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01.
arXiv (CS.CL) 2026-06-18

TopBench: A Benchmark for Implicit Predictive Reasoning in Tabular Question Answering

Large Language Models (LLMs) have advanced Table Question Answering, where most queries can be answered by extracting information or simple aggregation. However, a common class of real-world queries is implicitly predictive, requiring the inference of unobserved answers from historical patterns rather than mere retrieval. These queries introduce two challenges: recognizing latent intent and reliable predictive reasoning over massive tables. To assess LLMs in such Tabular questiOn answering with implicit Prediction tasks, we introduce TopBench, a benchmark consisting of 779 samples across four sub-tasks, ranging from single-point prediction to decision making, treatment effect analysis, and complex filtering, requiring models to generate outputs spanning reasoning text and structured tables. We evaluate diverse models under both text-based and agentic workflows. Experiments reveal that current models often struggle with intent recognition, defaulting to just lookups. Deeper analysis identifies that accurate intent disambiguation serves as the prerequisite for leading these predictive behaviors. Furthermore, elevating the upper bound of prediction precision requires the integration of more sophisticated modeling or reasoning capabilities.

02.
arXiv (CS.CV) 2026-06-25

Enhancing Brain MRI Anomaly Detection and Reasoning with ROI Rethink and Synthetic Data

Medical vision-language models typically generate diagnoses through single-pass inference without indicating which image regions support their conclusions. This lack of spatial grounding limits clinical utility: outputs cannot be audited, and models may hallucinate findings on normal scans. We present BrReMark (Brain Rethink via ROI Marking), a framework that introduces explicit region marking into brain MRI diagnosis. The model first generates hypotheses about potential abnormalities and grounds them through explicit bounding box marking, then verifies conclusions by re-examining the marked evidence. Training combines supervised fine-tuning on structured reasoning trajectories with reinforcement learning using a composite reward over localization accuracy and diagnostic reasoning. Furthermore, we integrate a domain randomization-based pathology synthesis augmentation strategy to improve the model's generalizability to out-of-distribution (OOD) data. On internal benchmark, BrReMark improves mAP50 from 0.74% to 37.54% compared to the base model, while achieving 21.57% Clinical F1 and 45.26% diagnostic accuracy. On NOVA OOD benchmark, it also achieves competitive overall performance with a 45.7% reduction in false positives compared to the state-of-the-art, indicating reduced hallucination on rare pathologies. These findings suggest that explicit hypothesis-verification grounding is a practical path toward trustworthy open-ended brain MRI diagnosis across both in-distribution and OOD settings.

03.
arXiv (CS.CV) 2026-06-16

A Survey on 3D Gaussian Splatting Applications: Segmentation, Editing, and Generation

In the context of novel view synthesis, 3D Gaussian Splatting (3DGS) has recently emerged as an efficient and competitive counterpart to Neural Radiance Field (NeRF), enabling high-fidelity photorealistic rendering in real time. Beyond novel view synthesis, the explicit and compact nature of 3DGS enables a wide range of downstream applications that require geometric and semantic understanding. This survey provides a comprehensive overview of recent progress in 3DGS applications. It first reviews the reconstruction preliminaries of 3DGS, followed by the problem formulation, 2D foundation models, and related NeRF-based research areas that inform downstream 3DGS applications. We then categorize 3DGS applications into three foundational tasks: segmentation, editing, and generation, alongside additional functional applications built upon or tightly coupled with these foundational capabilities. For each, we summarize representative methods, supervision strategies, and learning paradigms, highlighting shared design principles and emerging trends. Commonly used datasets and evaluation protocols are also summarized, along with comparative analyses of recent methods across public benchmarks. To support ongoing research and development, a continually updated repository of papers, code, and resources is maintained at https://github.com/heshuting555/Awesome-3DGS-Applications.

04.
arXiv (CS.LG) 2026-06-11

RePAIR: Predictive Self-Supervised Representation Learning in Chess

arXiv:2606.11860v1 Announce Type: new Abstract: In this paper, we introduce Representation Prediction via Autoencoding using Iterative Refinement (RePAIR) - a novel self-supervised representation learning architecture that synthesizes Masked Autoencoders (MAE), Joint Embedding Predictive Architectures (JEPA), and Bidirectional Encoder Representations from Transformers (BERT). We demonstrate how it can be used to encode objects in sequential data like consecutive chess positions into compact yet meaningful representations. The basic principle of the architecture is to mask large portions of a sequence of latent states, similar to BERT and MAE. Then, we apply a lightweight Predictor to the latent representations that repairs gaps in the sequence in a lower-dimensional embedding space akin to JEPA. Our experiments in the domain of chess show that the Encoder refines the board representations such that meaningful chess concepts emerge clustered in the latent space. Furthermore, reconstructions of the masked board states show that the model is able to reason about the piece movements without relying on costly reinforcement learning methods. Lastly, we find that the resulting representation space allows for quick and intuitive dissections of chess games by observing the game path trajectories in this semantically rich space.

