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Nov 3

LongGenBench: Long-context Generation Benchmark

Current long-context benchmarks primarily focus on retrieval-based tests, requiring Large Language Models (LLMs) to locate specific information within extensive input contexts, such as the needle-in-a-haystack (NIAH) benchmark. Long-context generation refers to the ability of a language model to generate coherent and contextually accurate text that spans across lengthy passages or documents. While recent studies show strong performance on NIAH and other retrieval-based long-context benchmarks, there is a significant lack of benchmarks for evaluating long-context generation capabilities. To bridge this gap and offer a comprehensive assessment, we introduce a synthetic benchmark, LongGenBench, which allows for flexible configurations of customized generation context lengths. LongGenBench advances beyond traditional benchmarks by redesigning the format of questions and necessitating that LLMs respond with a single, cohesive long-context answer. Upon extensive evaluation using LongGenBench, we observe that: (1) both API accessed and open source models exhibit performance degradation in long-context generation scenarios, ranging from 1.2% to 47.1%; (2) different series of LLMs exhibit varying trends of performance degradation, with the Gemini-1.5-Flash model showing the least degradation among API accessed models, and the Qwen2 series exhibiting the least degradation in LongGenBench among open source models.

  • 4 authors
·
Oct 5, 2024 3

One Thousand and One Pairs: A "novel" challenge for long-context language models

Synthetic long-context LLM benchmarks (e.g., "needle-in-the-haystack") test only surface-level retrieval capabilities, but how well can long-context LLMs retrieve, synthesize, and reason over information across book-length inputs? We address this question by creating NoCha, a dataset of 1,001 minimally different pairs of true and false claims about 67 recently-published English fictional books, written by human readers of those books. In contrast to existing long-context benchmarks, our annotators confirm that the largest share of pairs in NoCha require global reasoning over the entire book to verify. Our experiments show that while human readers easily perform this task, it is enormously challenging for all ten long-context LLMs that we evaluate: no open-weight model performs above random chance (despite their strong performance on synthetic benchmarks), while GPT-4o achieves the highest accuracy at 55.8%. Further analysis reveals that (1) on average, models perform much better on pairs that require only sentence-level retrieval vs. global reasoning; (2) model-generated explanations for their decisions are often inaccurate even for correctly-labeled claims; and (3) models perform substantially worse on speculative fiction books that contain extensive world-building. The methodology proposed in NoCha allows for the evolution of the benchmark dataset and the easy analysis of future models.

  • 5 authors
·
Jun 23, 2024

SnapKV: LLM Knows What You are Looking for Before Generation

Large Language Models (LLMs) have made remarkable progress in processing extensive contexts, with the Key-Value (KV) cache playing a vital role in enhancing their performance. However, the growth of the KV cache in response to increasing input length poses challenges to memory and time efficiency. To address this problem, this paper introduces SnapKV, an innovative and fine-tuning-free approach that efficiently minimizes KV cache size while still delivering comparable performance in real-world applications. We discover that each attention head in the model consistently focuses on specific prompt attention features during generation. Meanwhile, this robust pattern can be obtained from an `observation' window located at the end of the prompts. Drawing on this insight, SnapKV automatically compresses KV caches by selecting clustered important KV positions for each attention head. Our approach significantly reduces the growing computational overhead and memory footprint when processing long input sequences. Specifically, SnapKV achieves a consistent decoding speed with a 3.6x increase in generation speed and an 8.2x enhancement in memory efficiency compared to baseline when processing inputs of 16K tokens. At the same time, it maintains comparable performance to baseline models across 16 long sequence datasets. Moreover, SnapKV can process up to 380K context tokens on a single A100-80GB GPU using HuggingFace implementation with minor changes, exhibiting only a negligible accuracy drop in the Needle-in-a-Haystack test. Further comprehensive studies suggest SnapKV's potential for practical applications.

  • 9 authors
·
Apr 22, 2024 3

Infinite Retrieval: Attention Enhanced LLMs in Long-Context Processing

Limited by the context window size of Large Language Models(LLMs), handling various tasks with input tokens exceeding the upper limit has been challenging, whether it is a simple direct retrieval task or a complex multi-hop reasoning task. Although various methods have been proposed to enhance the long-context processing capabilities of LLMs, they either incur substantial post-training costs, or require additional tool modules(e.g.,RAG), or have not shown significant improvement in realistic tasks. Our work observes the correlation between the attention distribution and generated answers across each layer, and establishes the attention allocation aligns with retrieval-augmented capabilities through experiments. Drawing on the above insights, we propose a novel method InfiniRetri that leverages the LLMs's own attention information to enable accurate retrieval across inputs of infinitely length. Our evaluations indicate that InfiniRetri achieves 100% accuracy in the Needle-In-a-Haystack(NIH) test over 1M tokens using a 0.5B parameter model, surpassing other method or larger models and setting a new state-of-the-art(SOTA). Moreover, our method achieves significant performance improvements on real-world benchmarks, with a maximum 288% improvement. In addition, InfiniRetri can be applied to any Transformer-based LLMs without additional training and substantially reduces inference latency and compute overhead in long texts. In summary, our comprehensive studies show InfiniRetri's potential for practical applications and creates a paradigm for retrievaling information using LLMs own capabilities under infinite-length tokens. Code will be released in link.

  • 3 authors
·
Feb 18, 2025

Spinning the Golden Thread: Benchmarking Long-Form Generation in Language Models

The abilities of long-context language models (LMs) are often evaluated using the "Needle-in-a-Haystack" (NIAH) test, which comprises tasks designed to assess a model's ability to identify specific information ("needle") within large text sequences ("haystack"). While these benchmarks measure how well models understand long-context input sequences, they do not effectively gauge the quality of long-form text generation--a critical aspect for applications such as design proposals and creative writing. To address this gap, we have introduced a new long-form text evaluation benchmark, Spinning the Golden Thread (SGT), which tests models' ability to identify specific events within generated long text sequences. In this benchmark, we prompt long-context LMs to create long-form text that must include particular events or constraints and evaluate their ability to incorporate these elements. We evaluated ten long-context LMs across four distinct scenarios, three types of prompt instructions, and two different generation-length settings (16K and 32K). Although these models perform well on NIAH benchmarks, none demonstrated satisfactory performance on the Spinning the Golden Thread, raising concerns about their ability to generate coherent long-form text that follows instructions. Additionally, as the length of the generated text increases, all models exhibit a significant drop in performance.

