We present our submission to the IJCAI 2025 'Counterfactual Routing Competition' (CRC 25). The goal of the competition is to find counterfactual explanations for the shortest path problem. This requires deciding what the minimal changes to a road network would make a route chosen by the user the optimal route. This enables explanations such as "Your suggested route would indeed have been optimal, if road X were not a bicycle path." Our solution models the problem as an integer program, iteratively incorporating constraints until an exact solution is found. In the final evaluation on held-out test instances, our method ranked fourth in solution quality and obtained its solution fastest on every instance, with an average runtime of 9.0 seconds compared to 118.8 seconds for the next-fastest submission.
General-purpose code embeddings power tools for code search, classification, and retrieval. Compact transformer encoders for code typically rely on either human-written docstrings (labor-intensive and inconsistent) or mined structural signals such as execution traces (setting-specific and costly to collect). We empirically study an alternative: contrastive pretraining of small encoders with synthetically generated natural-language descriptions emphasizing code functionality and intent, paired with code in a dual-encoder framework at training and discarded at inference. We benchmark this approach against pretraining-based baselines, generalist LLMs, and embedding-specific models on eight retrieval, classification, and generation tasks across C, C++, and Java. Synthetic semantic supervision yields statistically significant gains over pretraining baselines of the same inference-time size on five of eight tasks, with parity on two more; once fine-tuned, it matches or exceeds zero-shot models two orders of magnitude larger on classification, and it stays on par with execution-aware supervision at matched pretraining data, suggesting a scalable, effective alternative to existing code-representation paradigms.
Kenneth Paulsen, Florian Tambon, Mike Papadakis et al.· 0 citations
Clinical trials in the UK can cost up to {\pounds}1.3 million, with approximately 90% drug failure rate. Toxicity is a major contributing factor in drug failure. Testing is time and cost intensive. In recent years, the use of artificial intelligence has been increasingly explored to aid in the prediction of drug toxicity, with extensive use of large language models (LLMs). However, LLMs can show considerable variation when minor changes are made to prompts, which raises concerns about their sensitivity to prompt engineering. Prompt engineering is used to optimise a prompt given to an LLM to generate the desired output. This paper proposes a method to analyse prompt engineering for drug toxicity prediction. The aim of the paper is to investigate the importance of prompt phrasing for drug toxicity prediction. LLMs were prompted to identify chemical properties of significance when predicting drug toxicity. Prompts were constructed to investigate; job role, prompt structuring, and rule interpretation. LLMs were then used to generate datasets, using the identified features from initial prompting, which were then passed to machine learning algorithms. The experiments show that the natural variance which occurs in LLMs outweighs any fine-tuning of prompts. There were, however, substantial improvements in model performance when using chemoinformatic code to extract features instead of using LLM-generated values. The proposed analysis methodology is applicable to a wide range of prompt types across different areas of bioinformatics.
Mia MacGregor, Aakash Welgamage Don, Mark Bartlett· 0 citations
Making science computable requires representations of both scientific knowledge and the physical world in which scientific claims are tested. A computable representation of the physical laboratory is established through typed research objects, capability-bound operations and a compositional workflow algebra. It provides the physical-world counterpart to machine-readable knowledge, expressing workflows as programs over evolving laboratory states with explicit dependencies, decisions, iteration and concurrency. The representation was implemented in a modular agentic robotic laboratory by binding formal operations to executable Function Skills. For diverse scientific intents, capability-relative workflows were generated, while stateful simulation propagated object transformations and verified operation preconditions and laboratory constraints before dispatch. The proposed representation and its engineering framework jointly establish a general computational interface between agent reasoning and capability-bound physical transformations, providing a foundation for end-to-end autonomous scientific discovery.
Xiaobo Li, Luyao Ge, Xiaohui Li et al.· 0 citations
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As LLMs increasingly act through tools, they must reconcile user instructions, parametric knowledge, and dynamic environmental observations before taking actions. We introduce KC-Bench, a controlled multi-turn benchmark for measuring this capability across world-knowledge conflicts, input inconsistencies, and multi-source temporal conflicts. Its 238 tasks are manually screened from more than 1,000 generated candidates and combine a user simulator, stateful tools, deterministic environment assertions, an open-source natural-language evaluator, and human trajectory verification. Evaluation of nine models, including DeepSeek-V4-Flash, GLM-5.2, and MiniMax-M3, shows substantial cross-domain variation: no model handles factual correction, identity consistency checking, and temporal conflict resolution reliably across all settings. In the simulated environments, missed conflicts can propagate to tool calls or synthetic protected-data flows. KC-Bench isolates this model-level behavior rather than ranking complete agent frameworks, and provides a reproducible diagnostic for developing conflict-aware reasoning and execution safeguards.
