Julian McAuley
Publications
Mechanist: AI as a Scientific Instrument for Discovering the Mechanisms of Intelligence
AI models have achieved remarkable success across diverse domains, yet the mechanisms underlying their capabilities and the risks they may pose remain poorly understood. As AI development becomes faster and increasingly automated, mechanistic exploration remains largely manual, widening the gap between what models can do and our ability to understand and control them. To bridge this gap, we introduce Mechanist, an agentic system that uses AI as a scientific instrument for the autonomous discovery of mechanisms underlying AI intelligence. To support autonomous mechanistic discovery, we construct an interpretability-focused knowledge graph of approximately 13,000 papers and integrate it with a multidisciplinary database of 43 million papers spanning 26 fields. We further curate a library of 32 foundational methods for mechanism analysis, causal intervention, and validation. Compared with Claude Code and existing AI-scientist systems, Mechanist generates more valuable mechanism hypotheses and executes experiments more reliably. Mechanist also demonstrates a progression from discovering model behaviors to explaining and controlling AI models. Specifically, Mechanist first uncovers a counterintuitive safety risk in scientific laboratories, showing that unsafe traits can transfer across modalities through apparently safe training data. Mechanist then develops a mechanism theory of belief, revealing how models represent world knowledge, form beliefs, infer the beliefs of others, and how these mechanisms emerge during pretraining. Finally, Mechanist translates these mechanistic insights into practical interventions that improve model performance across diverse scenarios and steer scientific foundation models toward generating DNA sequences with specified properties.
Filesystem-Based Memory for LLM Agents: Organization, Evolution, and Sustainability
Deployed LLM agents increasingly keep their long-term memory as a filesystem: a directory tree of markdown files that the agent itself reads, writes, and reorganizes through generic file tools. Yet research has largely passed over this medium: prior systems design bespoke memory representations and study retrieval over them, leaving the default's two working assumptions untested: that an agent can keep a growing store organized as memories accumulate, conflict, and go stale, and that this organization pays. We present the first systematic exploration of filesystem-based memory for LLM agents. We formalize the setting as three roles around one memory filesystem: a management agent integrates and organizes incoming content, a search agent answers queries with cited sources, and an execution agent supplies task trajectories that are distilled into skills, unifying declarative memory and skills in a single store. Across long-conversation benchmarks and embodied tasks, we vary memory shape (agent-organized hierarchy, verbatim dump, chunk retrieval), stream scale, tool harness (sandboxed shell, memory-tool-style functions, varied search tooling), and the strengths of the management and search agents, tracking answer quality, cost, and store health as memory grows. What organization reliably buys is search economy: organized stores roughly halve retrieval cost where material is large. Today's agents, however, fall short of the default's promise: in our growth study, organization erodes for all but the strongest management agent, and no agent we measure converts organization itself into better answers. And the model is not the only lever over a store's shape: changing the tool set alone reshapes the store as strongly as swapping the model. The study turns the filesystem default from an assumption into a design space for agent memory.
How Hard Does It Think? Analyzing Step-Aware Reasoning Energy in LLM Chain-of-Thought Trajectories
Understanding how computational effort is allocated across individual chain-of-thought (CoT) reasoning steps remains an open challenge: existing interpretability methods rely on output-level signals or collapse processing depth into a single trajectory-level scalar, leaving step-wise effort opaque. We propose Step-Aware Reasoning Energy (SARE), a geometric framework that quantifies effort at the granularity of individual CoT steps via Centered Kernel Alignment (CKA) between Gram matrices of token hidden states across adjacent transformer layers, capturing inter-token relational structure without requiring eigenvector alignment or cluster correspondence. SARE further contextualizes this energy within reasoning's semantic progression by modeling CoT trajectories as transitions among latent semantic states. Across six reasoning benchmarks and three open-weight LLMs, we find that reasoning energy is highly non-uniform across step types, exhibiting phase-like transitions invisible to trajectory-level metrics; incorrect trajectories show systematically lower energy at critical reasoning junctions; and SARE-based features match or outperform output-based confidence baselines in most settings, indicating that internal geometric dynamics encode predictive information beyond surface-level signals.