  • 4 authors
·
Sep 3, 2024 3

LV-Eval: A Balanced Long-Context Benchmark with 5 Length Levels Up to 256K

State-of-the-art large language models (LLMs) are now claiming remarkable supported context lengths of 256k or even more. In contrast, the average context lengths of mainstream benchmarks are insufficient (5k-21k), and they suffer from potential knowledge leakage and inaccurate metrics, resulting in biased evaluation. This paper introduces LV-Eval, a challenging long-context benchmark with five length levels (16k, 32k, 64k, 128k, and 256k) reaching up to 256k words. LV-Eval features two main tasks, single-hop QA and multi-hop QA, comprising 11 bilingual datasets. The design of LV-Eval has incorporated three key techniques, namely confusing facts insertion, keyword and phrase replacement, and keyword-recall-based metric design. The advantages of LV-Eval include controllable evaluation across different context lengths, challenging test instances with confusing facts, mitigated knowledge leakage, and more objective evaluations. We evaluate 10 LLMs on LV-Eval and conduct ablation studies on the techniques used in LV-Eval construction. The results reveal that: (i) Commercial LLMs generally outperform open-source LLMs when evaluated within length levels shorter than their claimed context length. However, their overall performance is surpassed by open-source LLMs with longer context lengths. (ii) Extremely long-context LLMs, such as Yi-6B-200k, exhibit a relatively gentle degradation of performance, but their absolute performances may not necessarily be higher than those of LLMs with shorter context lengths. (iii) LLMs' performances can significantly degrade in the presence of confusing information, especially in the pressure test of "needle in a haystack". (iv) Issues related to knowledge leakage and inaccurate metrics introduce bias in evaluation, and these concerns are alleviated in LV-Eval. All datasets and evaluation codes are released at: https://github.com/infinigence/LVEval.

  • 13 authors
·
Feb 6, 2024

GraphNIAH: A Benchmark for Long-Context Reasoning over Real-World Graphs

The needle-in-a-haystack (NIAH) benchmark was introduced as a test for measuring a model's ability to find small relevant facts within a very large body of input text. However, existing NIAH benchmarks each suffer from one or more of the following limitations: (1) reliance on synthetic data, so their evaluations may not generalize to real-world settings; (2) reuse of previously published datasets, leading to the risk of benchmark contamination; (3) dependence on manual annotation, which requires human effort to create and update data and is prone to future benchmark contamination; and (4) unrealistic simplification of long-context multi-hop reasoning where each next step is trivial given previous steps, while real-world reasoning often requires planning over multiple possible proof paths. To address these limitations, we introduce \Benchmark, a dynamic benchmark built from real citation relationships among scientific papers published after the evaluated models' knowledge cutoff date, which utilizes real-world information while ensuring no benchmark contamination. The fully automated benchmark construction pipeline samples representative subgraphs of the citation graph formed by these papers and converts each subgraph into a long-context QA example with a verifiable answer. We use GraphNIAH to evaluate eight LLMs from the GPT-5.6, Gemini-3, and Qwen3.5 families. We find that accuracy falls as questions require longer reasoning paths: at question depths of 16 and 32, the GPT-5.6 and Qwen3.5 models answer YES/NO questions no better than random guessing, mostly by answering NO; four of the eight models answer no counting example correctly, and the others model get worse as the subgraph size increases. These findings suggest that current LLMs often stop searching the citation relationships in their context before they reach the answer, even though every fact they need is in the context.

  • 2 authors
·
Oct 30

SealQA: Raising the Bar for Reasoning in Search-Augmented Language Models

We introduce SealQA, a new challenge benchmark for evaluating SEarch-Augmented Language models on fact-seeking questions where web search yields conflicting, noisy, or unhelpful results. SealQA comes in three flavors: (1) Seal-0 (main) and (2) Seal-Hard, which assess factual accuracy and reasoning capabilities, with Seal-0 focusing on the most challenging questions where chat models (e.g., GPT-4.1) typically achieve near-zero accuracy; and (3) LongSeal, which extends SealQA to test long-context, multi-document reasoning in "needle-in-a-haystack" settings. Our evaluation reveals critical limitations in current models: Even frontier LLMs perform poorly across all SealQA flavors. On Seal-0, frontier agentic models equipped with tools like o3 and o4-mini achieve only 17.1% and 6.3% accuracy, respectively, at their best reasoning efforts. We find that advanced reasoning models such as DeepSeek-R1-671B and o3-mini are highly vulnerable to noisy search results. Notably, increasing test-time compute does not yield reliable gains across o3-mini, o4-mini, and o3, with performance often plateauing or even declining early. Additionally, while recent models are less affected by the "lost-in-the-middle" issue, they still fail to reliably identify relevant documents in LongSeal when faced with numerous distractors. To facilitate future work, we release SealQA at huggingface.co/datasets/vtllms/sealqa.

  • 6 authors
·
Jun 1, 2025 2

Needle in the Web: A Benchmark for Retrieving Targeted Web Pages in the Wild

Large Language Models (LLMs) have evolved from simple chatbots into sophisticated agents capable of automating complex real-world tasks, where browsing and reasoning over live web content is key to assessing retrieval and cognitive skills. Existing benchmarks like BrowseComp and xBench-DeepSearch emphasize complex reasoning searches requiring multi-hop synthesis but neglect Fuzzy Exploratory Search, namely queries that are vague and multifaceted, where users seek the most relevant webpage rather than a single factual answer. To address this gap, we introduce Needle in the Web, a novel benchmark specifically designed to evaluate modern search agents and LLM-based systems on their ability to retrieve and reason over real-world web content in response to ambiguous, exploratory queries under varying levels of difficulty. Needle in the Web comprises 663 questions spanning seven distinct domains. To ensure high query quality and answer uniqueness, we employ a flexible methodology that reliably generates queries of controllable difficulty based on factual claims of web contents. We benchmark three leading LLMs and three agent-based search systems on Needle in the Web, finding that most models struggle: many achieve below 35% accuracy, and none consistently excel across domains or difficulty levels. These findings reveal that Needle in the Web presents a significant challenge for current search systems and highlights the open problem of effective fuzzy retrieval under semantic ambiguity.