Yaxing Lyu, Sheng-Jie Zhou, Binbin Toh et al.· 0 citations
Audio-video diffusion models rely on cross-modal attention to coordinate text, sound, and visual content, yet this same mechanism can introduce subtle and systematic semantic leakage. We study these models by probing and analyzing the ``attention triangle,'' comprising the three cross-attention edges connecting the text, audio, and video streams, and examine how semantic information is routed across modalities during generation. Our analysis reveals that routing along the audio-video edge is bidirectional: audio can influence video generation, while video can influence audio generation. This edge is shaped by biases encoded in the model's parameters and emerges as a major contributor to leakage: when prompts are in tension with learned priors, cross-modal interactions may override the intended conditioning and reroute semantics toward visually canonical but incorrect outcomes. These effects suggest that semantic artifacts arise not merely from attention spreading beyond its intended target, but from structured, bias-driven interactions along specific pathways. Building on this perspective, we extract attention-derived signals that expose how semantics are distributed and grounded across modalities, and use them as a diagnostic tool to both analyze and deliberately incur leakage under controlled conditions. This enables us to probe the internal dynamics of cross-modal routing and isolate the role of individual interactions. We further leverage these signals to guide inference-time interventions that encourage more consistent cross-modal alignment. Extensive experiments support our analysis and demonstrate improved semantic grounding while preserving generation quality.
Sagi Polaczek, Noa Kraicer, Gal Metzer et al.· 0 citations
The growing scale of academic peer review has motivated the use of Large Language Models (LLMs) as review assistants, yet LLMs can generate fluent but unsupported claims that undermine review reliability. Existing hallucination benchmarks are not designed for peer review, where verification requires grounding claims in long, technical papers. We introduce HalluPeer, a benchmark for detecting hallucinations in scientific peer reviews, providing aligned triples of paper content, human-written reviews, and hallucination-injected reviews, annotated for detection, classification, and localization. Our pipeline induces a peer-review-specific hallucination taxonomy, identifies review contexts, and injects hallucinations with automated filtering. Experiments on 12K papers and 38K reviews show that existing detectors struggle to separate hallucinations from legitimate critique, while evaluation on authentic reviews demonstrates that HalluPeer-defined hallucination patterns occur in real peer reviews, highlighting the critical need for source-aware verification. Our project page can be found in https://github.com/Lin-TzuLing/HalluPeer.git
Tzu-Ling Lin, Dong-Ting Yao, Teng-Fang Hsiao et al.· 0 citations
Policy analysis requires more than predicting whether a proposal will pass: it requires identifying who will be affected, how those actors respond, and what follows. LLM-based policy simulations model these processes at scale, but their validity is hard to establish when plausible behaviour is never compared with observed outcomes. We introduce GPS-Bench, an evidence-grounded benchmark for governance policy simulation that links policies to relevant actors, actor actions and downstream impacts using legislative records, lobbying disclosures, regulatory documents, corporate filings, economic data and other public evidence. Actors are reconstructed from the dated record rather than prompted as archetypes, so a persona is an evidence object with provenance; a human-annotated pool forms the Gold evaluation set, while cases labelled by a separate LLM from retrieved evidence are treated as Silver supervision and never as test labels. Because every inference mode reads the same grounded state and emits the same schema, GPS-Bench turns "does multi-agent simulation help?" into a controlled comparison: we contrast joint reasoning, independent and communicating actor agents, graph-based methods and weight-level fine-tuning over one policy state. Fine-tuning on the grounded record gives the strongest actor-level impact prediction, and decomposition does not beat it; what decomposition adds is mechanism. Agents hold private, non-identical evidence, each seeing its own exposure clause, and address named partners with concrete joint proposals, what they offer, what they need in return, and why acting together beats acting alone, so the coalitions that form can be checked against the commitments the record holds. GPS-Bench therefore gives a common empirical setting for studying when evidence, actor modelling and multi-agent interaction improve the prediction and interpretation of policy outcomes.
Linh Le, Melanie Bui, My Chiffon Nguyen et al.· 0 citations
We present Dalek, a closed machine designed for agents that realizes self-maintenance, self-evolution, self-reproduction, and self-organization on any substrate satisfying a general host contract. The machine is built from three primitives---actors, messages, and channels. Four obligations---a host boundary, a construction language, admissible transitions, and rule heredity---give its boundary, identity, and closure a structural basis.
Von Neumann's 1948 self-reproducing automaton supplies a hereditary constructional core: a self-description together with a constructor, a copier, and a controller. Dalek combines this core with the four obligations and rederives its medium for a text-and-message agent substrate, adding explicit structures for boundary, identity, history, and growth. A large language model and a compiler occupy the payload position and form a general capability producer. New capabilities are authored, compiled, installed into the description, and inherited by descendants. The same path produces the machine's own organs and even its runtime, closing heredity and evolution within the machine.
