat the report as a well-organised lead list, never a verified synthesis.

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Section 04

Systematic Prompting

Not magic words — a repeatable structure, an iteration habit, and a routine for evaluating what comes back.

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Systematic Prompting

CRIT: A Prompt Structure That Travels


CContextyour field, your question, the material you are supplying
RRole & registerwho the output is for, how it should read
IInstructions & constraintsformat, length, scope — and what to do when unsure
TTaskone specific request, plus how you will check the result

Then iterate: a prompt is a first draft, not an incantation.

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Systematic Prompting

Weak Prompt → Strong Prompt


Weak

"Summarise the literature on AI adoption by researchers."

no field · no window · no shape · nothing about being unsure — an invitation to invent references [5]

Strong (CRIT)

"I study scholarly communication and have attached three survey papers. Writing for a departmental seminar audience, use only the attached papers — if a figure is not in them, say so rather than estimating. Produce a 200-word synthesis with a page reference for every claim."

abstention is permitted, not penalised [4]

— Context  ·  — Role & register  ·  — Instructions & constraints  ·  — Task

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Systematic Prompting

What the Evidence Says About Prompting


retired"Think step by step"huge gains in 2022 [12] — built-in by default now, save the instruction [2]
oversoldPersonas162 personas × 2,410 questions: no accuracy gain [14] — set register with roles, not correctness
highest valuePermission to say "I don't know"the single instruction that most reduces invented answers [4]

Prompting is a documented literature — 58 techniques catalogued [13]. Context, constraints and retrieval buy correctness.

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Systematic Prompting

Evaluate Every Output: The Four Checks


flowchart LR
  A["1 · Grounding
where did this come from?
nothing retrieved = nothing checked"]:::n --> B["2 · Citations
does every reference resolve
to a record you can open?"]:::n --> C["3 · Claim-to-source
does the source say
what the output claims?"]:::n --> D["4 · Omission
what was left out?
summaries lose caveats first"]:::n classDef n fill:#23204c,stroke:#d9b36c,color:#eceaf8,font-size:19px

Checks 2–4: [5] [7] [6] [18] — a real link can still carry a false claim; open the record, don't trust the format.

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Live Demo & Takeaways

What We Do Next — and What You Take Home


AOne question, asked naively and then with CRITtwo tools, side by side
BA citation trap, set live — then the checks, whatever the model doesrefusal, real references, or fabrication: the checks are the lesson [5] [7]
You leave with: CRIT · the map · the taxonomy · a hallucination checklistnext session: literature discovery — Tier 2 against Tier 3, head to head
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References

References (1–15)


  1. OpenAI (2026). What are tokens and how to count them?help.openai.com — accessed 2026-07-27
  2. Anthropic (2026). Models overview & Fable 5 model docs. Claude Platform Docs.platform.claude.com — accessed 2026-09-02
  3. Google (2026). Gemini 3 Developer Guide. Gemini API.ai.google.dev — accessed 2026-07-27
  4. Kalai, Nachum, Vempala & Zhang (2025). Why Language Models Hallucinate. arXiv:2509.04664.arxiv.org — accessed 2026-07-27
  5. Walters & Wilder (2023). Fabrication and errors in the bibliographic citations generated by ChatGPT. Sci Rep 13, 14045.doi.org/10.1038/s41598-023-41032-5 — accessed 2026-07-27
  6. Zhao et al. (2026). LLM hallucinations in the wild. arXiv:2605.07723.arxiv.org — accessed 2026-09-02
  7. Rao & Callison-Burch (2026). BibTeX Citation Errors in Scientific Publishing Agents. COLM 2026.arxiv.org/abs/2604.03159 — accessed 2026-09-02
  8. Rao et al. (2026). Detecting and Correcting Reference Hallucinations in Commercial LLMs and Deep Research Agents. arXiv:2604.03173.arxiv.org — accessed 2026-09-02
  9. Liu et al. (2024). Lost in the Middle: How Language Models Use Long Contexts. TACL 12.aclanthology.org — accessed 2026-07-27
  10. OpenAI (2026). Reasoning models. OpenAI API guide.developers.openai.com — accessed 2026-07-27
  11. Walden & Wanner (2026). Reasoning Models Will Sometimes Lie About Their Reasoning. arXiv:2601.07663.arxiv.org — accessed 2026-07-27
  12. Wei et al. (2022). Chain-of-Thought Prompting Elicits Reasoning in Large Language Models. NeurIPS 2022.arxiv.org — accessed 2026-07-27
  13. Schulhoff et al. (2025). The Prompt Report: A Systematic Survey of Prompting Techniques. arXiv:2406.06608.arxiv.org — accessed 2026-07-27
  14. Zheng et al. (2024). When "A Helpful Assistant" Is Not Really Helpful. Findings of EMNLP 2024.aclanthology.org — accessed 2026-07-27
  15. Mohammadi et al. (2026). Is generative AI reshaping academic practices worldwide? IP&M 63(1).doi.org — accessed 2026-07-27
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References

References (16–31)


  1. Wiley (2025). AI Adoption Jumps to 84% Among Researchers (ExplanAItions wave 2; n = 2,430).newsroom.wiley.com — accessed 2026-07-27; still latest wave 2026-09-02
  2. Ruediger, McCracken & Skinner (2024). Adoption of Generative AI by Academic Biomedical Researchers. Ithaka S+R.sr.ithaka.org — accessed 2026-07-27
  3. Lieberum et al. (2025). LLMs for conducting systematic reviews: on the rise, but not yet ready for use. J Clin Epidemiol 181.jclinepi.com — accessed 2026-07-27
  4. Consensus (2025). Welcome to Consensus.consensus.app — accessed 2026-07-27
  5. Elicit (2026). Elicit: AI for scientific research.elicit.com — accessed 2026-07-27
  6. SCiNiTO (2026). What is SCiNiTO?scinito.ai — accessed 2026-07-27
  7. Google (2026). Gemini Notebook (formerly NotebookLM).notebooklm.google — accessed 2026-07-27
  8. Google (2026). Gemini Deep Research Agent. Gemini API.ai.google.dev — accessed 2026-07-27
  9. OpenAI (2025). Introducing deep research.openai.com — accessed 2026-07-27
  10. ICMJE (2025). Defining the Role of Authors and Contributors, §4 AI-Assisted Technology.icmje.org — accessed 2026-07-27
  11. NIH (2023). Generative AI Prohibited for the NIH Peer Review Process (NOT-OD-23-149).grants.nih.gov — accessed 2026-07-27
  12. Anthropic (2026). System Card: Claude Opus 5.anthropic.com — accessed 2026-09-02
  13. Anthropic (2026). System Card: Claude Fable 5 & Claude Mythos 5.anthropic.com — accessed 2026-09-02
  14. OpenAI (2026). GPT-5.6 August update. Deployment Safety Hub.deploymentsafety.openai.com — accessed 2026-09-02
  15. Consensus (2026). Consensus MCP server. Developer docs.docs.consensus.app — accessed 2026-09-02
  16. Research Solutions (2026). Research Solutions Launches Scite MCP. Press release.researchsolutions.investorroom.com — accessed 2026-09-02