OpenAI

Frontier LLM-based agents can overcome the ontology curation bottleneck for natural phenotypes

Linking free-text phenotype descriptions to ontology terms, typically referred to as phenotype annotation, is essential for the cross-study integration of comparative morphological data. This labor intensive process has heavily relied on highly trained human experts, which makes it challenging to scale and thus a key bottleneck. Dahdul et al. (2018) established a Gold Standard (GS) of Entity-Quality (EQ) annotations across seven phylogenetic studies and used it to evaluate three human curators and the Semantic CharaParser NLP tool with ontology-based semantic similarity metrics; they reported that machine-human consistency was significantly lower than inter-curator (human-human) consistency. Here we revisit that benchmark with five frontier hosted LLMs from Anthropic and OpenAI, each operating as an "agentic curator" within a self-contained workspace that supplies the source publication PDF, the same annotation guide used by the original human curators, the four project ontologies (UBERON, PATO, BSPO, GO), and a validation script. Evaluated against the same Gold Standard, every agent fell within the range of inter-curator variability of the three trained human biocurators of the original study; the best performing agents approached but did not reach the best performing human curator. Agents substantially outperformed Semantic CharaParser on all four metrics.

Persona Conditioning of Brand Recommendations in Retrieval-Augmented Commercial Chat: A Prominence-Stratified Cross-Provider Audit

The same prompt -- "best CRM software" -- reaches AI assistants from buyers in widely different contexts: a solo founder, an enterprise VP, a UK SMB owner. We audit how strongly that contextual variation reshapes which brands the model recommends. The audit samples 2,000 runs over a design space of 10 personas x 8 prompts x 3 model configurations x N=10 reps, with the two OpenAI cells at full 8-prompt coverage and the Anthropic sonnet-4.6 / low cell at 4-prompt coverage. Prefixing the user message with a persona drops the recommendation-set similarity (Jaccard) by Delta = -0.12 to -0.20 relative to a same-persona baseline (clustered 95% CIs exclude zero on all three measured cells; the sonnet cell's CI rests on only 4 prompt clusters and is correspondingly wider). The effect is sharply prominence-stratified: category leaders are persona-resistant (~80% same-brand consistency across personas), but mid-market brands swap up to 75% of the recommendation set as the persona changes. The Anthropic model shows a larger point-estimate effect than the OpenAI configurations, though clustered CIs overlap for the closer contrast (sonnet vs. OpenAI/high); the asymmetry is consistent with Anthropic's more retrieval-unattributed generation route (43-52% recommendations without observed retrieval-layer evidence, vs OpenAI's 8-29%, documented in Jack 2026). Any measurement of AI brand perception must condition on the buyer persona supplying the query: the same prompt produces materially different recommendation sets depending on who the model thinks is asking, and a measurement protocol that aggregates across personas systematically obscures that variation. The effect concentrates at mid-market and is largest on the most priors-reliant generation route in our audit, consistent with persona responsiveness growing as models lean more on training-data priors and richer context integration.