Lesion segmentation in medical images plays a critical role in clinical diagnosis and treatment planning. Despite significant advances, lesion segmentation remains challenging due to two major factors: (1) complex background interference; (2) diverse lesion morphology. Existing encoder-decoder based methods mainly focus on enhancing feature extraction or redesigning decoding strategies. However, they lack early prior guidance and feature reconfiguration during the encoding stage, limiting their effectiveness in handling these challenges. To address these limitations, we propose FreNet, a feature reconfiguration framework with visual priors, which performs pixel-level reconfiguration before encoding and feature-level reconfiguration during encoding for precise medical lesion segmentation. To suppress background responses, we propose an Implicit Prior Neural Network (IPNN), which models a continuous spatial field and leverages visual prior from SAM to reconfigure input image before encoding stage. To better handle diverse lesion morphology, we design a Dual-domain Feature Reconfiguration (DFR) module to progressively reconfigure backbone features during encoding stage. Within DFR, the Frequency Decoupling Module (FDM) decouples backbone features in frequency domain to enhance foreground-background discriminability, while the Spatial Localization Module (SLM) spatially relocates and improving spatial stability after frequency decoupling. Extensive experiments on 9 medical image segmentation benchmarks across three imaging modalities demonstrate that FreNet significantly outperforms state-of-the-art (SOTA) methods. On the challenging ETIS dataset, our method achieves Dice improvements of 5.0% over SOTA method and 7.2% over SAM.
Yinan Liu, Jiankang Hong, Zhen Gao et al.· 0 citations
Neonatal respiratory diseases are a major cause of neonatal morbidity and mortality, posing substantial challenges in clinical practice. Despite recent advances, existing Multimodal Large Language Models (MLLMs) face two key limitations in neonatal diagnosis: (1) domain gap arising from predominantly adult training data; (2) insufficient integration of multidimensional clinical context for accurate diagnosis. To address these challenges, we collect two real-world clinical datasets (NeoCXR and NeoCXR-EV) and propose NeoRed, to the best of our knowledge, the first MLLM tailored for neonatal respiratory disease, filling the gap in neonatal diagnostic reports generation. To enhance joint diagnosis from heterogeneous clinical context and chest X-rays, we design a novel Knowledge-Logic-Alignment (KLA) framework which constrains model behavior from three perspectives: 1) Knowledge Prior Injection (KPI) incorporates neonatologist-inspired diagnostic priors into multimodal representations, guiding disease-specific attention across modalities; 2) Diagnostic Logic Constraint (DLC) aligns the semantics of generated reports with multimodal diagnostic logic; and 3) Visual Semantic Alignment (VSA) establishes semantic correspondence between visual features and imaging conclusions. Extensive experiments demonstrate that NeoRed enables accurate neonatal diagnostic reports generation, achieving ROUGE-L of 53.29% and Clinical Efficacy F1 score of 65.19% on NeoCXR, outperforming existing MLLMs. NeoRed also preserves competitive report generation performance on adult benchmarks (MIMIC-CXR and IU-Xray). Datasets will be available upon application.
Yinan Liu, Hongtai Xia, Haoran Xu et al.· 0 citations
Multimodal language models achieve near-ceiling scores on food recognition benchmarks, yet it remains unclear whether this success reflects genuine cultural understanding or mere visual matching. To probe this distinction, we introduce CulturalMenuBench, a benchmark of 4,870 items in 10 languages across 18 regions; its 10 tasks pair final-dish and step-by-step cooking images with ingredients, procedural text, and regional labels, spanning basic recognition to process-grounded cultural attribution. Evaluating 12 models exposes a substantial knowledge-application gap: models exceeding 94% on standard multiple-choice tasks drop to at most 56% when attributing dishes to Chinese regional cuisines, despite an identical four-way format. Diagnostic analyses explain why: error patterns are consistent with random guessing, accuracy tracks visual distinctiveness rather than cultural structure, and models classify cuisines more accurately from dish names alone than from images (+7-18 points). The knowledge is thus present but cannot be activated through visual input. An ablation confirms these tasks genuinely require procedural evidence: removing sequential cooking images selectively degrades process-grounded tasks while others remain stable. Overall, CulturalMenuBench shows that near-perfect recognition can conceal an inability to apply cultural knowledge, motivating training that explicitly connects perception, procedure, and cultural context. Code and data are publicly available.
Bo Zeng, Linfeng Gao, Peiqin Lin et al.· 0 citations