05.
arXiv (CS.AI) 2026-06-16

ToolMenuBench: Benchmarking Tool-Menu Filtering Strategies for Reliable and Efficient LLM Agents

arXiv:2606.15508v1 Announce Type: new Abstract: Tool-augmented large language model agents increasingly operate over large tool libraries, but existing evaluations often focus on whether a model can call a tool correctly rather than how the visible tool menu shapes reliability, efficiency, and safety-relevant risk exposure. We introduce ToolMenuBench, a benchmark for evaluating tool-menu construction in multi-step LLM agents. ToolMenuBench varies tool-menu size, distractor type, state-dependent task structure, and risk exposure, and reports both filter-level and downstream agent metrics, including visible-tool count, risky-tool exposure, task success, wrong-tool calls, premature actions, and token usage. In a controlled evaluation across seven model backends, three tool-menu sizes, six filtering methods, and seven evaluation settings, CMTF improves task success from 32.1% under all-tools exposure to 85.7%, while reducing average token usage by roughly 98%. Causal minimal tool filtering achieves the strongest overall tradeoff, reducing visible tools, wrong-tool calls, premature actions, and risky-tool exposure relative to unfiltered exposure, lexical filtering, state-aware filtering, and broader causal-path baselines. ToolMenuBench provides a reusable evaluation framework for studying the agent-interface problem: which tools should be visible, when they should be visible, and under what cost or risk constraints.

06.
arXiv (CS.AI) 2026-06-16

Optimising Temporary Accommodation Placement Across London with AI-Powered SaaS in E-Governance Systems

arXiv:2606.16652v1 Announce Type: cross Abstract: Temporary accommodation has become a major fiscal and administrative pressure for English local authorities, particularly in London, where demand and costs have risen sharply. This paper documents the creation and use of DOMUS, a cloud-based, AI-enabled decision-support system built from scratch at the University of East London and customised for the needs of London Borough of Newham to support statutory Temporary accommodation placement. DOMUS integrates household case records, policy-constrained affordability and suitability rules, and live private-rental listings within a single governance-aligned workflow. The system combines transparent, rule-based filtering with large language model-assisted search to standardise the application of bedroom need, affordability thresholds, geographic preferences, and accessibility requirements, while preserving officer discretion and audibility. Household and property attributes are encoded into policy-consistent representations prior to AI-assisted ranking and explanation. A pilot deployment in Newham's secure environment evaluated operational performance relative to manual workflows. Results indicate substantial reductions in search time, improved adherence to key placement constraints, and high staff satisfaction, while maintaining statutory compliance and role-based accountability. Beyond TA, the paper frames DOMUS as replicable digital public infrastructure: a modular, cloud-native Software-as-a-Service architecture that can be deployed across other UK boroughs and adapted to other public administration tasks characterised by scarcity, rule-bound eligibility, and high stakes. The findings demonstrate the feasibility of scalable, ethically governed AI deployment in local government and contribute to debates on AI-enabled public value creation in e-governance.

07.
arXiv (CS.LG) 2026-06-24

Posterior Sampling Reinforcement Learning with Gaussian Processes for Continuous Control: Sublinear Regret Bounds for Unbounded State Spaces

arXiv:2603.08287v2 Announce Type: replace-cross Abstract: We analyze the Bayesian regret of the Gaussian process posterior sampling reinforcement learning (GP-PSRL) algorithm. Posterior sampling is a heuristic for decision-making under uncertainty that has been used to develop successful algorithms for a variety of continuous control problems. However, theoretical work on GP-PSRL is limited. All known regret bounds either have a sub-optimal growth rate, require strong smoothness assumptions, or fail to properly account for the fact that the set of possible system states is unbounded. Through a recursive application of the Borell-Tsirelson-Ibragimov-Sudakov inequality, we show that, with high probability, the states actually visited by the algorithm are contained within a ball of near-constant radius. We then use the chaining method to control the regret suffered by GP-PSRL under weak smoothness conditions. Our main result is a Bayesian regret bound of the order $\widetilde{\mathcal{O}}(H\sqrt{\gamma_TT})$, where $H$ is the horizon, $T$ is the number of time steps and $\gamma_T$ is the expected information gain. With this result, we resolve the limitations with prior theoretical work on PSRL, and provide the theoretical foundation and tools for analyzing PSRL in complex settings.

