Agency with AI
Lecture 2: Reading Matters
Shen Shen
[date]
Outline
Part 1: the boundary, and why research
Part 2: reading with AI
Part 3: the term ahead
Two questions, one model, same care in the prompting
[capture: a 6.390 question. "Derive the ridge-regression closed form." The answer comes back crisp, correct, textbook-grade.]
[capture: a boundary question, about the instructor's own unpublished exam analysis. The answer comes back fluent, structured, and wrong.]
Side by side, they look the same: register, structure, confidence. Fluency does not drop at the boundary; correctness does.
The wrongness is visible here only because this is the instructor's own data. You cannot bluff someone about their own data.
The drop as we cross the boundary
Coursework lives where the answer key exists. Research lives where it runs out.
The obvious version, nodded away: a model trained on the known is less reliable past the boundary of the known.
The working version: the drop is invisible. Nothing in the answer marks the crossing. Locating yourself relative to the boundary is your job, and it cannot be delegated to the thing being graded.
Guard 1: not "AI is useless for research." Past the boundary it still helps with the known parts. The drop says where verification stops being free, never where the tool stops helping.
Guard 2: the boundary moves; yesterday's boundary is in tomorrow's training set. At the current boundary, you are the one who has to know.
The drop can run opposite to difficulty
Strongest where research looks hardest: standard derivations, code, prior work. All known.
Weakest where it looks easy: is this question interesting? has it been tried? is the result surprising?
Delegating by felt difficulty delegates backwards.
The mechanism behind the drop (training objective, context limits, sampling) gets its mathematics in week eight.
You should be objecting right about now
Co-Scientist (Nature, May 2026) generates and ranks novel hypotheses; one matched an unpublished wet-lab result in two days. Claude Science (June 2026) runs research workflows with a reviewer agent checking every citation. So is the model great past the boundary now?
[image, left: coscientist-cycle.webp, the Generate → Debate → Evolve tournament. Dark background; frame on a dark card.]
[image, right: claude-science-artifact-repro.jpg, the workbench with the Review tab. Same dark-card treatment.]
The tournament is cheap generation plus a filter, and the wet lab was the answer key. Lit review, generation, ranking got cheap; verification is the bottleneck; taste is still ours. These systems are that same drop, built at scale. Current as of July 2026.
Why UROP
The boundary, crossed safely: an advisor, and a question nobody has answered.
The W1 map stops being a diagram: fundamentals, tools, and pipeline exercised together.
Taste does not delegate. What is worth working on, when a result smells wrong, what to read next.
Taste forms by doing the work, and by watching people who have it.
Research starts anywhere: an itch, a dataset, an advisor's half-broken code, a replication that failed.
But a contribution is a claim about the field: this is new. That claim is only earned by reading.
Reading is not step one. It is the standing obligation, due whenever the idea arrives.
Outline
Part 1: the boundary, and why research
Part 2: reading with AI
Part 3: the term ahead
A paper is a delta claim
A paper is a delta claim with evidence attached.
Placement: what does it build on, what does it push against?
Delta: what exactly is new, and compared to what?
Everything else in the paper is support.
The four-beat recipe
MOTIVATION what hurt · SOLUTION the move · OLD IDEA what it descends from · DELTA what is genuinely new
A paper is built from exactly these: introduction, method, related work, contribution claims. Reading one means extracting the four and auditing the fourth.
The delta is allowed to be "nothing, honestly". That is the lens working.
Typical exceptions, usually one of these when a paper resists: a phenomenon paper (no solution beat); a many-ancestor paper (placement is a graph, the recipe holds one edge); and the frame is for claims, not process.
And the recipe has a lineage: DARPA has asked these questions since the mid-1970s. We repurposed a proposal-writing tool for claim-auditing and added the nothing-honestly clause. That is our delta on it.
The research machine, as first imagined
1945: the memex. Not answers, trails: a reader building association paths through the literature.
