arXiv:2609.10055v1 Announce Type: new Abstract: Biomedical ontology normalization maps free-text expressions to standardized concepts, enabling consistent integration and analysis of biomedical data. This task remains challenging because lexical variation and subtle distinctions among hierarchically related concepts can obscure concept boundaries. We present OntologyAligner, a three-stage framework that combines ontology-aligned retrieval, large language model candidate reranking, and selective hierarchy-guided refinement. We also construct PhenoNormBench, a unified benchmark comprising 13,390 samples from seven Human Phenotype Ontology datasets. OntologyAligner achieved state-of-the-art performance on HPO normalization, with 88.78% Macro Top-1 Accuracy and 86.75% Micro Top-1 Accuracy, exceeding the strongest baseline by 4.85 and 5.07 percentage points, respectively. Ablation analyses showed complementary contributions from all three stages, and sensitivity analyses demonstrated stability across candidate-set sizes and model backbones. Applications to MONDO, MEDIC, and NCBITaxon further established portability to other ontologies. OntologyAligner offers a generalizable framework for accurate mapping of biomedical text to structured ontology concepts. PhenoNormBench and the code are publicly available at https://github.com/zhelishisongjie/OntologyAligner.

arXiv:2609.04298v2 Announce Type: replace Abstract: Evaluating agents on the growing number of agentic benchmarks is challenging because they often require complex environments and agent integrations. We introduce Harbor Adapters, a unified evaluation infrastructure for agentic benchmarks. Our work makes three contributions. First, we develop benchmark adapters that port more than 80 benchmarks to evaluate arbitrary agents, and validate them through rigorous code review and parity experiments. Second, we conduct a large-scale evaluation of 8 models spanning capability tiers across 54 benchmarks; every model is run with Terminus-2 and with one of 3 native harnesses. This enables a broader analysis of agent capabilities and failure modes than was previously possible. Third, we introduce Harbor-Index, a curated set of 82 difficult, diverse, and high-quality tasks spanning 29 benchmarks, refined from the adapted suite through difficulty filtering, AI and human audit, and an audit-and-fix loop. Harbor-Index preserves the challenge and breadth of large-scale agentic evaluations while being affordable to run; no evaluated model-harness configuration exceeds 30% pass rate, and the strongest (GPT-5.5 with Codex) reaches 28.0%. We release the adapters, evaluation results, in-depth analysis, and Harbor-Index as open-source artifacts to support more reliable and comprehensive evaluation of language-model agents.

arXiv:2512.13168v4 Announce Type: replace Abstract: We introduce FinWorkBench (a.k.a. Finch), a benchmark for evaluating agents on real-world, enterprise-grade finance and accounting workflows that interleave data entry, structuring, formatting, web search, cross-file retrieval, calculation, modeling, validation, translation, visualization, and reporting. Finch is built from authentic enterprise workspaces from Enron (15,000 files and 500,000 emails) and other financial institutions spanning 2000 to 2025, preserving the in-the-wild messiness of multimodal artifacts such as tables and charts across diverse domains including budgeting, trading, and asset management. We propose a workflow construction process that combines LLM-assisted mining of workflows from authentic enterprise environments with expert annotation. Specifically, we use LLM-assisted, expert-verified derivation of workflows from real-world email threads and spreadsheet version histories, followed by meticulous workflow annotation requiring more than 700 hours of expert effort. This process yields 172 composite workflows with 384 tasks, involving 1,710 spreadsheets with 27 million cells, along with PDFs and other artifacts, capturing the intrinsically messy, long-horizon, knowledge-intensive, and collaborative nature of enterprise work. We conduct both human and automated evaluations of frontier AI systems, including GPT 5.1, Claude Sonnet/Opus 4.5, Gemini 3 Pro, Grok 4, and Qwen 3 Max. GPT 5.1 Pro spends an average of 16.8 minutes per workflow yet passes only 38.4% of workflows. Comprehensive case studies further highlight the challenges that real-world enterprise workflows pose for AI agents.

arXiv:2509.06326v2 Announce Type: replace-cross Abstract: As on-device LLMs(e.g., Apple on-device Intelligence) are widely adopted to reduce network dependency, improve privacy, and enhance responsiveness, verifying the legitimacy of models running on local devices becomes critical. Existing attestation techniques are not suitable for billion-parameter Large Language Models (LLMs), struggling to remain both time- and memory-efficient while addressing emerging threats in the LLM era. In this paper, we present AttestLLM, the first-of-its-kind attestation framework to protect the hardware-level intellectual property (IP) of device vendors by ensuring that only authorized LLMs can execute on target platforms. AttestLLM leverages an algorithm/software/hardware co-design approach to embed robust watermarking signatures onto the activation distributions of LLM building blocks. It also optimizes the attestation protocol within the Trusted Execution Environment (TEE), providing efficient verification without compromising inference throughput. Extensive proof-of-concept evaluations on LLMs from Llama, Qwen, and Phi families for on-device use cases demonstrate AttestLLM's attestation reliability, fidelity, and efficiency. Furthermore, AttestLLM enforces model legitimacy and exhibits resilience against model replacement and forgery attacks.