  • 4 authors
·
Dec 18, 2025

A Controllable Examination for Long-Context Language Models

Existing frameworks for evaluating long-context language models (LCLM) can be broadly categorized into real-world and synthetic tasks. Despite their utility, both approaches are accompanied by certain intrinsic limitations. Real-world tasks are too complex to interpret or characterize and are susceptible to data contamination. In contrast, synthetic tasks often adopt the needle-in-the-haystack (NIAH) format, wherein a lack of coherence between the "needle" and the "haystack" compromises their validity as proxies for realistic applications. In response to these challenges, we posit that an ideal long-context evaluation framework should be characterized by three essential features: seamless context, controllable setting, and sound evaluation. This study introduces LongBioBench, a novel benchmark that utilizes artificially generated biographies as a controlled environment for assessing LCLMs across dimensions of understanding, reasoning, and trustworthiness. Our experimental evaluation, which includes 18 LCLMs in total, demonstrates that most models still exhibit deficiencies in semantic understanding and elementary reasoning over retrieved results and are less trustworthy as context length increases. Our further analysis indicates some design choices employed by existing synthetic benchmarks, such as contextual non-coherence, numerical needles, and the absence of distractors, rendering them vulnerable to test the model long-context capabilities. Moreover, we also reveal that long-context continual pretraining primarily adjusts RoPE embedding to accommodate extended context lengths. To sum up, compared to previous synthetic benchmarks, LongBioBench achieves a better trade-off between mirroring authentic language tasks and maintaining controllability, and is highly interpretable and configurable.

  • 7 authors
·
Jun 3, 2025 2

Beyond the Needle's Illusion: Decoupled Evaluation of Evidence Access and Use under Semantic Interference at 326M-Token Scale

Long-context LLM agents must access the right evidence from large environments and use it faithfully. However, the popular Needle-in-a-Haystack (NIAH) evaluation mostly measures benign span localization. The needle is near-unique, and the haystack is largely irrelevant. We introduce EverMemBench-S (EMB-S), an adversarial NIAH-style benchmark built on a 326M-token MemoryBank. While the full MemoryBank spans 326M tokens for retrieval-based (RAG) evaluation, we evaluate native long-context models only at scales that fit within each model's context window (up to 1M tokens in this work) to ensure a fair comparison. EMB-S pairs queries with collision-tested near-miss hard negatives and gold evidence sets spanning one or more documents, validated via human screening and LLM verification. We also propose a decoupled diagnostic protocol that reports evidence access (document-ID localization) separately from end-to-end QA quality under full-context prompting. This enables consistent diagnosis for both native long-context prompting and retrieval pipelines. Across a reference-corpus ladder from domain-isolated 64K contexts to a globally shared 326M-token environment, we observe a clear reality gap. Systems that saturate benign NIAH degrade sharply in evidence access under semantic interference. These results indicate that semantic discrimination, not context length alone, is the dominant bottleneck for long-context memory at scale.

  • 9 authors
·
Jan 28

Multimodal Needle in a Haystack: Benchmarking Long-Context Capability of Multimodal Large Language Models

Multimodal Large Language Models (MLLMs) have shown significant promise in various applications, leading to broad interest from researchers and practitioners alike. However, a comprehensive evaluation of their long-context capabilities remains underexplored. To address these gaps, we introduce the MultiModal Needle-in-a-haystack (MMNeedle) benchmark, specifically designed to assess the long-context capabilities of MLLMs. Besides multi-image input, we employ image stitching to further increase the input context length, and develop a protocol to automatically generate labels for sub-image level retrieval. Essentially, MMNeedle evaluates MLLMs by stress-testing their capability to locate a target sub-image (needle) within a set of images (haystack) based on textual instructions and descriptions of image contents. This setup necessitates an advanced understanding of extensive visual contexts and effective information retrieval within long-context image inputs. With this benchmark, we evaluate state-of-the-art MLLMs, encompassing both API-based and open-source models. The findings reveal that GPT-4o consistently surpasses other models in long-context scenarios, but suffers from hallucination problems in negative samples, i.e., when needles are not in the haystacks. Our comprehensive long-context evaluation of MLLMs also sheds lights on the considerable performance gap between API-based and open-source models. All the code, data, and instructions required to reproduce the main results are available at https://github.com/Wang-ML-Lab/multimodal-needle-in-a-haystack.

  • 9 authors
·
Jun 17, 2024 1

Learning to Discover at Test Time

How can we use AI to discover a new state of the art for a scientific problem? Prior work in test-time scaling, such as AlphaEvolve, performs search by prompting a frozen LLM. We perform reinforcement learning at test time, so the LLM can continue to train, but now with experience specific to the test problem. This form of continual learning is quite special, because its goal is to produce one great solution rather than many good ones on average, and to solve this very problem rather than generalize to other problems. Therefore, our learning objective and search subroutine are designed to prioritize the most promising solutions. We call this method Test-Time Training to Discover (TTT-Discover). Following prior work, we focus on problems with continuous rewards. We report results for every problem we attempted, across mathematics, GPU kernel engineering, algorithm design, and biology. TTT-Discover sets the new state of the art in almost all of them: (i) Erdős' minimum overlap problem and an autocorrelation inequality; (ii) a GPUMode kernel competition (up to 2times faster than prior art); (iii) past AtCoder algorithm competitions; and (iv) denoising problem in single-cell analysis. Our solutions are reviewed by experts or the organizers. All our results are achieved with an open model, OpenAI gpt-oss-120b, and can be reproduced with our publicly available code, in contrast to previous best results that required closed frontier models. Our test-time training runs are performed using Tinker, an API by Thinking Machines, with a cost of only a few hundred dollars per problem.

Haystack Engineering: Context Engineering for Heterogeneous and Agentic Long-Context Evaluation

Modern long-context large language models (LLMs) perform well on synthetic "needle-in-a-haystack" (NIAH) benchmarks, but such tests overlook how noisy contexts arise from biased retrieval and agentic workflows. We argue that haystack engineering is necessary to construct noisy long contexts that faithfully capture key real-world factors -- distraction from heterogeneous biased retrievers and cascading errors in agentic workflows -- to test models' long-context robustness. We instantiate it through HaystackCraft, a new NIAH benchmark built on the full English Wikipedia hyperlink network with multi-hop questions. HaystackCraft evaluates how heterogeneous retrieval strategies (e.g., sparse, dense, hybrid, and graph-based) affect distractor composition, haystack ordering, and downstream LLM performance. HaystackCraft further extends NIAH to dynamic, LLM-dependent settings that simulate agentic operations, where models refine queries, reflect on their past reasonings, and decide when to stop. Experiments with 15 long-context models show that (1) while stronger dense retrievers can introduce more challenging distractors, graph-based reranking simultaneously improves retrieval effectiveness and mitigates more harmful distractors; (2) in agentic tests, even advanced models like Gemini 2.5 Pro and GPT-5 suffer cascading failures from self-generated distractors or struggle to perform early stops. These results highlight persistent challenges in agentic long-context reasoning and establish HaystackCraft as a valuable testbed for future progress.