08.
arXiv (CS.AI) 2026-06-15

Safety-Contract Graph Multi-Agent Reinforcement Learning for Autonomous Network Security Response

arXiv:2606.13832v1 Announce Type: cross Abstract: Autonomous network-security response systems promise to reduce Security Operations Centre (SOC) reaction latency, but reward-only multi-agent reinforcement learning (MARL) can improve security reward while remaining non-deployable. We present a safety-contract graph MARL framework and instantiate it as ACD$^3$-GAT (Adaptive Constrained Counterfactual Decisioning with a Graph Attention Network encoder), an architecture that separates simulator observations from reusable operational budgets, constrained optimization, graph state encoding, and counterfactual action screening. We evaluate the method in CAGE Challenge 4, where agents operate under budgets for Mean Time to Recover (MTTR), false-positive response, and firewall change-management disruption. Across the benchmark, every unconstrained method violates the SOC downtime budget in 100% of evaluated episodes, with mean downtime proxy costs of 311-430 against a budget of 50. This complements prior CAGE Challenge 4 findings by showing that reward-only learning lacks operational discipline. Constrained MAPPO-GAT (C-MAPPO-GAT) isolates Lagrangian operational-cost control and budget-aware screening, while ACD$^3$-GAT adds budget context, CVaR tail-risk estimation, opponent-belief state, and Graph Counterfactual Risk Propagation (G-CRP). The replicated comparison includes three 200-episode seeds for IPPO, MAPPO-GAT, C-MAPPO-GAT, and ACD$^3$-GAT. C-MAPPO-GAT reduces downtime violation from 100% to 0.3% and mean downtime cost from 355.4 to 15.5 relative to MAPPO-GAT. ACD$^3$-GAT reduces mean downtime cost to 48.2 with a 13.8% violation rate, placing it on the safety-contract frontier rather than at the most conservative compliance point. Topology-seed and coupled adaptive Red-process stress tests preserve this contrast and show lower worst adaptive degradation for safety-constrained policies than reward-only MAPPO-GAT.

09.
arXiv (CS.CV) 2026-06-12

PaLMR: Towards Faithful Visual Reasoning via Multimodal Process Alignment

Reinforcement learning has recently improved the reasoning ability of Large Language Models and Multimodal LLMs, yet prevailing reward designs emphasise final-answer correctness and consequently tolerate process hallucinations–cases where models reach the right answer while misperceiving visual evidence. We address this process-level misalignment with PaLMR, a framework that aligns not only outcomes but also the reasoning process itself. PaLMR comprises two complementary components: a perception-aligned data layer that constructs process-aware reasoning data with structured pseudo-ground-truths and verifiable visual facts, and a process-aligned optimisation layer that constructs a hierarchical reward fusion scheme with a process-aware scoring function to encourage visually faithful chains-of-thought and improve training stability. Experiments on Qwen2.5-VL-7B show that our approach substantially reduces reasoning hallucinations and improves visual reasoning fidelity, achieving state-of-the-art results on HallusionBench while maintaining strong performance on MMMU, MathVista, and MathVerse. These findings indicate that PaLMR offers a principled and practical route to process-aligned multimodal reasoning, advancing the reliability and interpretability of MLLMs.

10.
arXiv (CS.LG) 2026-06-19

Matching Markets meet Cumulative Prospect Theory: Towards Optimal and Adversarially Robust Learning

