Md. Asif Uddin

    Chapter 9 IV.9

    LLM Systems

    Retrieval, chunking and ranking decide what the model is given, and no amount of capacity recovers a document that was never retrieved.

    A model in a system is one component.

    How this chapter is built

    M2Substantive

    The derivations are the chapter. A reader who skips the algebra has not learned it.

    basics2/9what the words mean
    concept2/2what to picture
    theory0/2why it works, and when it does not
    mathematics0/9derive it, then compute it
    practice0/6build 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

    Deployed models are rarely used alone. The components around them — an index, a chunking rule, a reranker — determine the input, and their failure modes are measurable independently of the model.

    Structure, affinity, and the speed between themCo-folding answers whether two molecules fit and runs fast. Free energy perturbation answers how tightly they hold and runs slowly enough to be a scheduling decision. Boltz-2 reaches comparable correlation to the second at the speed of the first.what each method answersco-foldingcan they fitfastFEPhow tightlyslowBoltz-2how tightlyfastPearson 0.62, >1000x fasterApproaching FEP is not matching FEP. A correlation of 0.62 supports ranking a library and choosing what tosynthesise. It does not support telling a chemist that compound 47 binds at 12 nanomolar.Knowing which decisions a number can carry is most of the skill in using it.
    Fig. 9 — Co-folding says whether two molecules fit, free energy perturbation says how tightly and runs slowly. Reaching the second at the speed of the first is what changes screening.

    What this chapter covers

    • RAG
    • Embeddings
    • Vector databases
    • Agents
    • Tools
    • Memory
    • Inference systems

    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.

    Inner products, norms and cosine similarity 0.LA.03 · Distributions, discrete and continuous 0.PR.01

    Notation

    • dModel width
    • TSequence length in tokens

    Propositions

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

    Worked problems

    0/3 problems0/3 variants0/6 exercisesowes 9 more

    Not yet written. At M2 this chapter owes 3 worked problems across 3 distinct variants, and 6 exercises, every one with a published solution. The build enforces that from the day the chapter is marked published.