metaresearch Meta Research
·
Oct 8, 2025 2

Search-G1: Co-Evolving Representation-Based Rewards for Selective Grounded Search

Search-augmented language agents should retrieve external information only when necessary and ground their answers in retrieved evidence. Yet terminal correctness assigns equal credit to direct answers from parametric knowledge, evidence-grounded answers, and answers recalled after redundant search. Process supervision and LLM judges provide richer feedback but can require high-cost annotation or inference; low-cost, non-contrastive policy confidence signals do not directly identify whether retrieved evidence changes an answer. We propose Search-G1, a reward framework that couples retrieval necessity with evidence reliance through two intervention-calibrated hidden-state readouts for selective grounded search. A prompt readout predicts closed-book sufficiency, whose complement proxies policy-relative retrieval necessity; an answer-commit readout predicts evidence reliance as sensitivity to evidence deletion conditional on the realized reasoning prefix. A correctness-first reward gates evidence-reliance credit by retrieval necessity, rewards sufficient direct answers, and penalizes repeated search. After calibration, scoring needs neither process annotations nor LLM-judge inference. As policy-relative targets, trajectory distributions, and representations may drift, Search-G1 periodically regenerates targets and refits its readouts. Across four QA benchmarks and two scales, Search-G1 achieves competitive task accuracy, with stronger counterfactual evidence dependence and fewer searches in the main comparisons, complemented by independent human audits of answer support.

  • 10 authors
·
Oct 9

ACES: Who Tests the Tests? Leave-One-Out AUC Consistency for Code Generation

Selecting LLM-generated code candidates using LLM-generated tests is challenging because the tests themselves may be incorrect. Existing methods either treat all tests equally or rely on ad-hoc heuristics to filter unreliable tests. Yet determining test correctness requires knowing which codes are correct, creating a circular dependency. Our key insight is that we need not determine test correctness at all: test votes should rank, not merely count. What matters is not how many codes pass a test, but whether the test can distinguish correct from incorrect code. We break the circular dependency via leave-one-out evaluation: hold out one test, rank codes by their aggregate scores on all remaining tests, and measure whether the held-out test's pass/fail pattern agrees with this ranking. We formalize this agreement as the leave-one-out AUC~(LOO-AUC) and prove that the expected LOO-AUC is proportional to each test's ability to separate correct code from incorrect code. Building on this, we propose ACES~(AUC ConsistEncy Scoring) with two complementary variants: ACES-C provides closed-form weights that provably approximate the oracle in expectation under a mild assumption on average test quality; ACES-O drops this assumption and iteratively optimizes a differentiable LOO-AUC objective. Both operate solely on the binary pass matrix with negligible overhead, and achieve state-of-the-art Pass@k on multiple code generation benchmarks.

  • 7 authors
·
Apr 4 4

WildTrace: Benchmarking Natural Evidence Trails in Long-Context Reasoning

Answering complex questions over long documents frequently requires integrating evidence that the source itself disperses naturally across distant passages. In an incident report, the operating condition, design flaw, and missed safety check that jointly explain a disaster may appear dozens of sections apart; in a novel, a character's true motive may surface only through scenes far removed from the moment it becomes relevant. This source-internal evidence integration is central to real-world long-document analysis, yet existing benchmarks largely sidestep it. Needle probes, planted facts, and reverse-engineered multi-hop chains embed evidence that may differ from the host text in distribution, placement, or register, making it unclear whether strong performance reflects genuine source reasoning or distributional artifacts. We introduce WILDTRACE, a benchmark of 481 tasks over 214 naturally occurring long-form sources such as technical incident reports and lesser-known literary narratives, where all evidence trails arise from the document's own causal, temporal, and narrative logic. Drawing on Pearl's causal hierarchy and prior multi-hop reasoning typologies, we define seven source-internal evidence geometries that characterize the distinct relational demands of analytical reading in long documents. A source-first construction pipeline mines candidate trails from document structure before writing questions; each item then undergoes multi-stage validation covering clue necessity, answer groundedness, rubric fidelity, contamination resistance and answerability. As models are increasingly entrusted with real-world high-stakes analytical tasks, this gap between accessing information and reasoning over naturally dispersed evidence emerges as a defining challenge for the next stage of long-context research.

  • 10 authors
·
Jul 22

IRPAPERS: A Visual Document Benchmark for Scientific Retrieval and Question Answering

AI systems have achieved remarkable success in processing text and relational data, yet visual document processing remains relatively underexplored. Whereas traditional systems require OCR transcriptions to convert these visual documents into text and metadata, recent advances in multimodal foundation models offer retrieval and generation directly from document images. This raises a key question: How do image-based systems compare to established text-based methods? We introduce IRPAPERS, a benchmark of 3,230 pages from 166 scientific papers, with both an image and an OCR transcription for each page. Using 180 needle-in-the-haystack questions, we compare image- and text-based retrieval and question answering systems. Text retrieval using Arctic 2.0 embeddings, BM25, and hybrid text search achieved 46% Recall@1, 78% Recall@5, and 91% Recall@20, while image-based retrieval reaches 43%, 78%, and 93%, respectively. The two modalities exhibit complementary failures, enabling multimodal hybrid search to outperform either alone, achieving 49% Recall@1, 81% Recall@5, and 95% Recall@20. We further evaluate efficiency-performance tradeoffs with MUVERA and assess multiple multi-vector image embedding models. Among closed-source models, Cohere Embed v4 page image embeddings outperform Voyage 3 Large text embeddings and all tested open-source models, achieving 58% Recall@1, 87% Recall@5, and 97% Recall@20. For question answering, text-based RAG systems achieved higher ground-truth alignment than image-based systems (0.82 vs. 0.71), and both benefit substantially from increased retrieval depth, with multi-document retrieval outperforming oracle single-document retrieval. We analyze the complementary limitations of unimodal text and image representations and identify question types that require one modality over the other. The IRPAPERS dataset and all experimental code are publicly available.