arXiv:2606.19883v1 Announce Type: new Abstract: We study a multi-agent multi-armed bandit problem in the competitive setup with two-sided matching markets under a human centric decision making model. To capture human preferences, we use cumulative prospect theory (CPT) that weighs the actions of the agent in a nonlinear fashion using a ($\alpha$-Hölder continuous) weight function. CPT has been widely used in behavioral economics and risk sensitive machine learning to emulate human preferences. We analyze the state-of-the-art learning algorithm with CPT weight distorted rewards and obtain a player optimal regret of $\mathcal{O}(K\log T \left(\frac{1}{\Delta}\right)^{2/\alpha})$, where $K$ denotes the number of arms, $T$ is the learning horizon, and $\Delta$ represents (suitably defined) players' minimum preference gap. Noticing the dependence on $\Delta$ to be sub-optimal, we further improve this regret by judiciously selecting the active set of arms during exploration, which removes the dependence on $K$ in the dominant term and achieves an improved (optimal) regret guarantees in the setting where the number of arms $K$ is significantly larger than the number of players $N$. In addition, we consider adversarial markets where the observed rewards of the agents may be corrupted. We propose and analyze algorithms for robust markets with CPT as risk sensitive measure in both settings where the total corruption budget is known and where it is unknown, and establish logarithmic player-optimal regret guarantees in both cases.

11.
arXiv (CS.AI) 2026-06-11

GPO: Learning from Critical Steps to Improve LLM Reasoning

arXiv:2509.16456v3 Announce Type: replace Abstract: Large language models (LLMs) are increasingly used in various domains, showing impressive potential on different tasks. Recently, reasoning LLMs have been proposed to improve the reasoning or thinking capabilities of LLMs to solve complex problems. Despite the promising results of reasoning LLMs, enhancing the multi-step reasoning capabilities of LLMs still remains a significant challenge. While existing optimization methods have advanced the LLM reasoning capabilities, they often treat reasoning trajectories as a whole, without considering the underlying critical steps within the trajectory. In this paper, we introduce Guided Pivotal Optimization (GPO), a novel fine-tuning strategy that dives into the reasoning process to enable more effective improvements. GPO first identifies the `critical step' within a reasoning trajectory - a point that the model must carefully proceed to succeed at the problem. We locate the critical step by estimating the advantage function. GPO then resets the policy to the critical step, samples the new rollout and prioritizes the learning process on those rollouts. This focus allows the model to learn more effectively from pivotal moments within the reasoning process to improve the reasoning performance. We demonstrate that GPO is a general strategy that can be integrated with various optimization methods to improve reasoning performance. Besides theoretical analysis, our experiments across challenging reasoning benchmarks show that GPO can consistently and significantly enhance the performance of existing optimization methods, showcasing its effectiveness and generalizability in improving LLM reasoning by concentrating on pivotal moments within the generation process.

12.
arXiv (CS.CV) 2026-06-16

XMedFusion: A Knowledge-Guided Multimodal Perception and Reasoning Framework for Autonomous Medical Systems

Autonomous medical and robotic systems increasingly rely on intelligent perception and reasoning capabilities to interpret visual data and support clinical decision making. Radiology report generation represents a critical component of such automated diagnostic workflows, yet existing end-to-end multimodal models often suffer from weak visual grounding, resulting in unreliable interpretations and omission of subtle clinical findings. This paper presents XMedFusion, a modular AI framework designed as an intelligent perception and reasoning module for autonomous medical systems. The proposed framework decomposes visual information into coordinated functional components that emulate expert-driven analysis, including a visual perception agent that extracts image-grounded evidence, a knowledge graph construction agent that structures clinically relevant findings, and a retrieval-guided drafting process that ensures a consistent reporting structure. A synthesis agent iteratively integrates visual and structured evidence through reasoning-driven verification to produce reliable and interpretable diagnostic outputs. Experimental evaluation on a public chest radiograph dataset demonstrates significant improvements over baseline vision-language models, achieving gains from 0.0493 to 0.3359 in BLEU-1, 0.0863 to 0.2440 in ROUGE-L, and 0.0829 to 0.1708 in METEOR, along with substantial improvements in semantic evaluation metrics such as Consistency (2.38 to 7.80) and Accuracy (2.34 to 6.93). The results highlight the effectiveness of structured multi-agent perception and reasoning for enhancing robustness, transparency, and automation in intelligent medical imaging systems, enabling integration into autonomous healthcare and robotic diagnostic workflows.