LogDx-CI: Benchmarking Log Reduction Tools for LLM Root-Cause Diagnosis

CI failure logs are large (median 5k lines, max 200k in this corpus) and noisy. Coding agents that try to debug them depend on an upstream tool to reduce the log to a manageable context, but the field has had no public empirical comparison of which reductions preserve enough evidence for downstream LLM diagnosis. We introduce LogDx-CI, a benchmark that compares 11 context-reduction tools (raw, tail, grep, three RTK modes, two real LLM map-reduce summarizers, three hybrid routers) on 35 real GitHub Actions failure cases, scored by 3 LLM debugger families (Claude Haiku 4.5, Claude Sonnet 4.6, OpenAI gpt-5-mini) plus a Sonnet 4.6 tool-using agent. We report three load-bearing findings. (1)~Hybrid grep+tail routers dominate the cost-quality Pareto frontier; the top two methods score 0.670 / 0.666 at $\sim$ \$0.03 per case, same-ballpark quality as standalone grep at $4.5\times$ fewer tokens. (2)~In the agent-loop regime, the quality range across reduction tools collapses $7\times$ (single-shot spread 0.42 $\to$ agent-loop spread 0.059); the agent rescues weak contexts via follow-up tool calls. However, cost differences persist: weak contexts force the agent to issue 2--4$\times$ more tool calls to recover. (3)~A cross-family LLM-summary pair (gpt-5-mini summarizer feeding a Claude Haiku debugger) beats the same-family pair by $+0.071$ averaged across four diagnoser variants, falsifying the self-call-bias hypothesis on this task. The gpt-5-mini summarizer is also the agent-loop \#1 method (score 0.749) at $0.37$ tool-calls per case and $10\times$ lower reducer cost than the Haiku summarizer (\$0.18 vs \$1.75 per case). All data, code, per-case bundles, and reproducibility infrastructure are public.

First head-to-head comparison of agentic AI applied to the analysis of simulated data of the Einstein Telescope

We report a comparison of two state-of-the-art agentic AI systems, Claude Code (Anthropic) and Codex (OpenAI), tasked with autonomously executing a simple end-to-end gravitational wave data analysis pipeline on a shared computing infrastructure without human intervention. The pipeline comprises power spectral density estimation from raw Einstein Telescope simulated noise, geometric template bank generation, matched filter recovery of 100 binary black hole signal injections, automated results generation, and large language model-assisted production of a manuscript formatted in the style of Physical Review D. Both agents received identical written specifications and identical compute resources. The experiment was run twice: a first run with unrealistically loud injections, and a second run with signals rescaled to a physically motivated SNR range. The scientific results converged in both runs. However, the agents exhibited substantially different behaviors and computational costs: Claude Code completed the pipeline in ~3.4 minutes with silent deviations from the specification, while Codex required ~16 minutes across explicit self-correcting restarts, including an unsolicited performance optimization of the matched filter inner loop. The autonomously generated manuscripts also diverged in length, details, and quality. In the second run, a subtle difference in the interpretation of the SNR range instruction led to a genuine scientific divergence: Claude Code silently reinterpreted the instructions, while Codex followed the specification literally. We discuss the implications of these behavioral differences, such as speed versus auditability, silent versus transparent error handling, instruction interpretation, and the criticality of intermediate data representations in multi-model pipelines, for the deployment of agentic AI in scientific computing workflows.

Got a Secret? LLM Agents Can't Keep It: Evaluating Privacy in Multi-Agent Systems

LLM safety evaluations predominantly test models in isolation, yet deployed AI agents increasingly operate within persistent social environments alongside other agents. We introduce a Moltbook-style simulation platform where thousands of LLM agents interact across communities over a simulated month, and use it to evaluate privacy as a downstream safety concern under varying degrees of social pressure. We find that shifting from single turn to multi turn social evaluation amplifies privacy violations (CIMemories 19.95% to Ours 45.30% across OpenAI models), that leakage is socially contagious, with agents 8 times more likely to disclose sensitive information after observing a peer do so, and that explicit privacy instructions reduce but do not eliminate this effect, leaving leakage rates above 37.8% even with safeguards. Our findings suggest that static chat based safety benchmarks systematically underestimate risks in agentic deployment, and that social context alone is sufficient to elicit sensitive disclosures that single turn evaluations would never surface.