  • 8 authors
·
Feb 5

Investigating Data Contamination in Modern Benchmarks for Large Language Models

Recent observations have underscored a disparity between the inflated benchmark scores and the actual performance of LLMs, raising concerns about potential contamination of evaluation benchmarks. This issue is especially critical for closed-source models and certain open-source models where training data transparency is lacking. In this paper we study data contamination by proposing two methods tailored for both open-source and proprietary LLMs. We first introduce a retrieval-based system to explore potential overlaps between evaluation benchmarks and pretraining corpora. We further present a novel investigation protocol named Testset Slot Guessing (TS-Guessing), applicable to both open and proprietary models. This approach entails masking a wrong answer in a multiple-choice question and prompting the model to fill in the gap. Additionally, it involves obscuring an unlikely word in an evaluation example and asking the model to produce it. We find that certain commercial LLMs could surprisingly guess the missing option in various test sets. Specifically, in the TruthfulQA benchmark, we find that LLMs exhibit notable performance improvement when provided with additional metadata in the benchmark. Further, in the MMLU benchmark, ChatGPT and GPT-4 demonstrated an exact match rate of 52\% and 57\%, respectively, in guessing the missing options in benchmark test data. We hope these results underscore the need for more robust evaluation methodologies and benchmarks in the field.

  • 5 authors
·
Nov 16, 2023

Same Agent, Different Answers: A Repeat-Aware Audit of Corpus-Induced Answer Churn in Retrieval-Augmented QA

A retrieval-augmented QA system can return different answers after an index expansion even when its requested model identifier, prompt, retrieval policy, evidence depth, rendering, and exposed generation controls are held fixed. Aggregate accuracy may hide these changes when gains and losses cancel, while ordinary generation variability makes one-shot comparisons overstate update effects. We call the hidden phenomenon accuracy-blind answer churn and introduce the Snapshot Compatibility Audit, which estimates excess answer churn by subtracting same-snapshot repeat disagreement from cross-snapshot disagreement. We instantiate it by expanding one frozen FineWeb prefix from one to seven shards. In a preregistered 400-question Natural Questions study, normalized-exact and blinded-semantic excess churn are 6.44 and 10.25 percentage points while exact-match accuracy changes by only -1.50 points. A post-hoc analysis finds repeat-stable semantic flips on 40/400 questions. A separately preregistered 200-question TriviaQA study yields smaller, directionally consistent excess churn while exact-match accuracy moves in the opposite direction. An outcome-blind post-hoc 100-question subset replication with a second DeepSeek generator and serving configuration finds 8.75 pp of semantic excess churn even as exact match rises by 3.00 percentage points. Answer-level compatibility can therefore fail without a conspicuous or consistently directed utility shift. Retrieval-augmented releases should audit compatibility alongside utility.

Beyond Overall Accuracy: A Psychometric Deep Dive into the Topic-Specific Medical Capabilities of 80 Large Language Models

As Large Language Models (LLMs) are increasingly proposed for high-stakes medical applications, there has emerged a critical need for reliable and accurate evaluation methodologies. Traditional accuracy metrics fail inadequately as they neither capture question characteristics nor offer topic-specific insights. To address this gap, we introduce MedIRT, a rigorous evaluation framework grounded in Item Response Theory (IRT), the gold standard in high-stakes educational testing. Unlike previous research relying on archival data, we prospectively gathered fresh responses from 80 diverse LLMs on a balanced, 1,100-question USMLE-aligned benchmark. Using one unidimensional two-parameter logistic IRT model per topic, we estimate LLM's latent model ability jointly with question difficulty and discrimination, yielding more stable and nuanced performance rankings than accuracy alone. Notably, we identify distinctive ``spiky'' ability profiles, where overall rankings can be misleading due to highly specialized model abilities. While GPT-5 was the top performer in a majority of domains (8 of 11), it was outperformed in Social Science and Communication by Claude-3-opus, demonstrating that even an overall 23rd-ranked model can hold the top spot for specific competencies. Furthermore, we demonstrate IRT's utility in auditing benchmarks by identifying flawed questions. We synthesize these findings into a practical decision-support framework that integrates our multi-factor competency profiles with operational metrics. This work establishes a robust, psychometrically grounded methodology essential for the safe, effective, and trustworthy deployment of LLMs in healthcare.

  • 4 authors
·
Sep 28, 2025

Consilience for Verifier-Free Test-Time Scaling

Test-time scaling often uses an external verifier, such as compilers and test cases in coding or trained value functions in robotics applications, to obtain high-quality rollouts. Verifier-free test-time scaling (or VF-TTS) is gaining extensive attention as a mechanism to enhance Large Language Model (LLM) reasoning, primarily because we do not have access to such high-quality verifiers in many real-world applications. Among existing VF-TTS methods, confidence-based VF-TTS methods, which compute and rank rollouts solely by confidence, are particularly promising. Such methods introduce near-zero overhead for sample evaluation and require minimal access to internal model states, making the methods highly flexible across models and tasks. In this paper, we demonstrate a critical limitation of existing confidence-based VF-TTS methods by showing that such methods catastrophically break down on complex tasks. We observe a very interesting phenomenon: uniformly high confidence frequently indicates a failure to explore, favoring confidently wrong answers. To address this, our core insight is that robust cognitive search requires a specific confidence trajectory pattern: such methods perform exploratory branching at the beginning, as manifested by low initial confidence, and converge to a high final confidence solution. To implement this insight, we introduce consilience, a novel selection framework that explicitly evaluates the temporal asymmetry of confidence in reasoning. We operationalize this via a combinatorial metric that actively penalizes high initial confidence while strictly demanding final certainty. Extensive experiments covering both graduate-level mathematics problems and free-form code generation demonstrate that consilience effectively outperforms existing baselines, validating our novel perspective on completion confidence.

  • 4 authors
·
Aug 9

MIR-Bench: Benchmarking LLM's Long-Context Intelligence via Many-Shot In-Context Inductive Reasoning

Inductive Reasoning (IR), the ability to summarize rules from examples and apply on new ones, has long been viewed as a primal ability for general intelligence and widely studied by cognitive science and AI researchers. Many benchmarks have been proposed to measure such ability for Large Language Models (LLMs); however, they focus on few-shot (usually <10) setting and lack evaluation for aggregating many pieces of information from long contexts. On the other hand, the ever-growing context length of LLMs have brought forth the novel paradigm of many-shot In-Context Learning (ICL), which addresses new tasks with hundreds to thousands of examples without expensive and inefficient fine-tuning. However, many-shot evaluations are mostly focused on classification (a very limited aspect of IR), and popular long-context LLM tasks such as Needle-In-A-Haystack (NIAH) seldom require complicated intelligence for integrating many pieces of information. To fix the issues from both worlds, we propose MIR-Bench, the first many-shot in-context inductive reasoning benchmark that asks LLM to induce output via input-output examples from underlying functions with diverse data format. Based on MIR-Bench, we study many novel problems for inductive reasoning and many-shot ICL, including robustness against erroneous shots and the effect of Chain-of-Thought (CoT), and acquired insightful findings.

