Md. Asif Uddin

    Chapter 6 VII.6

    Perturbation

    A perturbation screen is an experiment in the exact sense of Book VI, and it identifies edges that observation leaves undecided.

    A perturbation is an intervention in the sense Book VI means.

    How this chapter is built

    M3Load-bearing

    The content is mathematics. Understanding is demonstrated by computation, not recall.

    basics3/11what the words mean
    concept2/2what to picture
    theory0/4why it works, and when it does not
    mathematics0/15derive it, then compute it
    practice0/9build it, break it, read the papers

    Five strands, not one. Mathematics is the spine; the other four are the body. A chapter cannot pay its way out of teaching with problems, nor out of problems with teaching.

    Before you start

    The problem

    This is where the two halves of the reader's training meet. A CRISPR knockout is a do-operator with a reagent, and the assumptions Book VI has to argue for are here satisfied by design.

    Three pretext tasks built from one unlabelled imageAn unlabelled image feeds three tasks whose answers are known by construction: predict a hidden region, decide whether two crops came from the same photo, and recover an applied rotation. No annotator is involved.one unlabelled imageno labelhide a regionwhat was there?take two cropssame photo or not?rotate itby how much?The answer is known because you performed the corruption. What the model has to learn in order to undo it isthe representation you were after, and the choice of corruption decides which representation you get.
    Fig. 6 — Three tasks whose answers are known by construction, because you performed the corruption yourself.

    What this chapter covers

    • CRISPR
    • Perturb-seq
    • Interventions
    • Perturbation response
    • Causal interpretation

    Apparatus

    The mathematics this chapter leans on, held in Book 0 so it can be assumed here without being taught here. Not a gate — follow a link when a step stops making sense.

    Bayes' rule 0.PR.04 · Estimators, bias and variance 0.ST.01 · Hypothesis tests 0.ST.03 · Multiple comparisons 0.ST.04

    Notation

    • do(·)The intervention operator
    • 𝔼Expectation
    • VarVariance
    • θ̂An estimate, as against the quantity it estimates
    • X (random)A random variable

    Propositions

    Not yet written. The topics above are the plan for this chapter; each will become a proposition with its own figure.

    Worked problems

    0/5 problems0/4 variants0/10 exercisesowes 15 more

    Not yet written. At M3 this chapter owes 5 worked problems across 4 distinct variants, and 10 exercises, every one with a published solution. The build enforces that from the day the chapter is marked published.