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arxiv: 2604.20331 · v2 · submitted 2026-04-22 · 💻 cs.CL · cs.AI· cs.LG

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Surrogate modeling for interpreting black-box LLMs in medical predictions

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Pith reviewed 2026-05-10 00:25 UTC · model grok-4.3

classification 💻 cs.CL cs.AIcs.LG
keywords surrogate modelingLLM interpretabilityblack-box modelsmedical predictionsbias detectionknowledge extractionprompting
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The pith

A surrogate modeling framework approximates LLM knowledge from input-output pairs to reveal variable influences and hidden biases in medical predictions.

A machine-rendered reading of the paper's core claim, the machinery that carries it, and where it could break.

This paper proposes a surrogate modeling framework to interpret the encoded knowledge inside black-box large language models by generating extensive input-output data through prompting across many simulated medical scenarios. The method then measures how strongly each input variable relates to the model's output predictions, allowing quantitative assessment of what the LLM has learned. In proof-of-concept experiments, the framework detected both associations that contradict standard medical knowledge and the continued presence of disproven racial assumptions in the model's responses. A reader would care because LLMs are increasingly proposed for medical use where their opaque reasoning could lead to incorrect or biased decisions. If the approach holds, it offers a practical test for reliability without needing direct access to model internals.

Core claim

The central claim is that for a hypothesis drawn from domain knowledge, the surrogate framework approximates the latent LLM knowledge space using only observable input-output pairs obtained through extensive prompting across a comprehensive range of simulated scenarios, thereby revealing the extent to which LLMs perceive each input variable in relation to the output and quantitatively exposing both associations that contradict established medical knowledge and the persistence of scientifically refuted racial assumptions within LLM-encoded knowledge.

What carries the argument

Surrogate modeling framework that approximates the LLM's latent knowledge space via extensive prompting to produce observable input-output pairs.

If this is right

  • The framework quantifies the influence of each input variable on LLM outputs in medical prediction tasks.
  • It identifies associations in LLM predictions that contradict established medical knowledge.
  • It detects persistence of refuted racial assumptions within the LLM's encoded knowledge.
  • This provides a practical red-flag indicator for safe and reliable use of LLMs in medical applications.

Where Pith is reading between the lines

These are editorial extensions of the paper, not claims the author makes directly.

  • The same surrogate approach could be applied outside medicine to check for encoded biases in LLMs used in other high-stakes domains.
  • If the approximations prove reliable, the framework could support targeted adjustments to LLM behavior based on detected flawed associations.
  • The findings imply that simply cleaning training data may not eliminate all problematic encoded assumptions.

Load-bearing premise

That extensive prompting across many simulated scenarios can accurately approximate an LLM's full latent knowledge using only the observable input-output pairs.

What would settle it

If altering an input variable in direct LLM queries produces output changes that the surrogate model does not predict, the approximation of latent knowledge would be shown as incomplete.

read the original abstract

Large language models (LLMs), trained on vast datasets, encode extensive real-world knowledge within their parameters, yet their black-box nature obscures the mechanisms and extent of this encoding. Surrogate modeling, which uses simplified models to approximate complex systems, can offer a path toward better interpretability of black-box models. We propose a surrogate modeling framework that quantitatively explains LLM-encoded knowledge. For a specific hypothesis derived from domain knowledge, this framework approximates the latent LLM knowledge space using observable elements (input-output pairs) through extensive prompting across a comprehensive range of simulated scenarios. Through proof-of-concept experiments in medical predictions, we demonstrate our framework's effectiveness in revealing the extent to which LLMs "perceive" each input variable in relation to the output. Particularly, given concerns that LLMs may perpetuate inaccuracies and societal biases embedded in their training data, our experiments using this framework quantitatively revealed both associations that contradict established medical knowledge and the persistence of scientifically refuted racial assumptions within LLM-encoded knowledge. By disclosing these issues, our framework can act as a red-flag indicator to support the safe and reliable application of these models.

Editorial analysis

A structured set of objections, weighed in public.

Desk editor's note, referee report, simulated authors' rebuttal, and a circularity audit. Tearing a paper down is the easy half of reading it; the pith above is the substance, this is the friction.

Referee Report

2 major / 2 minor

Summary. The manuscript proposes a surrogate modeling framework to interpret black-box LLMs by approximating their latent knowledge via input-output pairs generated through extensive prompting over simulated scenarios. Surrogate models (linear or tree-based) are then fit to these pairs, with coefficients or feature importances interpreted as quantitative measures of how the LLM 'perceives' each input variable's relation to the output. Proof-of-concept experiments in medical predictions are presented as demonstrating the framework's ability to uncover associations that contradict established medical knowledge as well as the persistence of refuted racial biases within the LLM's encoded knowledge.