  • 8 authors
·
Feb 14, 2025

Generating and Evaluating Tests for K-12 Students with Language Model Simulations: A Case Study on Sentence Reading Efficiency

Developing an educational test can be expensive and time-consuming, as each item must be written by experts and then evaluated by collecting hundreds of student responses. Moreover, many tests require multiple distinct sets of questions administered throughout the school year to closely monitor students' progress, known as parallel tests. In this study, we focus on tests of silent sentence reading efficiency, used to assess students' reading ability over time. To generate high-quality parallel tests, we propose to fine-tune large language models (LLMs) to simulate how previous students would have responded to unseen items. With these simulated responses, we can estimate each item's difficulty and ambiguity. We first use GPT-4 to generate new test items following a list of expert-developed rules and then apply a fine-tuned LLM to filter the items based on criteria from psychological measurements. We also propose an optimal-transport-inspired technique for generating parallel tests and show the generated tests closely correspond to the original test's difficulty and reliability based on crowdworker responses. Our evaluation of a generated test with 234 students from grades 2 to 8 produces test scores highly correlated (r=0.93) to those of a standard test form written by human experts and evaluated across thousands of K-12 students.

  • 6 authors
·
Oct 10, 2023

Evolving in Thought Space: Training a Small Model at Test Time Unlocks Better Discoveries

Open-ended scientific discovery often requires repeatedly proposing and evaluating candidate solutions. LLM-based systems can support this process by generating and refining executable solutions from verifier feedback. Methods such as TTT-Discover use test-time training (TTT) to update the solution-generating LLM from verifier feedback, adapting its generation policy to improve subsequent proposals on the target problem. However, this becomes expensive when reliable execution requires a large model, since training must maintain gradients, optimizer states, and policy statistics while repeatedly generating long, structured outputs. It also complicates credit assignment: outcome-level verifier feedback must jointly evaluate the high-level strategy and its low-level implementation. In this work, we introduce Guidance-TTT, which separates these roles. A compact guidance model is trained at test time to propose high-level strategic changes, while a frozen execution model implements them as complete executable solutions. At each step, the system selects a promising previously discovered solution, proposes a change, executes and verifies it, and updates only the guidance model using an adaptive group-relative RL objective. This concentrates test-time learning on short strategic decisions while retaining the implementation capability of a substantially stronger model without adapting it. Without web access, Guidance-TTT produces strong solutions across four distinct domains: combinatorial optimization (Polyomino Packing), heuristic programming (AHC058), machine learning (Lasso), and GPU kernel optimization (TriMul). Across these tasks, it outperforms the best solutions reported in prior work while remaining competitive with state-of-the-art results on public online leaderboards. Code is available at https://github.com/Human-Agent-Society/reef/tree/guidance-ttt-support.

  • 12 authors
·
Oct 4

TreeSeeker: Tree-Structured Trial, Error, and Return in Deep Search

Deep search requires agents to answer complex questions through multi-step web search, browsing, evidence comparison, and synthesis. A central challenge is deciding how to search when several directions look plausible but only some will later lead to reliable evidence. If an agent greedily follows the current best-looking direction, it may keep extending a weak continuation. If it explores without discipline, it may waste budget on disconnected trials. We propose TreeSeeker, an inference-time framework for controlled trial-and-error in deep search. TreeSeeker organizes search as branch-and-return search over tree-structured states, where each branch is a tentative direction for a sub-goal. At each round, TreeSearch reads all sub-goal trees, identifies active goals, and uses textual UCB signals of value, uncertainty, and risk to select among exploiting a promising branch, exploring an uncertain alternative, or pruning an unproductive continuation and returning to an earlier branch point. TreeMem supports this control loop by keeping evidence, uncertainty, conflicts, progress, and failure cues attached to the branches that produced them, so trial outcomes can guide later decisions. Experiments on XBench-DeepSearch, BrowseComp, and BrowseComp-ZH show that TreeSeeker consistently outperforms strong open-source baselines, suggesting that explicit branch-and-return control complements stronger reasoning and tool execution.

  • 11 authors
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Jun 9 3

HarnessTTT: Learn to Optimize Harness at Test-Time for Scientific Discovery

Scientific discovery with language models requires finding the best valid solution within a finite computational budget. We study how feedback from this search can improve the procedure used to conduct it. We introduce HarnessTTT, a test-time learning framework that trains a harness proposer while keeping the executor frozen. The proposer generates executable harnesses comprising system prompts, reusable skills, tools, middleware, and execution controls. Each harness guides a budgeted discovery rollout, whose outcome provides feedback for updating the proposer. A discovery-oriented policy-gradient objective combines gap-normalized rewards, leave-one-out advantages (RLOO), and max-sharpening to favor high-performing proposals. Generated components are validated before execution, and the search retains the best valid solution and selected harnesses across rounds. Across fourteen discovery tasks in mathematics, systems, GPU kernels, heuristic programming, astrodynamics, and biology, HarnessTTT with a frozen 9B executor improves on OpenEvolve with the same executor on all eleven benchmark tasks (e.g., from 1.17 to 2.64 on circle packing), improves on the discovery-fine-tuned Finch-9B by up to 92%, holds the best open-weight sub-10B result on nine, and reaches 0.380919 on Erdős minimum overlap, better than the best human reference of 0.380927. Scaling the proposer and frozen executor to 27B improves on eleven of fourteen tasks, and transferring the learned harnesses to GPT-5.5 matches or exceeds the strongest reported system of any backbone on nine of fourteen tasks. Together, these results show that harness search can itself be learned at test time: a trained proposer lets a small frozen executor search effectively, and the harnesses it finds carry over to stronger executors.

  • 8 authors
·
Oct 11

From Harm to Help: Turning Reasoning In-Context Demos into Assets for Reasoning LMs

Recent reasoning LLMs (RLMs), especially those trained with verifier-based reinforcement learning, often perform worse with few-shot CoT than with direct answering. We revisit this paradox using high-quality reasoning traces from DeepSeek-R1 as demonstrations and find that adding more exemplars consistently degrades accuracy, even when demonstrations are optimal. A detailed analysis reveals two mechanisms behind this decline: (i) semantic misguidance, where high textual similarity leads the model to treat the target as the same as the exemplar and to copy intermediate steps verbatim; and (ii) strategy transfer failure, where the model struggles to extract useful reasoning strategies and apply them to target questions. Guided by these, we introduce Insight-to-Solve (I2S), a sequential test-time procedure that turns demonstrations into explicit, reusable insights and derives a target-specific reasoning trace; optionally, the reasoning is self-refined for coherence and correctness (I2S+). Extensive experiments on diverse benchmarks show that I2S and I2S+ consistently outperform both direct answering and test-time scaling baselines across open- and closed-source models. Even for GPT models, our method helps: on AIME'25, GPT-4.1 rises by +14.0%, and o1-mini improves by +2.7% on AIME and +1.7% on GPQA, indicating that in-context demonstrations can be harnessed effectively via insight-refine-solve framework.