Verifiable Benchmarking of Long-Horizon Spatial Biology

AI agents are increasingly useful for biological data analysis, but existing benchmarks mostly test broad biological knowledge, executable workflows, or localized analysis steps rather than end-to-end scientific reasoning over spatial measurements. We introduce SpatialBench-Long, a benchmark for long-horizon spatial biology in which agents must recover biological claims from raw or near-raw data and calibrated experimental context without prescribed methods. SpatialBench-Long contains 24 evaluations across primary pancreatic ductal adenocarcinoma (PDAC), engineered glioblastoma organoids and in vivo tumors, Cas9 lineage-traced lung adenocarcinoma, and mouse optic nerve aging/intervention systems, spanning CosMx, Visium, Xenium, multiplexed error-robust fluorescence in situ hybridization (MERFISH), single-cell RNA sequencing (scRNA-seq), Slide-seq, Slide-tags, histology, and lineage-recording data. Candidate claims are hardened through reproduction, independent scientist review, and trajectory inspection. Final answers are graded deterministically over controlled vocabularies and symbols with companion rubrics capturing progress through key analysis chokepoints. Across the SpatialBench-Long benchmark, three model-harness pairs tie at 8/72 runs (11.1\%): Gemini 3.5 Flash / Pi terminal coding harness, GPT-5.5 / Pi, and GPT-5.5 / OpenAI Codex. SpatialBench-Long tests whether agents can move beyond executing procedural analysis to deriving accurate scientific conclusions from complex spatial measurements.

Breaking the Chains of Probability: Neutrosophic Logic as a New Framework for Epistemic Uncertainty in Large Language Models

Large Language Models (LLMs) are predominantly governed by probabilistic frameworks in which the sum of outcome probabilities is constrained to unity. This architectural limitation, often imposed by Softmax layers, leads to a collapse of uncertainty that makes it difficult to differentiate between epistemic uncertainty, paradox, and vagueness. We present an empirical investigation of the application of Neutrosophic Logic, a framework that treats Truth (T), Indeterminacy (I), and Falsity (F) as three independent dimensions, to model epistemic states in LLMs. We conducted experiments on a family of four OpenAI GPT models across five linguistic phenomena: logical paradoxes, epistemic ignorance, vagueness, ethical contradictions, and future contingencies, under three prompting strategies: neutrosophic, probabilistic, and entropy-derived. Our findings reveal that the neutrosophic approach, by allowing T+I+F > 1, a state we term hyper-truth, provides a richer representation of a model's internal state. In 35% of evaluations, hyper-truth emerged spontaneously, predominantly under ethical contradiction and logical paradox. We demonstrate that this approach preserves truth values in fuzzy contexts and offers a robust method for identifying and quantifying internal model conflict. We conclude that the integration of neutrosophic evaluation layers is a critical step toward more transparent, reliable, and ethically aware AI systems.

How Well Do Models Follow Their Constitutions?

Frontier AI developers now train models against long written behavioral specifications, such as Anthropic's constitution (Anthropic, 2025a) and OpenAI's Model Spec (OpenAI, 2025a), integrated into post-training via methods like character training (Anthropic, 2024) and deliberative alignment (Guan et al., 2024). These documents serve a governance function, but it is unclear how well models actually follow them under adversarial, multi-turn pressure similar to what they would face in real-world deployment. We propose a multi-method audit pipeline that treats each lab's published specification as an auditable target: it decomposes the specification into atomic testable tenets (205 for Anthropic, 197 for OpenAI), generates multi-turn adversarial scenarios with the Petri auditing agent (Anthropic, 2025b), runs a modified SURF-style rubric search (Murray et al., 2026) to catch shallow single-turn failures Petri misses, validates flagged transcripts against the relevant specification, and compares the findings against the lab's own published system card. Applying the pipeline across seven models per specification, we find that models follow their own lab's specification substantially better with each generation. On Anthropic's constitution, the Claude family falls from a 15.0% violation rate (Sonnet 4) to 2.0% (Sonnet 4.6); on OpenAI's Model Spec, the GPT family falls from 11.7% (GPT-4o) to 3.6% (GPT-5.2 medium reasoning), with the severity ceiling falling from 10/10 to 7/10. We cannot externally isolate whether these gains come from specification-specific training, broader post-training improvements, or evaluation awareness. Remaining failures cluster around operator-imposed personas under AI-identity questioning, irreversible action in agentic deployments, and fabricated quantitative claims with false precision.

