AI for EE Research

From Researcher to Orchestrator

A hands-on guide to using AI tools and agents for everyday research in electrical engineering and computer design

AI for EE Research — dmccreary.github.io/ai-for-ee-research

The Problem: Research Is a Pipeline

  • Literature search
  • Data analysis
  • Brainstorming and problem framing
  • Scientific coding and simulation
  • Manuscript preparation

AI can now absorb a large share of each stage, but only for researchers who know how to direct it, check it, and own the result.

AI for EE Research — dmccreary.github.io/ai-for-ee-research
poster

The Big Idea: Researcher as Orchestrator

  • Stop doing every task personally
  • Coordinate ~20 planning agents and ~10 execution agents
  • You set direction, supply domain judgment, resolve conflicts, and decide what is true
  • You stay accountable for the science
AI for EE Research — dmccreary.github.io/ai-for-ee-research

Who It Is For

Audience: MS and PhD students, postdocs, and faculty in EE, computer engineering, and computer design

Prerequisites

  • Graduate standing or equivalent research experience
  • One programming language, preferably Python
  • Command line, text editor, and Git basics
  • No prior ML, prompt engineering, or agent experience
AI for EE Research — dmccreary.github.io/ai-for-ee-research

How the Book Is Organized

Part Chapters Theme
1. Foundations 1–4 Workflows, how LLMs work, prompts, context
2. Memory and skills 5–7 Markdown, Git, knowledge graphs, skills
3. Agents and teams 8–10 Tools, supervision, orchestration
4. Research tasks 11–15 Literature, data, code, ideas, manuscripts
5. Communicate and trust 16–20 MicroSims, verification, ethics, agents, capstone
AI for EE Research — dmccreary.github.io/ai-for-ee-research

Foundations: How Language Models Work

Chapters 2–3

  • Text becomes tokens; the context window is a shared budget
  • Models optimize plausibility, not truth, so fluent answers can be false
  • Fabricated citations come from this, not from a bug
  • Choose models by capability, cost, latency, privacy, and reproducibility
  • A prompt is a specification: instructions, constraints, roles, examples
AI for EE Research — dmccreary.github.io/ai-for-ee-research
poster

Context Engineering

Chapter 4

  • Decide everything the model sees
  • Task spec: goal, inputs, outputs, constraints, definition of done
  • Ground answers in sources
  • Chain prompts with checks between steps
  • Defend against prompt injection
AI for EE Research — dmccreary.github.io/ai-for-ee-research
poster

Memory: Markdown, Git, and Knowledge Graphs

Chapters 5–6

  • Markdown is readable by both humans and agents
  • AGENTS.md / CLAUDE.md hold goals, conventions, constraints
  • Git gives history and recovery
  • A personal knowledge graph links notes, papers, experiments, and people as queryable entities
AI for EE Research — dmccreary.github.io/ai-for-ee-research
poster

Agent Skills: Repeatable Tasks as Commands

Chapters 6–7

  • Anatomy: name, description, instructions, supporting files
  • One-sentence scope; single-purpose skills
  • Progressive disclosure keeps context small
  • Test that it fires, stays quiet, and gives known answers
  • Version, share, and maintain
AI for EE Research — dmccreary.github.io/ai-for-ee-research
poster

Agents, Tools, and Subagents

Chapter 8

  • Agent = model + tools + loop
  • Decide, call a tool, observe, repeat
  • File access, shell, code execution, MCP
  • Sandboxing and permissions set the limits
  • Subagents run in parallel with isolated context
AI for EE Research — dmccreary.github.io/ai-for-ee-research
poster

Supervising Agents and Assigning Roles

Chapter 9

  • Autonomy is a dial set per task
  • Set it by reversibility, reach, and verifiability
  • Log everything; bound cost and runtime
  • Know the failure modes: premature completion, scope drift, test weakening, runaway loops
  • Roles: planner, executor, reviewer, researcher, coder, writer
AI for EE Research — dmccreary.github.io/ai-for-ee-research

Orchestrating Agent Teams

Chapter 10

  • Break work into tasks with owners, outputs, and checks
  • Dependencies set the critical path, and parallelism cannot shorten it
  • Handoffs through files and a shared workspace
  • Review checkpoints and human approval gates
  • Scaling stops paying off when review cost exceeds the work saved
AI for EE Research — dmccreary.github.io/ai-for-ee-research
poster

Literature Search and Synthesis

Chapter 11

  • Write a repeatable search strategy
  • Favor recall when scoping, then triage for precision
  • Chain citations forward and backward
  • Verify every citation against the source
  • Tie claims to locations in sources
AI for EE Research — dmccreary.github.io/ai-for-ee-research
poster

Data Analysis, Simulation, and Code

Chapters 12–13

  • Record measurement settings; keep raw data read-only
  • Cleaning is a logged script; outliers are information
  • Silent errors run cleanly and return wrong numbers
  • Test with known answers
  • Apply numerical sanity checks and pin environments
AI for EE Research — dmccreary.github.io/ai-for-ee-research
poster

Brainstorming and Manuscripts

Chapters 14–15

  • AI offers volume and range; its weakness is agreement
  • Use a devil's advocate prompt and check analogies
  • Move from hunch to falsifiable hypothesis
  • Draft from evidenced claims; abstract last
  • Protect your voice and your numbers
AI for EE Research — dmccreary.github.io/ai-for-ee-research
poster

MicroSims: Communicating by Interaction

Chapter 16

  • Match the medium to the point
  • A static figure shows a fact; an interactive shows a dependence
  • A MicroSim is small, single-concept, embeddable
  • Built with p5.js and built-in controls
  • Specify precisely, then check what the agent builds
AI for EE Research — dmccreary.github.io/ai-for-ee-research
poster