13.
arXiv (quant-ph) 2026-06-16

Entangled states are typically incomparable

arXiv:2406.03335v2 Announce Type: replace Abstract: Consider a bipartite quantum system, where Alice and Bob jointly possess a pure state $|\psi\rangle$. Using local quantum operations on their respective subsystems, and unlimited classical communication, Alice and Bob may be able to transform $|\psi\rangle$ into another state $|\phi\rangle$. Famously, Nielsen's theorem [Phys. Rev. Lett., 1999] provides a necessary and sufficient algebraic criterion for such a transformation to be possible (namely, the local spectrum of $|\phi\rangle$ should majorise the local spectrum of $|\psi\rangle$). In the paper where Nielsen proved this theorem, he conjectured that in the limit of large dimensionality, for almost all pairs of states $|\psi\rangle, |\phi\rangle$ (according to the natural unitary invariant measure) such a transformation is not possible. That is to say, typical pairs of quantum states $|\psi\rangle, |\phi\rangle$ are entangled in fundamentally different ways, that cannot be converted to each other via local operations and classical communication. Via Nielsen's theorem, this conjecture can be equivalently stated as a conjecture about majorisation of spectra of random matrices from the so-called trace-normalised complex Wishart-Laguerre ensemble. Concretely, let $X$ and $Y$ be independent $n \times m$ random matrices whose entries are i.i.d. standard complex Gaussians; then Nielsen's conjecture says that the probability that the spectrum of $X X^\dagger / \operatorname{tr}(X X^\dagger)$ majorises the spectrum of $Y Y^\dagger / \operatorname{tr}(Y Y^\dagger)$ tends to zero as both $n$ and $m$ grow large. We prove this conjecture, and we also confirm some related predictions of Cunden, Facchi, Florio and Gramegna [J. Phys. A., 2020; Phys. Rev. A., 2021].

14.
medRxiv (Medicine) 2026-06-10

Trajectories of brain structure and function in young adult carriers of genetic frontotemporal dementia variants

Background and Objectives: Converging evidence hints at neurodevelopmental effects in genetic frontotemporal degeneration (FTD). In cross-sectional studies, for some genes, young adult FTD variant carriers show differences in brain volumes and cognition compared to familial non-carriers. However, longitudinal trajectories may more sensitively capture FTD-related neurodevelopmental vs. neurodegenerative changes than cross-sectional approaches. This study examined longitudinal trajectories of brain volumes, executive function, and plasma biomarkers in young adult carriers compared to familial non-carriers, as measures of neurodevelopmental and neurodegenerative outcomes of FTD-causing variants. Methods: This longitudinal cohort study comprised participants, aged 18-30 years, from the FTD Prevention Initiative across Europe, Canada, and the USA. Genetic groups included C9orf72 (47%), MAPT (30%), and GRN (23%). Linear mixed-effects models were computed to assess longitudinal outcomes across age between groups, controlling for sex, scanner (for brain volumes), and education (for executive function); random effects accounted for between-subject variability nested within family membership. Results: Variant carriers (n=147) and familial non-carriers (n=113) did not differ in age (mean{+/-}SD, 25.9{+/-}3.2 years), sex (53% female), or number of visits (2.1{+/-}1.7). Young adult C9orf72 repeat expansion carriers exhibited smaller thalamic volumes than non-carriers at the reference age of 26 years (b=-982.8mm3, SE=317.0, p=0.0046, f2=0.32), with relatively stable trajectories across ages 18-30 (i.e., no change over time). Trajectories of rostral anterior cingulate volumes differed in C9orf72 carriers and non-carriers across age, where carriers showed relatively stable trajectories and non-carriers showed age-appropriate declines (b=64.4mm3, SE=29.9, p=0.035, f2=0.07). For MAPT and GRN, there were little to no differences in total brain, cortical, or subcortical volumes between groups and over time. No longitudinal differences were observed between carriers and non-carriers in executive function, or plasma NfL or GFAP for any genetic group. Discussion: C9orf72 repeat expansions were linked to smaller average thalamic volumes and stable trajectories between ages 18 to 30, supporting potential neurodevelopmental origins. The modest evidence supporting an absence of difference in neurodegenerative biomarkers and executive function suggests minimal early neurodegeneration and functional preservation in young adulthood.

15.
arXiv (quant-ph) 2026-06-24

Active interference suppression in frequency-division-multiplexed quantum gates via off-resonant microwave tones

arXiv:2601.14547v3 Announce Type: replace Abstract: The increasing number of control lines connecting quantum processors to external electronics constitutes a major bottleneck in the realization of large-scale quantum computers. Frequency-division multiplexing is expected to enable control of multiple qubits through a single microwave cable; however, interference from off-resonant microwave tones hinders precise qubit control. Here, we propose an active interference suppression method for frequency-division-multiplexed simultaneous gates on microwave-controlled qubits. We demonstrate that the deliberate incorporation of off-resonant microwave tones improves single-qubit gate fidelity. In particular, the gate infidelity scales inversely with the square of the number of microwave tones when off-resonant orthogonal or quasi-orthogonal tones are incorporated. Furthermore, we show that fast oscillations, neglected under the rotating wave approximation, degrade the gate fidelity, and that this degradation can be mitigated through optimized frequency allocation. The proposed approach is simple and effective for improving the performance of frequency-division-multiplexed quantum gates.