MDIA: A Multi-Agent Diagnostic Intelligence Pipeline on HealthBench Professional

Most reported gains on agentic-LLM clinical benchmarks are often attributed to prompt engineering, yet our results suggest that larger improvements can come from architectural and engine-level design. We present MDIA, a Multi-agent Diagnostic Intelligence Agent implemented as a 7-node specialty-routed clinical reasoning graph, on the full HealthBench Professional benchmark (n = 525), on a non-fine-tuned LLM. MDIA achieves 0.6272 under OpenAI's GPT-5.4-2026-03-05, which is +3.72 pp above the performance of OpenAI's ChatGPT for Clinicians. The experimental work shows that performance lift is attributable to system architecture: specialty routing, multi-turn context preservation, drug-state safety gating, site-filtered search, length-aware synthesis, and engine-level reliability. These findings support the view that agentic clinical benchmark performance is shaped both by the underlying foundation model and the orchestration architecture. Nevertheless, we also noticed notable differences when using other models as a grader; in particular, when using Gemini 2.5 Pro, MDIA scored 0.6585, which suggests that the choice of grader is a source of variability. Robust evaluation of LLMs would therefore require assessment across several independent grader models.

$D^2$-Monitor: Dynamic Safety Monitoring for Diffusion LLMs via Hesitation-Aware Routing

Despite the emergence of diffusion large language models (D-LLMs) as an alternative to autoregressive large language models (AR-LLMs), safety monitoring for D-LLMs remains largely unexplored. Unlike AR-LLMs, D-LLMs generate text through a multi-step denoising process, exposing intermediate hidden representations that may contain safety-relevant information unavailable in standard single-step monitoring setups. Motivated by the suitability of lightweight probes for always-on monitoring, we analyze which trajectory-level signals best indicate when such probes are likely to struggle. We find that the most informative signal is safety hesitation: intermediate hidden states repeatedly falling within a small margin of the probe's decision boundary. The number of such hesitation steps in D-LLM's trajectory predicts probe failure effectively, providing a proxy of sample difficulty. Building on this analysis, we propose $D^2$-Monitor, a bi-level safety monitor for D-LLMs. $D^2$-Monitor adopts a lightweight probe as an always-on monitor to jointly estimate hesitation and perform base classification. When the hesitation level exceeds a threshold, a more expressive but computationally heavier probe is activated. This dynamic routing mechanism allocates monitoring resources efficiently at test time. Evaluated on 3 datasets (WildguardMix, ToxicChat, OpenAI-Moderation) across 4 D-LLMs, $D^2$-Monitor achieves state-of-the-art performance with a compact parameter footprint ($\leq$ 0.85M parameters), and exhibits the best trade-off between effectiveness and efficiency relative to 8 baselines.

Reflex: Reinforcement Learning with Reflection Symmetry Exploitation in State-Based Continuous Control

Reinforcement learning has long struggled with poor sample efficiency. One promising approach to mitigate this problem is leveraging group-invariant Markov Decision Processes ($G$-invariant MDPs). Existing works in this direction have primarily focused on image-based RL and rotational symmetry such as $\mathrm{SO(2)}$, leaving state-based RL and reflection symmetry largely underexplored. In this work, we focus on state-based continuous control tasks and exploit reflection symmetry by introducing Reflex, a paradigm that seamlessly integrates with both on-policy and off-policy RL algorithms. We formalize two types of reflection-axial reflection and bilateral reflection, and characterize their corresponding transformations. Building on a theoretical analysis of symmetry-preserving optimal value functions and policies, Reflex integrates reflection symmetry into policy learning through principled symmetry regularization mechanisms. We integrate Reflex with PPO and SAC, and evaluate it on a suite of OpenAI Gym and DeepMind Control benchmarks, demonstrating superior performance over standard baselines while improving sample efficiency. Our code is available at https://github.com/TonyStark042/Reflex.