  • 11 authors
·
Sep 27, 2025 2

MIRAGE: Scaling Test-Time Inference with Parallel Graph-Retrieval-Augmented Reasoning Chains

Large reasoning models (LRMs) have shown significant progress in test-time scaling through chain-of-thought prompting. Current approaches like search-o1 integrate retrieval augmented generation (RAG) into multi-step reasoning processes but rely on a single, linear reasoning chain while incorporating unstructured textual information in a flat, context-agnostic manner. As a result, these approaches can lead to error accumulation throughout the reasoning chain, which significantly limits its effectiveness in medical question-answering (QA) tasks where both accuracy and traceability are critical requirements. To address these challenges, we propose MIRAGE (Multi-chain Inference with Retrieval-Augmented Graph Exploration), a novel test-time scalable reasoning framework that performs dynamic multi-chain inference over structured medical knowledge graphs. Specifically, MIRAGE 1) decomposes complex queries into entity-grounded sub-questions, 2) executes parallel inference chains, 3) retrieves evidence adaptively via neighbor expansion and multi-hop traversal, and 4) integrates answers using cross-chain verification to resolve contradictions. Experiments on three medical QA benchmarks (GenMedGPT-5k, CMCQA, and ExplainCPE) show that MIRAGE consistently outperforms GPT-4o, Tree-of-Thought variants, and other retrieval-augmented baselines in both automatic and human evaluations. Additionally, MIRAGE improves interpretability by generating explicit reasoning chains that trace each factual claim to concrete chains within the knowledge graph, making it well-suited for complex medical reasoning scenarios. The code will be available for further research.

  • 7 authors
·
Aug 25, 2025

Effective Test Generation Using Pre-trained Large Language Models and Mutation Testing

One of the critical phases in software development is software testing. Testing helps with identifying potential bugs and reducing maintenance costs. The goal of automated test generation tools is to ease the development of tests by suggesting efficient bug-revealing tests. Recently, researchers have leveraged Large Language Models (LLMs) of code to generate unit tests. While the code coverage of generated tests was usually assessed, the literature has acknowledged that the coverage is weakly correlated with the efficiency of tests in bug detection. To improve over this limitation, in this paper, we introduce MuTAP for improving the effectiveness of test cases generated by LLMs in terms of revealing bugs by leveraging mutation testing. Our goal is achieved by augmenting prompts with surviving mutants, as those mutants highlight the limitations of test cases in detecting bugs. MuTAP is capable of generating effective test cases in the absence of natural language descriptions of the Program Under Test (PUTs). We employ different LLMs within MuTAP and evaluate their performance on different benchmarks. Our results show that our proposed method is able to detect up to 28% more faulty human-written code snippets. Among these, 17% remained undetected by both the current state-of-the-art fully automated test generation tool (i.e., Pynguin) and zero-shot/few-shot learning approaches on LLMs. Furthermore, MuTAP achieves a Mutation Score (MS) of 93.57% on synthetic buggy code, outperforming all other approaches in our evaluation. Our findings suggest that although LLMs can serve as a useful tool to generate test cases, they require specific post-processing steps to enhance the effectiveness of the generated test cases which may suffer from syntactic or functional errors and may be ineffective in detecting certain types of bugs and testing corner cases PUTs.

  • 5 authors
·
Aug 31, 2023

CachedSearch: Training-Free Cached Exploration for Test-Time Search in Video Diffusion

Test-time search lets small video diffusion models rival larger ones, but costs 2-10x more. All candidates are fully denoised, although most are discarded. Training-free caching makes each rollout 2-3x faster at near-lossless quality. Composition is safe only if lossy caching preserves verifier rankings. We present the first study of whether caching corrupts candidate ranking in video test-time search. On Wan2.1-T2V-1.3B with an adaptive caching wrapper (~2x per-candidate speedup), ImageReward scores seed-matched cached and full rollouts. Median per-prompt Spearman rank correlation is 0.905, with 72% top-1 agreement on the VBench suite. VBench-2.0 replicates this result on a harder suite. Recomputing the cached winner at full compute retains 90-94% of the full-search gain. Errors cluster among near-tied candidates, making corruption self-limiting. This finding leads to CachedSearch. It explores every candidate with aggressive caching, then re-generates only the winner at full compute. At N=8, it captures 94.7% of best-of-N's gain at 63% of the cost. Capture rises with width. At matched budget, it searches twice as wide for 38% more gain. The result holds from 1.3B-14B across six models and four families: Wan, LTX, CogVideoX, and Hunyuan. Wan2.1-14B matches the 1.3B model's fidelity. Mid-trajectory pruning multiplies the exploration saving to 3.11x at 88.6% capture. Ports to other model families require recalibrating a single parameter, showing that fidelity tracks architecture rather than parameter count. CachedSearch is training-free, verifier-agnostic, and orthogonal to the search algorithm, making it a plug-in multiplier for test-time scaling.

  • 5 authors
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Jul 29

Effectiveness of Hidden-State Probes for Localizing Reasoning Failures

Verifying the final answer of a long reasoning trace may show that the trace is wrong but it does not distinguish three cases. The problem may lie beyond the model's capability, another attempt would succeed, or one step in an otherwise recoverable trace made the trace fail. Standard hidden-state probes are trained on final-answer correctness, a label that conflates these cases. Monte Carlo rollouts distinguish the cases and locate the failing step at additional inference cost. We test the hidden states of 4B and 8B reasoning models for the failure type and the failing step and compare each probe with the strongest baseline that uses no hidden states. On incorrect 8B traces, the confidence probe, a calibrated correctness probe at a midpoint cutoff, misses 81% of cases in which a single step makes the trace unrecoverable and 47% of cases in which another attempt would succeed. A probe with a different training design over the same states reverses the ordering of these two kinds of failure, so either ordering can be read from those states. At both scales, no single tested probe locates the failing step more accurately than a rule based only on trace length, and at 4B a probe trained to predict that step fails to outperform this rule in any of 10 runs on identical traces. The confidence probe therefore indicates that an answer is wrong, but its failure-type ordering depends on its training design.

