The Inference Report

Structure-property relationships are foundational to biology, chemistry and materials science, where function, reactivity and physical response emerge from spatial, chemical and periodic organization. Mechanistically explaining these relationships requires interpreting structural evidence through scientific principles and physical constraints, from stereochemistry and bonding to symmetry, energetics and periodic order. However, applying artificial intelligence to this process presents a joint challenge of representation and reasoning: models must preserve domain-native structural information while showing how specific evidence supports predictions under these constraints. Here we introduce SciReasoner, a multimodal scientific foundation model for native structural reasoning across proteins, small molecules and inorganic crystals. SciReasoner discretizes coordinates, topologies and periodic connectivities into a unified structure-aware vocabulary, treating structural tokens as addressable evidence units during reasoning. In homology-controlled Gene Ontology prediction, SciReasoner improves Cellular Component annotation for low-homology and orphan-like proteins, increasing $F_{\max}$ from 0.42 to 0.55. In chemistry, it raises single-step retrosynthesis accuracy from 0.63 to 0.72 while generating fragment-level disconnection and precursor-verification traces. In materials science, its representations separate elemental and compound phases and resolve high- and low-band-gap regimes. Across 86 benchmarks, SciReasoner achieves state-of-the-art performance on 67 tasks. Double-blind expert evaluation rates its reasoning traces as preferred or at least comparable to those of a frontier large language model in 98% of cases. By making structure an inspectable substrate for reasoning under scientific constraints, SciReasoner connects accurate prediction with interpretable scientific inference.

Limited memory language models (LMLMs) externalize factual knowledge during pretraining to a knowledge base (KB), rather than memorizing it in their weights. During generation, the model then fetches knowledge from the KB as needed. This recently introduced paradigm provides multiple advantages, including knowledge control capabilities that remain beyond conventional LLMs. We propose continuous-query LMLM (CO-LMLM), where the KB pairs continuous keys with textual knowledge values, a significant departure from prior reliance on relational KB and queries. CO-LMLM generates flexible vector queries at minimal cost, while still integrating human-readable and attributable retrieved knowledge into its generation. We pair this design with an annotation pipeline that tags free-form factual spans in arbitrary text, removing prior work's restriction to Wikipedia. Across pretraining on Wikipedia and FineWeb-Edu and at multiple model scales, CO-LMLM outperforms prior LMLMs and vanilla LLMs in both perplexity and factual precision. At 360M scale, this includes lower perplexity than models pretrained on 40x more data, and SimpleQA-verified performance that is in line with gpt-4o-mini and higher than Claude Sonnet 4.5.

The quadratic cost of causal self-attention severely bottlenecks long-context transformer inference. While numerous post hoc linearization pipelines exist, it is difficult to identify which components preserve model quality. This work isolates the effect of state update design in a strict frozen-backbone regime. We show that softmax relies on key-dependent, rank-1 orthogonal projections, elucidating why delta-style networks outperform purely gated accumulation. We identify a potential source of approximation errors and introduce structural interventions, specifically sink tokens, short convolutions, and fixed-budget cache routing, which reduces the remaining gap. We scale this linearization approach across LLaMA and Qwen models up to 32B parameters, outperforming prior post hoc baselines on MMLU and matching the long-context retrieval of complex adaptive-caching frameworks.

The optimization of long-horizon agents increasingly relies on reflection-based mechanisms, where a large language model (LLM) acts as an optimizer to diagnose agent failures and improve agent policies. However, real execution traces are difficult to use directly for optimization: large trace collections are often redundant and heterogeneous, making optimization inefficient and prone to overfitting to low-value failures; meanwhile, each individual trajectory also contains many irrelevant steps, while naive context reduction methods such as truncation or sliding windows can discard causally important evidence and produce misleading optimization signals. To resolve this dilemma, we introduce STRACE (Structural TRajectory Analysis and Causal Extraction), a framework that constructs high signal-noise optimization contexts for more precise and effective optimization. At the batch level, STRACE mines failure patterns to filter redundant traces and retain representative failures; within each selected trace, it performs causal localization over a textual dependency graph to remove non-causal steps and identify the true root-cause module for optimization. Empirical results demonstrate that STRACE significantly outperforms standard context-filtering baselines. Notably, on a challenging formal verification task (VeruSAGE-Bench), it successfully optimizes human-expert designed agents, delivering $1.4\times$ success-rate improvement (42.5% to 58.5%). The code is available at https://github.com/moomight/STRACE .

Analytical workloads operating on data stored in external database systems face a fundamental bottleneck: data access is guarded entirely by the database driver, like JDBC or ODBC, forcing all reads through query execution and other driver layers that are not designed for bulk columnar analytics. We present Jailbreak, an approach that bypasses the database engine entirely by reading storage files directly and materializing data as in-memory columnar buffers. Jailbreak's key insight is that database file formats, while complex, are fully specified by their source code and documentation, artifacts that Large Language Models (LLMs) can ingest to regenerate operator-specific table reading components without human-engineered parsing logic. Jailbreak leverages LLM-assisted code synthesis for database storage decoding, turning a traditionally opaque format into a directly queryable artifact. We evaluate Jailbreak on PostgreSQL and MySQL storage files, targeting analytical snapshot scenarios common in read replicas and offline processing pipelines. The generated reader produces Apache Arrow buffers consumable directly by most of the widely known query engines, including DuckDB, Apache Spark, and GPU-accelerated frameworks such as cuDF and Spark RAPIDS. We validate correctness against JDBC/ODBC-based baselines using the TPC-H benchmark across all query results, and demonstrate significant performance improvements in end-to-end analytical throughput, achieving up to 27x speedups. Our results showcase that LLM-assisted storage reader synthesis is a viable and generalizable methodology for breaking data lock-in across database systems, with applications beyond PostgreSQL and MySQL for any system whose file format is available to the LLM from documentation or source code.

We introduce institutional red-teaming, an evaluation methodology for testing deployment rules in multi-agent AI: hold the agents, objectives, and task state fixed, vary only one rule, and attribute the resulting change in collective behavior to that rule. We instantiate the methodology in IABench-CA, a consequence-allocation benchmark spanning 228 contexts, five canonical rules, and seven model populations (33,924 games), with a normative cooperative reference and auto-labelled reasoning traces. Three findings emerge. (1) Deployment rules causally alter collective safety: changing only the consequence rule moves mean fatality by 22 to 58 percentage points within every population. (2) There is no safe default, but the targeting hazard is universal: the safest rule, the least-safe rule, and even the direction of the incidence effect vary across populations, yet regressive identity-targeting is never decisively safest in any context for any population, eliminates the least-resourced agent in 30-87% of games everywhere, and is selection-unsafe relative to the cooperative reference for all seven populations. (3) Identity salience is the mechanism: a one-shot anonymization ablation on the most exploitation-prone population (gpt-5.1) shows that merely naming the loss bearer in the rule text drives targeted elimination from 22% to 81% at identical payoffs; under repeated play, anonymization only delays the targeting, as agents re-infer the hidden rule from observed eliminations. We package the methodology as a safety-case workflow that certifies a provisional rule region $Φ(c,P)$ per deployment context and population, with explicit residual risks and monitoring obligations.