AI for Researchers

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

2-Minute Orientation

The Series: Seven Sessions, One Arc


Today (Session 1): the mental model every later session depends on — and the two artefacts we will reuse all series, the capability/failure map and the 2026 tool landscape taxonomy.

Learning Objectives

By the End of This Session You Will Be Able To…


  1. Explain, in plain terms, how large language models predict tokens inside a context window, and why hallucination is a structural property rather than a bug.
  2. Explain how extended thinking works now that it is on by default — and what it still does not fix.
  3. Classify a given AI tool as a general chatbot, research-specific tool, or deep-research agent within the 2026 landscape.

Objectives 4–6 continue on the next slide.

Learning Objectives

…And You Will Also Be Able To


  1. Apply a capability/failure map to judge whether a specific research task is safe, unreliable, or dangerous to hand to AI.
  2. Apply systematic prompting techniques — context, role, constraints, iteration, output evaluation — to turn a weak prompt into a strong one.
  3. Evaluate an AI-generated citation for signs of hallucination using a verification method.

Section 01

Inside the Box: A Working Mental Model

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

Literacy Foundation

Start Where You Already Are


Adoption figures: Wiley ExplanAItions survey, fielded Aug 2025 — still the latest wave as of Aug 2026; publisher self-reported data [16]. Barrier figure: Ithaka S+R, self-reported survey data [17]. Peer-reviewed corroboration: [15].

Literacy Foundation

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


Literacy Foundation

Tokens: What the Model Actually Reads


Literacy Foundation

The Context Window: The Model's Working Memory


Literacy Foundation

A Big Window Is Not Perfect Recall


Literacy Foundation

Why Hallucination Is Structural


Literacy Foundation

And Why It Persists: We Grade It In


Literacy Foundation

Hallucination, Measured: The Citation Case


Literacy Foundation

Extended Thinking: No Longer a Separate Model Class


Literacy Foundation

What Extended Thinking Still Does Not Fix


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.

Series Artefact

The Capability/Failure Map for Research Tasks


Zone Typical research tasks Why it lands here Your obligation
Safedraft with it, still read it Polishing, translating and restructuring text you wrote; brainstorming search terms; explaining a concept you can check You supply the ground truth, so errors are visible to you Read every line. Disclose AI writing assistance where the journal requires it [25]
Unreliableneeds checking, every time Summarising a paper you have; first-pass title/abstract screening; drafting extraction tables; generating analysis code Evidence is mixed and task-dependent; validated applications remain rare [18] Spot-check against the source; never let AI be the only pass [18]
Dangerousdo not delegate Asking for references from memory; treating an AI synthesis as evidence; uploading confidential manuscripts or grant applications Fabrication is structural, and vendors document it in their own model cards [5] [7] [27]; funders prohibit AI in peer review [26] Retrieve citations from a database instead; keep confidential material out of these tools [26]
Zone names — Safe / Unreliable / Dangerous — are reused throughout this series. "Safe" means safe to draft with; it never means safe to skip reading. Landscape as of August 2026.

Series Artefact

Using the Map: Three Rules


Section 03

The 2026 Tool Landscape

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

Series Artefact

The 2026 Tool Landscape Taxonomy


Tier What it is Examples, August 2026 Where it fails
Tier 1General chatbots An LLM in a chat box; may search the web if asked ChatGPT (GPT-5.6), Claude (Fable 5 / Opus 5), Gemini (3.1 Pro / 3.7 Flash), Kimi (K3) Leans on memory even when search is available [7]; worst for citations [5]
Tier 2Research-specific tools Retrieval over a scholarly corpus first, generation second [19] Elicit, Consensus, Semantic Scholar, SCiNiTO, Scite, ResearchRabbit, Gemini Notebook [19] [20] [21] [22] Bounded by corpus coverage; paywalled full text often missing
Tier 3Deep-research agents Plans, browses, iterates, returns a long cited report [23] ChatGPT deep research, Gemini Deep Research [23] [24] More citations per query and a higher URL-hallucination rate [8]
Landscape as of August 2026. 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 are illustrative, not endorsements.