16.
arXiv (CS.LG) 2026-06-17

ResAware: Cross-Environment Website Fingerprinting via Resource-Privileged Distillation

arXiv:2606.17462v1 Announce Type: new Abstract: While Website Fingerprinting (WF) attacks achieve high accuracy in controlled laboratory settings, they often degrade substantially in real-world environments due to spatio-temporal drift, browser heterogeneity, proxy obfuscation and etc. This limitation stems from their sole reliance on low-level traffic features that are noisy and highly sensitive to environmental perturbations. To address this problem, we propose ResAware, a cross-environment resource-aware distillation framework under a training-rich/inference-poor asymmetric setting. Specifically, ResAware trains a teacher model on resource-level features, and then distills the resulting privileged knowledge into a student model through heterogeneous knowledge distillation. At deployment time, the student model performs inference using only encrypted traffic, incurring zero additional cost. We evaluate ResAware on a large-scale dataset collected over five months from six globally distributed vantage points, comprising more than $160{,}000$ paired samples. The results show that ResAware significantly enhances the cross-environment robustness of diverse WF baselines. Under a 150-day temporal drift, for example, ResAware improves the F1-score of Var-CNN from $72.77\%$ to $81.49\%$ and the open-world $TPR@1\%FPR$ from $22.40\%$ to $27.20\%$. Our results demonstrate that resource-level supervision improves WF robustness without expanding online observation capabilities.

17.
arXiv (CS.CV) 2026-06-24

Bengal-HP_RU: A Dataset of Bengal People For Head Pose Estimation

Existing head pose datasets predominantly feature subjects of Western or East Asian origin, leaving South Asian populations, particularly Bengali individuals, largely underrepresented. We introduce Bengal-HP_RU, the first publicly available head pose dataset centred on Bengali subjects, comprising 12,894 labelled head images annotated with continuous yaw, pitch, and roll values. Images were collected from Wikimedia Commons under free licences and processed through an automated pipeline followed by manual label correction. The dataset is partitioned by Wikimedia uploader identity to prevent data contamination, yielding 10,494 training and 2,400 test images across 296 unique uploaders. Bengal-HP_RU exhibits substantial diversity in subject age, gender, occlusion, illumination, and background, reflecting realistic in-the-wild conditions. The dataset is publicly available at https://doi.org/10.17632/xbw9kr37jb.2.

18.
arXiv (CS.CL) 2026-06-24

Ensemble Learning for Large Language Models in Text and Code Generation: A Survey

Generative Pretrained Transformers (GPTs) are foundational Large Language Models (LLMs) for text generation. However, individual LLMs often produce inconsistent outputs and exhibit biases, limiting their representation of diverse language patterns. The closed-source nature of many powerful LLMs further restricts industry applications due to data privacy concerns. Inspired by successes in text generation, LLM ensemble techniques are now increasingly explored for code generation. This article reviews these emerging ensemble approaches to enhance understanding, encourage further research, and promote practical implementation in both text and code generation. We categorize LLM ensembles into seven main methods - weight merging, knowledge fusion, mixture-of-experts, reward ensemble, output ensemble, routing, and cascading - analyzing capabilities of those approaches. Our findings highlight key benefits such as improved diversity representation, enhanced output quality, and greater application flexibility. These insights aid model selection for real-world tasks and crucially, lay groundwork for extending ensemble strategies to multimodal LLMs.