What got built instead came in two waves: retrieval (search engines), then generation (LLMs).
Neither builds your trails.
The connection graph is still the researcher's own artifact. Your term-long lineage map is one.
Search-shaped vs. AI-shaped reading
Search handed you documents and made you judge them. The skill: source evaluation.
AI hands you an answer and invites you to accept it. The skill becomes interrogation.
The retrieval half’s lineage is next, worked by hand on three tiny documents. The generation half adds its own failure: an answer supported by nothing that was retrieved.
Documents are vectors, relevance is an angle
TF-IDF and cosine, worked by hand · toy corpus, by construction
MOTIVATION The whole corpus, three documents:
d1 "gradient descent converges"
d2 "gradient descent diverges"
d3 "transformers attend"
Goal: a number that says how relevant any two texts are to each other. The 1975 answer: turn each document into a vector, measure the angle.
Every retrieval system you have used, and the R in RAG, descends from this idea.
The reference formulas
SOLUTION Coordinate for term \( t \) in document \( d \): count times rarity.
\[ w_{t,d} = \mathrm{tf}(t,d)\,\cdot\,\mathrm{idf}(t), \qquad \mathrm{idf}(t) = \ln\!\frac{N}{\mathrm{df}(t)} \]
\( \mathrm{tf} \): how often \( t \) appears in \( d \). \( \mathrm{df} \): how many of the \( N \) documents contain \( t \). Common everywhere → idf near 0; rare → large.
Similarity of two vectors: the cosine of their angle.
\[ \cos\theta = \frac{u \cdot v}{\lVert u\rVert\,\lVert v\rVert} \]
Why the angle: the norms mean a long document cannot win by being long.
Why the log, and what idf secretly is
SOLUTION Room question first. What is the idf of a word that appears in all three documents?
\( \mathrm{idf} = \ln(3/3) = 0 \): a word that appears everywhere carries zero distinguishing information, and the formula sends it to exactly zero. The hand-written stopword lists of pre-1972 systems fall out of a statistic.
And the log is not decoration: df\( /N \) estimates \( P(t) \), so
\[ \mathrm{idf}(t) = -\ln P(t) \]
Surprisal: each word weighted by how many bits its presence carries. (Shannon returns in W8.)
OLD IDEA Proposed on intuition in 1972; theorists were still arguing why in 2004. Practice preceded theory. (And the highest-idf strings in a real corpus are typos, hence BM25.)
Worked, end to end
df("gradient") = 2 → \( \mathrm{idf} = \ln(3/2) \approx 0.405 \); df("converges") = 1 → \( \ln 3 \approx 1.099 \)
\( v_1 = (0.405,\; 0.405,\; 1.099,\; 0) \) over (gradient, descent, converges, diverges)
\( v_2 = (0.405,\; 0.405,\; 0,\; 1.099) \)
\( v_1 \cdot v_2 = 0.405^2 + 0.405^2 + 1.099\cdot 0 + 0 \cdot 1.099 \approx 0.328 \)
\( \lVert v_1 \rVert = \sqrt{0.405^2 + 0.405^2 + 1.099^2} = \sqrt{1.536} \approx 1.239 = \lVert v_2 \rVert \)
\( \cos\theta = \dfrac{0.328}{1.239 \times 1.239} \approx 0.21 \)
0.21, low, despite sharing two of three words. IDF already decided the shared words are boilerplate here. Crude judgment about what matters, done with a logarithm, in 1975.
The failure that motivates fifty years of successors
DELTA "Converges" and "diverges" occupy different coordinates: their product term is exactly zero. The vectors cannot see that they are the two most related words on the board.
The classic false drop: a relevant document missed because it uses different words for the same thing.
Embeddings are the fix with the same geometry: replace one-hot coordinates with learned dense ones, where converges and diverges land close. The cosine formula is untouched. RAG is this fix wired to a generator.