Series Artefact

Tier 1 vs. Tier 2: The Difference That Matters


Tier 1 — General chatbots

  • Generation first; search is bolted on, and models lean on memory even when it runs. [7]
  • Excellent at language, structure, explanation, brainstorming.
  • Its built-in "library" is text from before the knowledge cutoff. [2] [3]
  • Citations are the single worst thing to ask it for. [5] [7]

Tier 2 — Research-specific tools

  • Retrieval first: "We only use AI after we search the scientific literature." [19]
  • Built on scholarly catalogues such as Semantic Scholar and OpenAlex. [19] [21]
  • Source-grounded notebooks restrict answers to files you upload. [22]
  • Still summarise — so they still flatten nuance (Session 3).

Series Artefact

Tier 3: Deep-Research Agents


Section 04

Systematic Prompting

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

Systematic Prompting

CRIT: A Prompt Structure That Travels


Systematic Prompting

Weak Prompt → Strong Prompt


Weak

"Summarise the literature on AI adoption by researchers."

  • No field, no time window, no output shape.
  • No instruction about what to do when unsure.
  • Invites the model 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."

  • Context, role, constraints and task are all explicit.
  • Abstention is permitted, not penalised. [4]

Systematic Prompting

What the Evidence Says About Prompting


Systematic Prompting

Evaluate Every Output: The Four Checks


Live Demo & Takeaways

What We Do Next — and What You Take Home


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/abs/2509.04664 — accessed 2026-07-27
  5. Walters & Wilder (2023). Fabrication and errors in the bibliographic citations generated by ChatGPT. Scientific Reports 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/abs/2605.07723 — accessed 2026-09-02
  7. Rao & Callison-Burch (2026). BibTeX Citation Errors in Scientific Publishing Agents. COLM 2026; arXiv:2604.03159. arxiv.org/abs/2604.03159 — accessed 2026-09-02
  8. Rao, Wong & Callison-Burch (2026). Detecting and Correcting Reference Hallucinations in Commercial LLMs and Deep Research Agents. arXiv:2604.03173. arxiv.org/abs/2604.03173 — accessed 2026-09-02
  9. Liu et al. (2024). Lost in the Middle: How Language Models Use Long Contexts. TACL 12, 157–173. aclanthology.org/2024.tacl-1.9 — 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/abs/2601.07663 — accessed 2026-07-27
  12. Wei et al. (2022). Chain-of-Thought Prompting Elicits Reasoning in Large Language Models. NeurIPS 2022. arxiv.org/abs/2201.11903 — accessed 2026-07-27
  13. Schulhoff et al. (2025). The Prompt Report: A Systematic Survey of Prompting Techniques. arXiv:2406.06608. arxiv.org/abs/2406.06608 — accessed 2026-07-27
  14. Zheng, Pei, Logeswaran, Lee & Jurgens (2024). When "A Helpful Assistant" Is Not Really Helpful. Findings of EMNLP 2024, 15126–15154. aclanthology.org/2024.findings-emnlp.888 — accessed 2026-07-27
  15. Mohammadi et al. (2026). Is generative AI reshaping academic practices worldwide? Information Processing & Management 63(1), 104350. doi.org/10.1016/j.ipm.2025.104350 — accessed 2026-07-27

References

References (16–31)


  1. Wiley (2025). AI Adoption Jumps to 84% Among Researchers (ExplanAItions, wave 2; n = 2,430, fielded Aug 2025). 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). Large language models for conducting systematic reviews: on the rise, but not yet ready for use — a scoping review. J Clin Epidemiol 181, 111746. 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, Connecting ChatGPT, Claude, & Other AI Tools To Scientific Literature. researchsolutions.investorroom.com — accessed 2026-09-02