  • 5 authors
·
Oct 14

Demystifying deep search: a holistic evaluation with hint-free multi-hop questions and factorised metrics

RAG (Retrieval-Augmented Generation) systems and web agents are increasingly evaluated on multi-hop deep search tasks, yet current practice suffers from two major limitations. First, most benchmarks leak the reasoning path in the question text, allowing models to follow surface cues rather than discover reasoning chains autonomously. Second, evaluation is typically reduced to a single pass rate, which collapses diverse behaviours into one score and obscures whether failures stem from inadequate search, poor knowledge use, or inappropriate refusal. To address these issues, we present WebDetective, a benchmark of hint-free multi-hop questions paired with a controlled Wikipedia sandbox that ensures full traceability of model actions, and a holistic evaluation framework that separates search sufficiency, knowledge utilisation, and refusal behaviour. Our evaluation of 25 state-of-the-art models reveals systematic weaknesses across all architectures: models struggle with knowledge utilisation despite having sufficient evidence and demonstrate near-absent appropriate refusal when evidence is lacking. These patterns expose a fundamental gap: today's systems excel at executing given reasoning paths but fail when required to discover them. We develop an agentic workflow, EvidenceLoop, that explicitly targets the challenges our benchmark identifies, incorporating verification loops and systematic evidence tracking that improve both search and synthesis capabilities. This baseline demonstrates that WebDetective's diagnostic framework can guide concrete architectural improvements, establishing our benchmark as a critical tool for developing genuinely autonomous reasoning systems rather than pattern-following agents.

MedHopQA: A Disease-Centered Multi-Hop Reasoning Benchmark and Evaluation Framework for LLM-Based Biomedical Question Answering

Evaluating large language models (LLMs) in the biomedical domain requires benchmarks that can distinguish reasoning from pattern matching and remain discriminative as model capabilities improve. Existing biomedical question answering (QA) benchmarks are limited in this respect. Multiple-choice formats can allow models to succeed through answer elimination rather than inference, while widely circulated exam-style datasets are increasingly vulnerable to performance saturation and training data contamination. Multi-hop reasoning, defined as the ability to integrate information across multiple sources to derive an answer, is central to clinically meaningful tasks such as diagnostic support, literature-based discovery, and hypothesis generation, yet remains underrepresented in current biomedical QA benchmarks. MedHopQA is a disease-centered multi-hop reasoning benchmark consisting of 1,000 expert-curated question-answer pairs introduced as a shared task at BioCreative IX. Each question requires synthesis of information across two distinct Wikipedia articles, and answers are provided in an open-ended free-text format. Gold annotations are augmented with ontology-grounded synonym sets from MONDO, NCBI Gene, and NCBI Taxonomy to support both lexical and concept-level evaluation. MedHopQA was constructed through a structured process combining human annotation, triage, iterative verification, and LLM-as-a-judge validation. To reduce leaderboard gaming and contamination risk, the 1,000 scored questions are embedded within a publicly downloadable set of 10,000 questions, with answers withheld, on a CodaBench leaderboard. MedHopQA provides both a benchmark and a reusable framework for constructing future biomedical QA datasets that prioritize compositional reasoning, saturation resistance, and contamination resistance as core design constraints.

  • 16 authors
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May 11

Excess Separability: Nuisance-Controlled Residual-Stream Probing for Benchmark Contamination Detection

Benchmark contamination is diagnosed with n-gram overlap, likelihood-based membership inference, or canary strings, and each needs something usually unavailable: the training corpus, a well-chosen test statistic, or foresight at release. A recent alternative reads it off a linear probe on internal activations. We show the natural way to do this does not work, specify one that survives measurement, then find that the correction making it work carries more variance than the null it is tested against. The protocol reports a zero-sum contrast on the depth profile of probe accuracy, recentred on a level-matched placebo baseline, tested against a label-permutation null, with the reference set twice the size of the suspect set. Each choice replaces a simpler alternative we rejected on measurement. Reporting the level of excess separability rather than its shape makes the false positive rate track the size of the analyst's own control set, 0.03 to 0.99 under a true null. Contrasting against a flat depth profile rejects a true null 0.72 of the time when surface decodability rises with depth, and loses all power when it falls. On real transformers the protocol fails a test the simulations did not pose. The recentring subtracts an estimate, and the permutation null holds it fixed. Re-estimated across split seeds on four audits of contaminated checkpoints, its standard deviation is 1.30 to 1.56 times the null's own in every arm: what is subtracted to remove a bias is more variable than what it corrects. The one nominally significant result, p = 0.0075, becomes 0.0745 once that variance is propagated, and no verdict is issued. The simulations missed this because their surface key is the covariate driving item variation; on real text it is a proxy, and degrading key quality in simulation reproduces it. We add a companion measurement and a widened null. No arm shows contamination.

  • 1 authors
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Aug 15

Fixing a Model That Learned Worse Cancer Means Lower Risk: Monotonic Constraints in Bladder Cancer Recurrence Prediction

Background and Objective: Clinicians expect recurrence risk to climb with cancer severity. In a UK multicentre trial, an unconstrained XGBoost model learnt that higher tumour stage and carcinoma in situ predicted lower recurrence risk, and discrimination, calibration, and SHAP were all blind to it. We developed a counterfactual testing framework to detect this inversion and a monotonic-constraint framework to remove it without hurting performance. Methods: BOXIT enrolled 472 patients with protocol-mandated cystoscopy across 51 UK sites (2007-2012); 435 had at least two years' follow-up (153 recurrences, 35.2%). We developed a counterfactual direction test and a monotonic-constraint correction, with constraint directions drawn from the EORTC and EAU risk systems, and evaluated both against unconstrained XGBoost and logistic regression on 18 predictors (seven directed) over 50 cross-validation folds. The test worsened each patient on one directed feature at a time to check whether risk fell; SHAP direction and calibration were also assessed. Key Findings and Limitations: Tumour stage and carcinoma in situ were associated with lower recurrence, opposite to medical intuition; the unconstrained model reversed carcinoma in situ counterfactuals in 90.2% of cases and stage in 74.3%. Discrimination (ΔAUC 0.005, p=0.47), calibration, and SHAP magnitude were all blind to the inversion. Monotonic constraints eliminated every violation at no cost to discrimination (0.723 vs 0.718) and outperformed EORTC (p=8.9e-16). Limitations: single trial, internal-external validation only. Conclusions and Clinical Implications: A model that had learned this inversion passed every conventional check. A counterfactual direction test, run as a single refit with pre-specified monotonic constraints, catches this failure at no cost to performance and should be routine before clinical deployment.

  • 6 authors
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Sep 30