Significance. If the surrogates can be shown to faithfully recover LLM behavior, the framework would offer a practical auditing method for detecting biases and factual inaccuracies in LLMs applied to high-stakes medical tasks, extending existing surrogate-based interpretability techniques to prompted LLM outputs. The quantitative focus on both contradictory associations and societal biases is timely given deployment concerns in healthcare. The approach is conceptually straightforward and leverages observable pairs without requiring internal access, but its current evidential support is limited by missing validation steps.

major comments (2)
  1. [§3] §3: The surrogate construction trains linear or tree-based models on prompted input-output pairs and interprets their parameters as LLM perceptions, yet no quantitative fidelity check is reported comparing surrogate predictions to the original LLM on held-out scenarios outside the prompting distribution. This validation is load-bearing for the central claim that the extracted associations reflect LLM-encoded knowledge rather than surrogate inductive bias or prompt artifacts.
  2. [Abstract] Abstract and experimental description: The claim that experiments 'quantitatively revealed both associations that contradict established medical knowledge and the persistence of scientifically refuted racial assumptions' is asserted without details on the medical hypotheses tested, number of simulated scenarios, method for quantifying contradictions against external benchmarks, or controls for prompt engineering sensitivity. These omissions prevent assessment of whether the data support the reported findings.
minor comments (2)
  1. [Abstract] The abstract and §1 repeat the motivation about LLMs encoding biases from training data; condensing this would improve readability without loss of content.
  2. [§3] Notation distinguishing the LLM's latent function f from the surrogate approximator g could be introduced explicitly in §3 to clarify the approximation step.

Simulated Author's Rebuttal

2 responses · 0 unresolved

We thank the referee for the thoughtful and constructive review. The comments highlight important aspects of validation and transparency that will improve the manuscript. We address each major comment below and will incorporate revisions as indicated.

read point-by-point responses
  1. Referee: [§3] The surrogate construction trains linear or tree-based models on prompted input-output pairs and interprets their parameters as LLM perceptions, yet no quantitative fidelity check is reported comparing surrogate predictions to the original LLM on held-out scenarios outside the prompting distribution. This validation is load-bearing for the central claim that the extracted associations reflect LLM-encoded knowledge rather than surrogate inductive bias or prompt artifacts.

    Authors: We agree that a direct fidelity assessment on held-out scenarios is necessary to substantiate that the surrogate captures LLM behavior rather than its own biases or prompt effects. The current proof-of-concept experiments focus on associations derived within the prompted distribution, but we recognize the gap. In the revised manuscript we will add a dedicated validation subsection that generates new scenarios outside the original prompting set, obtains LLM outputs on them, and reports quantitative agreement metrics (e.g., prediction correlation or classification accuracy) between the surrogate and the LLM. This addition will directly address the load-bearing concern. revision: yes

  2. Referee: [Abstract] Abstract and experimental description: The claim that experiments 'quantitatively revealed both associations that contradict established medical knowledge and the persistence of scientifically refuted racial assumptions' is asserted without details on the medical hypotheses tested, number of simulated scenarios, method for quantifying contradictions against external benchmarks, or controls for prompt engineering sensitivity. These omissions prevent assessment of whether the data support the reported findings.

    Authors: We acknowledge that the abstract and high-level experimental description lack sufficient specifics for independent evaluation. Although the body of the manuscript describes the medical prediction tasks and scenario generation, we will revise the abstract to concisely state the hypotheses examined, the scale of the simulated scenarios, the external medical benchmarks used to identify contradictions, and the prompt-variation controls performed. We will also expand the methods/results sections with explicit quantification procedures and sensitivity results to ensure the claims are fully supported and verifiable. revision: yes

Circularity Check

1 steps flagged

Surrogate interpretations of LLM perceptions reduce to fits on prompted input-output pairs

specific steps
  1. fitted input called prediction [Abstract]
    "this framework approximates the latent LLM knowledge space using observable elements (input-output pairs) through extensive prompting across a comprehensive range of simulated scenarios. Through proof-of-concept experiments in medical predictions, we demonstrate our framework's effectiveness in revealing the extent to which LLMs 'perceive' each input variable in relation to the output."

    The latent space is operationally replaced by prompted pairs; a surrogate is then fitted to those pairs and its coefficients/importances are presented as the LLM's perceptions. Because the surrogate is optimized directly on the pairs, any revealed associations (e.g., racial assumptions or contradictions with medical knowledge) are by construction the surrogate's explanation of the prompted data rather than an independently validated recovery of internal LLM structure.

full rationale

The paper defines its core contribution as a surrogate framework that generates input-output pairs via prompting to approximate latent LLM knowledge, then trains simplified models (linear, tree-based) on those pairs to extract variable importances as 'perceptions.' This matches the fitted-input-called-prediction pattern because the extracted associations are statistically forced by the surrogate fit to the very data used to stand in for the LLM; the abstract presents this as revealing LLM-encoded knowledge (including medically contradictory associations) without describing held-out fidelity checks against the original LLM on new scenarios. The derivation chain therefore reduces the claimed explanation of latent space to modeling the prompted observations by construction. No self-citation load-bearing or uniqueness theorems appear; the circularity is limited to the surrogate step itself.

Axiom & Free-Parameter Ledger

0 free parameters · 0 axioms · 0 invented entities

The abstract does not enumerate any free parameters, axioms, or invented entities. The approach implicitly assumes that domain-derived hypotheses and prompting can stand in for internal model states, but no explicit ledger is provided.

pith-pipeline@v0.9.0 · 5513 in / 1294 out tokens · 36582 ms · 2026-05-10T00:25:37.479135+00:00 · methodology

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Reference graph

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