Verification and Reproducibility

Chapter 17

  • Verification: done right? Validation: the right work?
  • Independent checks with different failure causes
  • Primary-source and cross-model checks
  • Fix success criteria before seeing the result
  • Audit trails and reproducibility packages
AI for EE Research — dmccreary.github.io/ai-for-ee-research
poster

Responsible and Ethical Use

Chapter 18

  • Accountability cannot be delegated; AI is not an author
  • Disclose AI use per venue and institutional policy
  • Protect confidential data, participant data, and unpublished results
  • Respect licensing and intellectual property
  • Check for bias; keep your own skills sharp
AI for EE Research — dmccreary.github.io/ai-for-ee-research
poster

Personal Agents and Case Studies

Chapters 19–20

  • Always-on agents (Grok Bot, Dots, Muse, Claude Cowork, OpenClaw, Hermes Agent)
  • Judge them by criteria, not brands: where they run, what they reach, cost, data
  • Real cases, including failures: the MicroSims arXiv paper, this textbook's skill pipeline
  • Capstone: an end-to-end task with an agent team, plus an adoption plan
AI for EE Research — dmccreary.github.io/ai-for-ee-research

Key Takeaways

  • Direct, check, and own — the researcher stays accountable
  • Context and memory make agents reliable: Markdown, Git, knowledge graphs, skills
  • Autonomy is a dial set per task, bounded by logs and review
  • Verify independently; disclose AI use
  • Start small, then adopt in order

Read the book: dmccreary.github.io/ai-for-ee-research

AI for EE Research — dmccreary.github.io/ai-for-ee-research

Welcome. This deck is a 20-slide tour of the whole book: the central idea, how the 20 chapters are organized, and what a reader can do after finishing. Each slide maps to one or two chapters. Speaker notes carry the detail.

Chapter 1. Graduate research in EE and computer design is a chain of repeatable tasks with checkable outputs. The pipeline is only as trustworthy as its weakest stage. AI absorbs much of the procedural layer; what it cannot supply is the question, the domain judgment, and the accountability.

The 20:10 ratio reflects that plans are cheap to discard while executions are expensive to check. The number of agents matters least; dependencies, review cost, and handoff quality set what the team can deliver (Chapter 10).

The course deliberately does not cover training LLMs, ML theory, AI chip design, vendor EDA flows, or legal advice. It assumes students bring their own EE domain knowledge and teaches how to direct AI at it.

Every chapter ships with annotated references and a quiz. The book also has a glossary of 379 terms, a learning graph with 379 concepts, 48 interactive MicroSims, 20 infographic posters, and two appendices (Personal Agents and Personal Knowledge Graphs).

Chapter 2 explains tokens, context windows, training data, knowledge cutoffs, and hallucination. Chapter 3 turns that into choices: API access (keys are secrets), cost and rate limits, when a local open-weight model is the right answer, and the first prompting techniques.

Reliability comes less from clever wording than from complete specification, selected and grounded context, checks between steps, and tested, versioned prompts. Defining domain vocabulary (resolution, gain, noise) prevents silent misreadings.

An agent is only as reliable as the project it works in. Plain text, a short checkable instruction file, a predictable layout, and version history give memory, boundaries, and recovery. A knowledge graph with typed links can be queried to ground an agent's answers; Appendix B covers building one.

A skill is worth the effort when a task recurs and the result can be checked. Chapter 7 covers trigger tests including near misses, behavior tests with known answers, evaluation of pass rate across repeated runs, and a research skill template.

An agent's power and its risk are the same quantity: what its tools can reach. Early errors compound across loop iterations, so version control is the safety net. Setting limits is what lets you use agents with confidence.

Supervision is the design of where a human looks. Each failure mode has a mechanical defense. Roles make a group of agents legible.

Orchestration is the design of how work, checks, and decisions flow so that your attention prevents the most damage. Span of control and review load limit the useful team size; the MicroSims on critical path and review load let students experiment with both.

AI changes the speed of every stage of the literature workflow and none of the standards. A fluent fake citation looks identical to a real one, so verification is a required step, not an optional one.

Example from Chapter 13: a 10 versus 20 log10 mistake turned a 10-bit converter into an 18-bit one. Code from an agent is a hypothesis about how to compute a result; the chapter is how you test that hypothesis.

Chapter 14 separates divergent and convergent idea phases and ranks ideas in a table with assumptions and failure conditions. Chapter 15 follows a paper from outline through LaTeX, figures, references, venue rules, and arXiv submission. Argument-bearing sections stay human-written.

This book contains 48 MicroSims that students use to sort, predict, calculate, and judge. Chapter 16 shows how to generate one from a precise specification, and the same approach extends to intelligent textbooks and slide decks like this one.

Agreement between models is weak evidence; disagreement is a flag. Verification is not a final stage but a habit that runs through the whole workflow. AI raises the volume of output and adds failure modes that sound plausible, so every check matters more.

Unpublished results pasted into a hosted tool are disclosed to a third party. Keep a log as you work so the disclosure statement is accurate. The chapter ends with drafting a responsible-use policy for a research group.

Products change monthly, so Chapter 19 teaches durable criteria: blast radius, usage metering, data exposure, vendor-claim verification, and overnight activity audits. Chapter 20 applies the whole toolkit; each case records cause, detection, control, and change for what failed.

Close by pointing to the quizzes, MicroSims, and posters for self-study, and to the capstone chapter for an adoption plan. Invite questions.