Search arXiv⌕ Search
Home/Archive/arXiv

arXiv · 2511.11324

NOVA: An Agentic Framework for Automated Histopathology Analysis and Discovery

Anurag J. Vaidya·Felix Meissen·Daniel C. Castro·Shruthi Bannur·Tristan Lazard·Drew F. K. Williamson·Faisal Mahmood·Javier Alvarez-Valle·Stephanie L. Hyland·Kenza Bouzid
View original source ↗Read source document ↗Export metadata ↓

Abstract

Digitized histopathology analysis involves complex, time-intensive workflows and specialized expertise, limiting its accessibility. We introduce NOVA, an agentic framework that translates scientific queries into executable analysis pipelines by iteratively generating and running Python code. NOVA integrates 49 domain-specific tools (e.g., nuclei segmentation, whole-slide encoding) built on open-source software, and can also create new tools ad hoc. To evaluate such systems, we present SlideQuest, a 90-question benchmark -- verified by pathologists and biomedical scientists -- spanning data processing, quantitative analysis, and hypothesis testing. Unlike prior biomedical benchmarks focused on knowledge recall or diagnostic QA, SlideQuest demands multi-step reasoning, iterative coding, and computational problem solving. Quantitative evaluation shows NOVA outperforms coding-agent baselines, and a pathologist-verified case study links morphology to prognostically relevant PAM50 subtypes, demonstrating its scalable discovery potential.

Explore related subjects

cs.CLcs.AI

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Anurag J. Vaidya, Felix Meissen, Daniel C. Castro, Shruthi Bannur, Tristan Lazard, Drew F. K. Williamson, Faisal Mahmood, Javier Alvarez-Valle, Stephanie L. Hyland, Kenza Bouzid. 2025-11-14. NOVA: An Agentic Framework for Automated Histopathology Analysis and Discovery. https://arxiv.org/abs/2511.11324

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

KEEP EXPLORING

Related papers

arXiv2026

The Metanym Game: An LLM Benchmark Without Ground Truth That Rises With the Models It Measures

We introduce a benchmark that is fully self-contained, needs no ground truth, and rises with the models it measures. Language models compete at making analogies and subjectively grade one another; nothing enters from outside. The benchmark reproduces GPQA Diamond, a keyed benchmark of expert-written questions, at r = 0.98, audited for a leak and found clean. We hypothesize that both benchmarks measure the same thing in different ways: a language model holds its knowledge as archetypal contexts, relationship patterns valid across many topic domains. GPQA instantiates the required knowledge in one domain; the Metanym Game instantiates one archetype into several domains, generating analogies, no reasoning required. The reasoning feature of an LLM hardly changes the game's ratings, while it lifts GPQA, which requires derivations. In the game, a player writes a context template whose slots, filled with a set of keywords from a topic domain, instantiate a factually true description of that domain; the instantiations are each other's metaphors, and keywords filling the same slot are metanyms, metaphorically synonymous. Correctness is settled sentence by sentence. Ground truth is replaced by the SVD of the factual rating matrix: its left and right singular vectors rate the players as judges and as generators, two ratings from one factorisation, to our knowledge a first for an LLM council of peers. On the subjective criteria, judges are weighted by their rating consistency under a swept calibration anchor. Generating and judging are different skills: on this roster the strongest generators were middling judges. A council of the five best issues the official ratings; its contestable seats keep it current, a candidate steering signal for self-improving AI. The paper is accompanied by a validating package that recomputes every number.

cs.CL↗
arXiv2026

SCoNE: Selective Context-aware Neuron Editing for Robust Retrieval-Augmented Generation

Retrieval-Augmented Generation (RAG) is highly sensitive to retrieval noise: when retrieved documents mix informative and irrelevant context, LLMs are easily distracted, leading to hallucinations. To overcome this, we propose SCoNE (Selective Context-aware Neuron Editing), a training-free model editing approach that improves retrieval noise robustness by selectively strengthening context-aware FFN neurons that are identified by both high attribution and high cross-input variability. SCoNE requires only a small number of mining samples, no fine-tuning, and no inference-time overhead. Across various knowledge-intensive question-answering benchmarks and two LLM backbones, SCoNE consistently outperforms competitive baseline methods. Our code is available at https://github.com/HYU-ARK-Lab/SCoNE.

cs.CL↗
arXiv2026

COT-TTS: Audio Context-Aware Text-to-Speech with Chain-of-Thought Reasoning

Recently, text-to-speech systems have made significant progress in speech expressiveness and controllability. However, the speaking style of generated speech typically relies on clear user-specified instructions. In natural conversations, speaking style should be naturally inferred from the preceding conversational context. Therefore, we propose COT-TTS, a context-aware, reasoning-based text-to-speech task. Given historical conversation audio, target text, and a reference speech, the system should comprehend the conversational context, infer an explicit intermediate reasoning, and finally synthesize the target speech with the specified timbre. To support this task, we constructed a large-scale bilingual conversational speech dataset comprising 9 million training samples, including a high-quality subset of 1 million samples. We further constructed a source-disjoint benchmark with 800 human-verified samples and established strong task-specific baselines. Additionally, we developed end-to-end autoregressive models with parameter sizes of 0.6B and 1.7B, generating emotion-labeled transcripts, editable speech style inferences, and speech tokens. Experimental results show that the proposed model achieves performance comparable to large-scale baseline systems with significantly fewer parameters. At the same time, the model performs well in terms of duration consistency and emotional consistency, and can generate appropriate emotional, stress, and rhythmic variations based on the conversational context. To facilitate future research, we will publicly release the data construction pipeline, dataset, trained models, and related resources. The demo page and additional resources are available at https://luckybian.github.io/COT-TTS

cs.CL↗