19.
bioRxiv (Bioinfo) 2026-06-23

VCBench: A Multi-Dimensional Benchmark for Single-Cell Foundation Models

Single-cell foundation models are increasingly positioned as virtual cells, yet their capabilities are assessed by fragmented, largely single-task benchmarks that obscure where these models improve on simple baselines. VCBench addresses this by synthesizing four independent virtual-cell frameworks into seven capability dimensions: perturbation response prediction, cross-species universality, gene regulatory network (GRN) inference, modality integration, temporal dynamics, multi-scale integration, and in silico experimentation. Each dimension is assessed for operational testability under current architectures and datasets: five admit direct or proxy evaluation, while multi-scale integration and in silico experimentation are structurally untestable as end-to-end tasks. We evaluate five foundation models (Geneformer, scGPT, UCE, TranscriptFormer, Arc State) against pre-registered linear and nearest-neighbor baselines across the five testable dimensions, and report three findings. First, the baselines match or exceed every foundation model on four of the five scored dimensions, replicating the reported competitiveness of linear baselines on perturbation prediction and extending it to cross-species transfer, GRN inference, and temporal ordering. Second, TranscriptFormer alone exceeds the strongest baseline on cross-modal RNA-to-protein prediction (53% Pearson improvement, with a documented contamination caveat) and is the only model to reach Level 2 in the pre-registered Virtual Cell (VC) Level rubric; the architectural choice behind this advantage simultaneously causes a spectral collapse that destroys its temporal-ordering performance, a tradeoff invisible to single-task benchmarks. Third, no foundation model publishes a complete cell-level training manifest, leaving data contamination undetectable to users. Alongside the benchmark, VCBench releases a Contamination Reporting Schema and contributes two further methodological tools: a common-label-set protocol that controls for class-count confounds in cross-species transfer, and a spread-error correlation probe for epistemic calibration.

20.
arXiv (CS.CL) 2026-06-15

A Computational Audit of Demographic Association Encoding in ClinicalBERT Language Predictions

Transformer-based clinical language models are increasingly integrated into high-stakes clinical decision support pipelines, yet the computational mechanisms through which demographic associations encoded in medical documentation propagate into model probability distributions remain empirically underspecified. We present a systematic computational audit of representational bias in ClinicalBERT (Alsentzer et al., 2019), a BERT-based model pretrained on MIMIC-III discharge summaries, employing two complementary probing methodologies: Log Probability Bias Analysis (LPBA), which quantifies demographic descriptor-induced shifts in masked token probability distributions across behavioral and evaluative semantic categories, and Masked Language Model-based analysis (MLM), which probes internal representational structure for demographic agency attribution encoding across 98 real clinical sentence templates and eight intersectional race-gender combinations. Corpus frequency analysis operationalizes the distinction between statistical disparity and bias amplification by benchmarking model outputs against empirical term frequencies in the MIMIC-III training corpus. Of 32 statistically significant findings, 65.6% contradict observed corpus distributions, rising to 80% for Black patients and 87.5% for agency attribution under MLM probing, providing direct empirical evidence that representational bias in ClinicalBERT operates predominantly through model-internal amplification rather than training data inheritance. Keywords: natural language processing, clinical documentation, algorithmic auditing, representational bias, health equity 1

21.
arXiv (CS.AI) 2026-06-11

Beyond Continuity: Simulation-free Reconstruction of Discrete Branching Dynamics from Single-cell Snapshots

arXiv:2605.00545v2 Announce Type: replace-cross Abstract: Inferring cellular trajectories from destructive snapshots is complicated by the challenges of stochasticity and non-conservative mass dynamics such as cell proliferation and apoptosis. Existing unbalanced Optimal Transport (OT) methods treat mass as a continuous fluid, performing inference at the population level. However, this macroscopic view often fails to capture the discrete, jump-like nature of birth-death events at single-cell resolution, which is essential for understanding lineage branching and fate decisions. We present Unbalanced Schrödinger Bridge (USB), a simulation-free framework for learning underlying dynamics that effectively integrates both stochastic and unbalanced effects which also models the discrete, jump-like birth-death dynamics at single-cell resolution. Theoretically, USB provides a tractable solution to the Branching Schrödinger Bridge (BSB) problem, offering a rigorous microscopic interpretation where individual cells undergo both Brownian motion and discrete birth-death jumps. Technically, the method implements an efficient solver by introducing a simulation-free training objective that effectively scales to high-dimensional omics data. Empirically, we demonstrate on both simulated and real-world datasets that USB not only achieves trajectory reconstruction performance better than or comparable to deterministic baselines but also uniquely enables realistic discrete simulation of birth-death dynamics at single-cell resolution.

