Search arXiv⌕ Search
Home/Archive/arXiv

arXiv · 2605.30826

Beyond Agreement: Scoring Panel-Surfaced Biomedical Entity Candidates for Curator Triage

Shuheng Cao·Ruiqi Chen·Renjie Cao·Zhenhao Zhang·Siyu Zhang·Tingting Dan
View original source ↗Read source document ↗Export metadata ↓

Abstract

Biomedical NER is deceptively simple for modern LLMs: plausible biomedical mentions are easy to surface, but corpus-convention correctness depends on annotation conventions, span boundaries, entity granularity, and type schemas. Multi-LLM agreement is a salience signal, not corpus-convention correctness. We introduce a candidate-level panel-output benchmark for panel-surfaced candidate verification, where the unit is an aligned candidate surfaced by an explicitly defined multi-model panel rather than a standalone extractor output. The benchmark aligns eight LLMs' predictions over five public biomedical NER datasets into a candidate master table. BioConCal is an in-domain supervised scorer that instantiates this layer with inference-time gold-free agreement, mention, surface-availability, and document features for a fixed candidate stream. In domain, BioConCal improves AUROC from 0.753 for raw agreement to 0.910. At a validation-selected 0.95 precision target it selects 1,340 candidates at empirical test precision 0.939, compared with 293 for raw agreement. This corresponds to candidate-level recall 0.592 and corpus-level recall 0.523 against a within-panel row-label ceiling of 0.883. The main benefit is not recovering entities missed by every panel member, but reshaping a noisy panel stream into a higher-yield review queue. Under entity-type shift, thresholds require target-domain validation, and exact character localization remains a separate deterministic post-processing step.

Explore related subjects

cs.CLcs.AI

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Shuheng Cao, Ruiqi Chen, Renjie Cao, Zhenhao Zhang, Siyu Zhang, Tingting Dan. 2026-05-29. Beyond Agreement: Scoring Panel-Surfaced Biomedical Entity Candidates for Curator Triage. https://arxiv.org/abs/2605.30826

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related papers

arXiv2026

DA-Cramming: Enhancing Cost-Effective Language Model Pretraining with Dependency Agreement Integration

Pretraining language models is still a challenge for many researchers due to its substantial computational costs. As such, there is growing interest in developing more affordable pretraining methods. One notable advancement in this area is the Cramming technique (Geiping and Goldstein, 2022), which enables the pretraining of BERT-style language models using just one GPU in a single day. Building on this innovative approach, we introduce the Dependency Agreement Cramming (DA-Cramming), an efficient framework that integrates information about dependency agreements into the pretraining process. Unlike existing methods that leverage similar semantic information during finetuning, our approach represents a pioneering effort focusing on enhancing the foundational language understanding with semantic information during pretraining. We meticulously design a dual-stage pretraining work flow with four dedicated submodels to capture representative dependency agreements at the chunk level, effectively transforming these agreements into embeddings to benefit the pretraining. Extensive empirical results demonstrate that our method significantly outperforms previous methods across various tasks.

cs.CL↗
arXiv2026

BigO(Bench): Can LLMs Generate Code with Controlled Time and Space Complexity?

We introduce BigO(Bench), a novel coding benchmark designed to evaluate the capabilities of generative language models in understanding and generating code with specified time and space complexities. This benchmark addresses the gap in current evaluations that often overlook the ability of models to comprehend and produce code constrained by computational complexity. BigO(Bench) includes tooling to infer the algorithmic complexity of any Python function from profiling measurements, including human- or LLM-generated solutions. BigO(Bench) also includes of set of 3,105 coding problems and 1,190,250 solutions from Code Contests annotated with inferred (synthetic) time and space complexity labels from the complexity framework, as well as corresponding runtime and memory footprint values for a large set of input sizes. We present results from evaluating multiple state-of-the-art language models on this benchmark, highlighting their strengths and weaknesses in handling complexity requirements. In particular, token-space reasoning models are unrivaled in code generation but not in complexity understanding, hinting that they may not generalize well to tasks for which no reward was given at training time.

cs.CL↗
arXiv2026

UR$^2$: Unify RAG and Reasoning through Reinforcement Learning

Large Language Models (LLMs) have shown strong capabilities through two complementary paradigms: Retrieval-Augmented Generation (RAG) for knowledge grounding and Reinforcement Learning from Verifiable Rewards (RLVR) for complex reasoning. However, existing attempts to unify these paradigms remain narrow in scope, typically limited to open-domain QA with fixed retrieval settings, which constrains generalization to broader domains. To address this limitation, we propose UR$^2$ (Unified RAG and Reasoning)), a general reinforcement learning framework that dynamically coordinates retrieval and reasoning. UR$^2$ introduces two key designs: a difficulty-aware curriculum that selectively invokes retrieval only for challenging instances, and a hybrid knowledge access strategy that combines domain-specific offline corpora with on-the-fly LLM-generated summaries. Together, these components mitigate the imbalance between retrieval and reasoning and improve robustness to noisy information. Experiments on open-domain QA, MMLU-Pro, medical, and mathematical reasoning tasks show that UR$^2$, built on Qwen-2.5-3/7B and LLaMA-3.1-8B, consistently outperforms existing RAG and RL baselines, and achieves performance comparable to GPT-4o-mini and GPT-4.1-mini on several benchmarks. Code, models, and data are available at https://github.com/Tsinghua-dhy/UR2.

cs.CL↗