Spider 2.0-AIFunc: Extending Real-World Text-to-SQL to AI-Native SQL Workflows
Major cloud data platforms now expose large language model capabilities as native SQL functions, enabling analysts to perform classification, filtering, sentiment analysis, extraction, similarity search, and aggregation within ordinary SQL queries. Yet existing text-to-SQL benchmarks evaluate only conventional SQL and provide no signal on whether models can generate such AI-native SQL. We introduce Spider 2.0-AIFunc, a benchmark of 465 verified instances across 125 real-world databases covering six types of AI functions on the Snowflake platform. Starting from an existing enterprise text-to-SQL benchmark, we construct Spider 2.0-AIFunc through an agent-based pipeline that rewrites source tasks into AI-native form, simultaneously transforming target queries and refining natural language instructions to make the intended AI-native solution explicit and reduce ambiguity. All instances pass a multi-round repeated execution protocol across temporally separated windows to confirm result stability before release. Evaluating ten state-of-the-art language models, we find that the strongest proprietary models reach 67-70% execution accuracy while the best open-source model achieves 58.1%, a gap driven primarily by errors in predicate specification, schema grounding, and AI function parameterization. Agent frameworks designed for traditional text-to-SQL challenges, such as schema retrieval and relevant table selection, do not transfer effectively to AI-native SQL: a minimal agent setup consistently matches or outperforms more elaborate alternatives, suggesting that the strategies these frameworks employ are less critical in this setting. Data are available at https://github.com/Leolty/Spider2-AIFunc .
CocoaBench: Evaluating Unified Digital Agents in the Wild
LLM agents now perform strongly in software engineering, deep research, GUI automation, and various other applications, while recent agent scaffolds and models are increasingly integrating these capabilities into unified systems. Yet, most evaluations still test these capabilities in isolation, which leaves a gap for more diverse use cases that require agents to combine different capabilities. We introduce CocoaBench, a benchmark for unified digital agents built from human-designed, long-horizon tasks that require flexible composition of vision, search, and coding. Tasks are specified only by an instruction and an automatic evaluation function over the final output, enabling reliable and scalable evaluation across diverse agent infrastructures. We also present CocoaAgent, a lightweight shared scaffold for controlled comparison across model backbones. Experiments show that current agents remain far from reliable on CocoaBench, with the best evaluated system achieving only 45.1% success rate. Our analysis further points to substantial room for improvement in reasoning and planning, tool use and execution, and visual grounding.
ThinkRouter: Efficient Reasoning via Routing Thinking between Latent and Discrete Spaces
Recent work explores latent reasoning to improve reasoning efficiency by replacing explicit reasoning trajectories with continuous representations in a latent space, yet its effectiveness varies across settings. Analysis of model confidence dynamics under latent reasoning reveals that thinking trajectories ending in incorrect answers contain fewer low-confidence steps than those ending in correct answers. Meanwhile, we suggest that soft embeddings aggregated by multiple low-confidence thinking alternatives may introduce and propagate noise, leading to high confidence in unreliable reasoning trajectories. Motivated by these observations, ThinkRouter, an inference-time confidence-aware routing mechanism is proposed to avoid high confidence and noise for efficient reasoning. ThinkRouter routes thinking to the discrete token space when model confidence is low, and to the latent space otherwise. Extensive experiments on STEM reasoning and coding benchmarks across diverse large reasoning models demonstrate that ThinkRouter outperforms explicit CoT, random routing, and latent reasoning baselines in terms of accuracy, achieving an average improvement of 19.70 points in Pass@1, while reducing generation length by up to 15.55%. Further comprehensive analysis reveals that ThinkRouter can calibrate errors arising from explicit CoT and latent reasoning, and accelerates end-of-thinking token generation by globally lowering model confidence.