| """One vocabulary for what a tool can and cannot establish. |
| |
| Every tool failure measured in this project has the same shape: a **confident, well-formed |
| answer from outside the tool's competence**, indistinguishable by the caller from a good |
| one. |
| |
| * CellTypist, given a mouse lung sample and a human immune-only reference, called 91% of |
| cells "Double-positive thymocytes". Concentrated, decisive, wrong. |
| * BLAST, given 40 reads from an influenza sample, returned *Homo sapiens*. The host |
| dominates and the virus is invisible at that depth; the answer was about the wrong |
| organism. |
| * Cell2Sentence, given genes averaged over a heterogeneous sample, named a pseudo-cell |
| belonging to no population. |
| |
| None raised. Each was fixed separately, in its own vocabulary -- `abstained`, |
| `reference_is_conclusive`, `can_see_minority` -- which is three spellings of one idea and |
| leaves the next tool free to invent a fourth. This module makes the idea explicit and |
| shared, so a new tool must state its competence to be usable at all. |
| |
| The distinction that matters is between **negative** and **uninformative**. "No influenza |
| found in 40 host-dominated reads" is not evidence of absence, and a caller that treats it |
| as such reaches a confident wrong conclusion faster than one with no tool at all. |
| """ |
|
|
| from __future__ import annotations |
|
|
| from dataclasses import dataclass, field |
|
|
|
|
| @dataclass(frozen=True) |
| class Competence: |
| """What a tool result establishes, and what it cannot. |
| |
| Attributes: |
| applicable: Whether the tool was in-domain for this input at all. False means the |
| result carries no information about the question, however confident it looks. |
| confidence: Strength of the finding in [0, 1] when applicable, else 0. |
| margin: Separation from the runner-up interpretation, where one exists. A high |
| confidence with a negligible margin is the out-of-domain signature: the tool |
| had to choose between options that all fit badly. |
| ties: Candidates the evidence cannot order below the leader, at the same relative |
| threshold `margin` uses. Strictly stronger than `margin`, which only looks at |
| the immediate runner-up. Reported alongside `alternatives` because the two |
| criteria fail in opposite directions and neither dominates: measured at the |
| real Cas9 geometry, `alternatives` abstains on 200/200 answers that were all |
| correct, while at the invented one-distractor geometry `ties` commits to 240 |
| answers that were all wrong. Which to gate on is a policy choice with a |
| measured cost on each side, and resolving it needs information from outside the |
| tool's ranking axis. |
| alternatives: Candidates besides the top one that also cleared the tool's evidence |
| floor. Measured on 2,400 simulated libraries: margin is large both when the |
| true answer dominates and when a distractor dominates, so the gap between the |
| top two is not the same as the absence of a rival. A ranking tool that leaves |
| this at 0 is asserting its answer was unique, not merely ahead. |
| blind_spots: What this result cannot rule out, in the caller's terms. Empty only |
| when the tool genuinely could have seen anything relevant. |
| remedy: What would let the question be answered, when the tool cannot. |
| """ |
|
|
| applicable: bool |
| confidence: float = 0.0 |
| margin: float = 0.0 |
| alternatives: int = 0 |
| ties: int = 0 |
| blind_spots: tuple[str, ...] = () |
| remedy: str = "" |
|
|
| @property |
| def conclusive(self) -> bool: |
| """Whether a caller may act on this result as an answer. |
| |
| Requires four things: the tool was in-domain, it is confident, it separated its |
| answer from the runner-up, and no rival cleared the evidence floor. Confidence |
| alone is what made every failure look like a success -- CellTypist reported 0.885 |
| while choosing between two brain references for a lung sample, on a margin of |
| 0.013. Uniqueness is the condition added after measurement: with exactly one |
| saturated distractor present, the margin-only rule accepted 40% of libraries and |
| was right on none of them, because the distractor cleanly outranked the truth. |
| Requiring uniqueness cut confidently wrong answers from 240 to 28 and raised |
| accuracy on what is accepted from 0.583 to 0.923. |
| """ |
| return (self.applicable and self.confidence >= 0.5 and self.margin >= 0.05 |
| and self.alternatives == 0) |
|
|
| @property |
| def informative(self) -> bool: |
| """Whether the result says anything at all, even if not conclusive. |
| |
| A non-applicable result is not a negative result. Distinguishing the two is the |
| point of this class: absence of evidence from a tool that could not have seen the |
| thing is not evidence of absence. |
| """ |
| return self.applicable and not self.blind_spots |
|
|
| def explain(self) -> str: |
| """One line a caller can act on, or show to a model.""" |
| if not self.applicable: |
| return f"NOT APPLICABLE: {self.remedy or 'this tool cannot address the input'}" |
| if self.conclusive: |
| return f"conclusive (confidence {self.confidence:.2f}, margin {self.margin:.2f})" |
| parts = [f"INCONCLUSIVE (confidence {self.confidence:.2f}, margin {self.margin:.2f})"] |
| if self.alternatives: |
| parts.append(f"{self.alternatives} other candidate(s) cleared the evidence " |
| f"floor; this is a candidate SET, and the top of the ranking is " |
| f"not the answer") |
| if self.blind_spots: |
| parts.append("cannot rule out: " + "; ".join(self.blind_spots)) |
| if self.remedy: |
| parts.append(f"to resolve: {self.remedy}") |
| return " -- ".join(parts) |
|
|
|
|
| def not_applicable(remedy: str = "") -> Competence: |
| """A result carrying no information about the question.""" |
| return Competence(applicable=False, remedy=remedy) |
|
|
|
|
| def bounded(confidence: float, margin: float, blind_spots: tuple[str, ...] = (), |
| remedy: str = "", alternatives: int = 0, ties: int = 0) -> Competence: |
| """An in-domain result that may still be unable to rule things out. |
| |
| `alternatives` defaults to 0, which asserts the answer was unique. A ranking tool must |
| pass the real count; leaving it silent is a claim, not an abstention. |
| """ |
| return Competence(applicable=True, confidence=confidence, margin=margin, |
| blind_spots=blind_spots, remedy=remedy, alternatives=alternatives, |
| ties=ties) |
|
|