The failure modes kept their shapes while changing names. A false drop in 1975 is a retrieval miss in RAG today. And idf is a frozen relevance weight, computed once from the corpus; attention is the same job, learned per query.
Two papers through the summarizer.
[capture: a canonical paper every training corpus digested. The summary comes back textbook-flavored, and contains things that are not in the PDF.]
[capture: a recent workshop paper. The summary comes back abstract-flavored: the paper's own advertising, limitations quietly dropped.]
"Summarize this paper" runs two different programs
Famous paper: reciting its reputation. From memory, not from your PDF.
Obscure paper: compressing its advertising. In the paper's own register.
Both miss the same thing: the delta lives between the paper and the field. A summary of one document does not contain it.
The famous-paper behavior is your first sighting of training-set contamination. It returns as a data question in W7 and an eval question in W9.
What AI summaries reliably drop or flatten.
Flattened novelty: every contribution sounds equally new, because the abstract said so
Missing compared-to-what: the claim without its baseline
Dropped limitations: the paragraph the authors were made to write, gone
Inherited register: the paper's marketing tone, repeated as fact
Fluent middle, wrong stakes: methods compressed correctly, significance misassigned
Citation blur: related work melted into "prior approaches"
The trap
Three different acts, at three different costs:
Agreeing is recognition.
Verifying is work: find the fragile claim, check it against the PDF.
Reading is the expensive one, and the only one that builds the trail; agreeing leaves no anchor.
A fluent summary is easy to agree with, and agreeing feels like having read the paper. That is the cheapest act, credited as the dearest.
Unwatched, the summary replaces the reading: students who lean on the assistant stop consulting other sources.
The same trap, new face
Reasoning models show their work: a visible thinking trace arrives with the answer.
The trace reads like your verification, pre-done. It is one more fluent artifact, from the same machine.
The story can be written after the fact: an answer reached one way, narrated another.
Reading the trace is not verifying the answer. The check comes from outside the trace, same as the summary, same as the paper.
Outline
Part 1: the boundary, and why research
Part 2: reading with AI
Part 3: the term ahead
The term ahead: one lineage per unit
skills → modularity and information hiding, 1972
MoE → mixtures of local experts, 1991
prompt evals → experimental design, 1935
Every new term gets the four-beat treatment when its week arrives: what hurt, the move, what it descends from, what is genuinely new. Sometimes the honest delta is "less than advertised." Sometimes it is something real. Telling them apart is the skill.
Commit to a question
You leave this week with one toy research question. Yours.
Past the boundary: no answer key exists; checking it takes evidence you produce.
Answerable, by you, this semester: you can name the data that would bear on it.
Wanted: your best bet on still caring in December. If interest dies, the writeup diagnoses why, and the diagnosis earns credit.
Committed as a draft: next week's lab locks it to your build; W7 finds its data, W9 measures it, W12 writes the one-page result.
This week's lab
An assigned paper. Produce the AI summary; that part is free.
The work: annotate the summary against the four beats and the failure list, correcting and supplying, with page references; placement and delta are beats three and four.
Three probing questions, aimed at the delta: what did the field use before, which experiment would break the claim, what limitation got dropped.
Then the toy question: three candidates, the boundary test on each (ask a model straight; if its confident answer checks against something that exists, it was textbook), partner critique, commit one.
Graded: the annotations and the questions, not the summary.
Summary
Research lives where the answer key runs out; the reliability drop there is invisible (fluency stays flat), and it can run opposite to felt difficulty.
A paper is a delta claim: read for placement and delta; the delta is what summaries are worst at.
"Summarize" runs two programs: reciting reputation, or compressing advertising. Grade its reading.
Agreeing is recognition, verifying is work, reading builds the trail.
A reasoning trace is an artifact, not a verification; the check comes from outside the trace.
The four beats are yours now: motivation, solution, old idea, delta.
One lineage per module ahead, and one toy research question that is yours.
Lec02
By Shen Shen
Lec02
Agency with AI, Lecture 2: Reading Matters