Which Models Are Our Models Built On? Auditing Invisible Dependencies in Modern LLMs

Tool-using LLM agents produce trajectories whose calls form a directed dependency graph: earlier tool outputs supply arguments to later calls. Whether this execution structure is represented inside the model is unknown; prior structural probes have targeted static code or chain-of-thought text, not an agent's run-time call graph. A low-capacity edge probe on the residual stream of Qwen3-32B decodes the tool-call dependency graph well above both a Hewitt--Liang random-label control and a positional baseline. A counterfactual contrast between value corruption and structural perturbation indicates the signal tracks abstract topology rather than identifier values, and replicates under an independent, non-substring oracle. The non-positional component replicates on three further interactive multi-hop benchmarks and attenuates as call order alone becomes a sufficient proxy for dependency, vanishing in single-shot planning. Per-layer activation patching shifts the probe at a later, non-patched boundary, evidence that the representation propagates rather than passively reads out, though the realised tool call does not move. To our knowledge this is the first structural probe of an LLM agent's runtime tool-call dependency graph. Our claims concern representation, not behavioural control, and span two model families and one primary domain.

LLM API calls have become a standard programming primitive, but they create a program boundary that disrupts traditional dataflow analysis. A runtime value may be inserted into a natural-language prompt through a template placeholder, transformed opaquely by the LLM, and returned as code, JSON, or text consumed by downstream logic. Existing analyses such as taint analysis and program slicing require a dataflow summary that describes how a callee maps inputs to outputs; an LLM call provides no such summary, breaking analysis at what we call the NL/PL boundary. We introduce PRISM, the first reachability model for this boundary. PRISM abstracts the missing dataflow summary of an LLM call as placeholder-to-output reachability. Because the LLM's internal transformation is opaque, the only observable signal is the input-output relationship, which spans an unbounded range of behaviors. PRISM therefore uses a finite taxonomy grounded in quantitative information flow theory. It classifies placeholder-output behavior into 25 labels along two dimensions: information preservation and output modality. Each label yields a reachability predicate for a placeholder. The model is sound with respect to its labeling, with residual error bounded empirically. PRISM is dependable and effective. Independent models and human annotators assign its labels consistently (Fleiss' kappa >= 0.72), and the labels cover 8,119 real-world pairs, leaving no pair unclassifiable; the Good-Turing discovery probability is 0.09%. For taint analysis, PRISM nearly doubles the conservative baseline and outperforms a direct LLM baseline, achieving F1 = 81.7%. Across six real OpenClaw CVEs, it detects every vulnerable flow and confirms every patch (F1 = 100%). In backward slicing, it removes about a quarter of irrelevant code without discarding any true dependency.

The pretraining data mixture of Large Language Models (LLMs) constitutes their "digital DNA", shaping model behaviors, capabilities, and failure modes. Yet this composition is rarely disclosed, making post-hoc auditing of data combination or provenance difficult. In this work, we formalize $\textbf{Data Mixture Surgery (DMS)}$: given only generated text from a target LLM, estimate the domain-level distribution of its pretraining corpus under a predefined taxonomy. We propose $\textbf{LLMSurgeon}$, a strong framework that casts DMS as an inverse problem under the label-shift assumption. Rather than directly aggregating classifier outputs, LLMSurgeon estimates a calibrated $\textit{soft}$ confusion matrix and solves a constrained inverse problem to correct systematic domain confusion and recover the latent mixture prior. To evaluate, we introduce $\textbf{LLMScan}$, a recipe-verifiable evaluation suite built from open-source LLMs with transparent pretraining mixtures. Across LLMScan, LLMSurgeon recovers domain mixtures with high fidelity under fixed protocols. Our work presents a practical, post-hoc approach for auditing the digital DNA of foundation models without access to their training data.