Separable Pathways for Causal Reasoning: How Architectural Scaffolding Enables Hypothesis-Space Restructuring in LLM Agents

We introduce CausaLab, a scalable environment for evaluating interactive causal discovery by LLM agents. Unlike prior evaluations, CausaLab evaluates both whether an agent can solve a problem using causal evidence and whether its answer is grounded in a faithful recovered causal mechanism. Each episode places an agent in a synthetic laboratory: it receives prior measurement records, intervenes on a manipulator crystal, and predicts the resonance frequency of a held-out reactor crystal governed by the same mechanism. The hidden data-generating process is a randomly sampled structural causal model (SCM), so success requires recovering both a causal graph and structural equations rather than recalling prior knowledge. Experiments show a persistent gap between prediction and mechanism recovery: in the purely observational 6-node setting, GPT-5.2-high reaches 92% task accuracy but only 0.471 all-edge $F_1$. Mixed observation-intervention strategies improve structural fidelity, while pure intervention remains difficult even for strong agents. We identify premature stopping as a major weakness and show that consistency verification mitigates it. CausaLab therefore separates predictive success from causal understanding and exposes current LLM agents' limits as experimental causal reasoners.

Humans intuitively solve complex problems by flexibly shifting among reasoning modes: they plan, execute, revise intermediate goals, resolve ambiguity through associative judgment, and apply formal procedures to well-specified subproblems. Current LLM agents lack this flexibility, as their scaffolds hard-code such reasoning decisions in advance. These scaffolds are effective when their prescribed structure matches the task, but brittle when solving the task requires adapting the structure of reasoning itself. We introduce Deep Reasoning -- an inference-time approach for constructing task-specific scaffolds through structured meta-reasoning. Deep Reasoning uses a formal language that represents meta-reasoning as executable decompositions over associative inference, formal computation, and recursive subproblem solving, enabling decomposition principles to be encoded as in-context examples that guide test-time scaffold construction. We instantiate this approach in a general-purpose agent (DOLORES) that distributes complex tasks across more controlled reasoning threads. We evaluate it against state-of-the-art scaffolding methods across four hard benchmarks: multi-hop reasoning, long-chain question answering, long-context aggregation, and deep research-style information seeking. DOLORES outperforms all evaluated scaffolds across three model sizes and two model families, improving over the strongest evaluated scaffold baseline by 24.8% on average. DOLORES distributes cognition across structured, lower-load reasoning threads, thereby reducing premature termination and hallucinations. This advantage can even bridge the scaling gap, with an 8B version surpassing all evaluated 32B baselines from the same family in more than half the settings. These results point toward future agentic systems that treat scaffolding as adaptive reasoning, constructing the structure each task requires just-in-time.

Building AI Scientist agents with Large Language Models (LLMs) has recently attracted growing attention. Since scientific discovery fundamentally relies on uncovering causal relationships from observations, the capability of causal thinking, i.e., distinguishing causation from correlation and recognizing hidden biases, is essential to LLM agents. Although a number of benchmarks exist for AI Scientists, none explicitly incorporate challenges from selection bias, measurement error, and hidden confounders that widely exist in real-world scientific discovery. To this end, we present CausalGame, a benchmark that evaluates the causal thinking capabilities of LLM agents through interactive games. CausalGame asks LLM agents to actively design experimental protocols, collect observation data, and derive a final solution with an explanation report. To emulate realistic scientific discovery challenges, we design 14 scenarios that incorporate selection bias, measurement error, and hidden confounders. Across 30 LLM agents, none demonstrates reliable causal thinking: the best model reaches only 68.0% survival against analytical optima of 78-85%, and merely 5-7% of sessions receive credits on the causal-reasoning rubrics. CausalGame provides a scalable and controlled testbed for evaluating the causal thinking of AI Scientist agents.