22.
arXiv (CS.AI) 2026-06-11

Mind the Perspective: Let's Reason Recursively for Theory of Mind

arXiv:2606.11724v1 Announce Type: new Abstract: Theory of Mind (ToM) reasoning requires inferring agents' beliefs from partial and asymmetric observations, which remains an open challenge for LLMs. Existing prompting-based approaches improve ToM reasoning through observable-event filtering or temporal belief chains, without explicitly modeling nested beliefs. We introduce RecToM, an inference-time framework for ToM reasoning that models nested beliefs via recursive perspective construction. RecToM constructs each character perspective from the preceding character perspective along the character chain specified by the question, reducing higher-order belief questions to actual-world questions within the final constructed perspective. We further provide a KD45 analysis showing that RecToM's perspective construction induces a well-formed belief modality beyond simple event filtering. Experiments on ToM benchmarks, including Hi-ToM, Big-ToM, and FanToM, across multiple LLM backbones show that RecToM consistently outperforms recent advanced approaches, achieving state-of-the-art performance. Notably, RecToM reaches 100\% accuracy on Hi-ToM with GPT-5.4 and Qwen3.5, a benchmark requiring higher-order ToM reasoning.

23.
arXiv (CS.AI) 2026-06-25

A Hybrid TGN-SEAL Model for Dynamic Graph Link Prediction

arXiv:2602.14239v3 Announce Type: replace-cross Abstract: Predicting links in sparse, continuously evolving networks is a central challenge in network science. Conventional heuristic methods and deep learning models, including Graph Neural Networks (GNNs), are typically designed for static graphs and thus struggle to capture temporal dependencies. Snapshot-based techniques partially address this issue but often encounter data sparsity and class imbalance, particularly in networks with transient interactions such as telecommunication call detail records (CDRs). Temporal Graph Networks (TGNs) model dynamic graphs by updating node embeddings over time; however, their predictive accuracy under sparse conditions remains limited. In this study, we improve the TGN framework by extracting enclosing subgraphs around candidate links, enabling the model to jointly learn structural and temporal information. Experiments on a sparse CDR, email, message dataset show that our approach increases average precision by at least 2% over standard TGNs, demonstrating the advantages of integrating local topology for robust link prediction in dynamic networks.

24.
arXiv (CS.AI) 2026-06-19

Navigating Unreliable Parametric and Contextual Knowledge: Explicit Knowledge Conflict Resolution for LLM Inference

arXiv:2606.20245v1 Announce Type: new Abstract: Large language models (LLMs) have achieved strong performance across a wide range of language-based tasks by leveraging both extensive parametric knowledge and in-context learning ability, enabling them to incorporate external information provided in the input prompt. However, the integration of external knowledge can introduce conflicts, not only between the model's internal parametric knowledge and the external information, but also among multiple pieces of external contexts. Existing approaches typically assume that either the model or the provided context is reliable, overlooking the possibility that both sources may contain errors, and avoid conflicts by privileging one source over the other, rather than actively resolving inconsistencies. To address these limitations, we propose a novel framework MACR for LLM knowledge conflict resolution that moves beyond the conventional binary choice paradigm and incorporates an explicit conflict-resolution mechanism based on a multi-agent reasoning approach. Specifically, we first propose an adaptive knowledge assessment and retrieval approach that employs a modified semantic entropy measure to quantify an LLM's confidence in its answer to a given query. Based on this confidence estimation, MACR either externalizes the model's internal knowledge as textual representations or retrieves relevant external knowledge when internal knowledge is insufficient, generating basic contexts for subsequent reasoning. Then we introduce an inductive multi-agent reasoning framework with three specialized agents that, respectively, induce explicit rules, analyze potential conflicts, and resolve inconsistencies across all available contexts. Empirical results demonstrate that MACR significantly outperforms state-of-the-art baselines across benchmarks, while also providing interpretable resolutions of explicit conflicts.

25.
arXiv (CS.AI) 2026-06-17

TuneAhead: Predicting Fine-tuning Performance Before Full Training Begins

arXiv:2606.17660v1 Announce Type: cross Abstract: Fine-tuning large language models (LLMs) is compute-intensive and error-prone: model performance depends sensitively on data quality and hyperparameter choices, and naïve runs can even degrade model performance. This raises a practical question:can we predict fine-tuning performance before committing to a full training run? We present TUNEAHEAD, a lightweight framework for pre-hoc prediction of fine-tuning performance. TUNEAHEAD encodes each candidate run as a meta-feature vector that combines static dataset descriptors with dynamic probe features from a short standardized probe. A predictor maps these features to performance estimates, while SHAP-based attributions provide interpretable diagnostics that reveal which specific features drive the prediction. Across 1,300+ fine-tuning runs on Qwen2.5-7B-Instruct, TUNEAHEAD consistently outperforms strong baselines such as Early-Stop Extrapolation and ProxyLM. On a held-out test set of 370 runs, TUNEAHEAD achieves an RMSE of 1.47 percentage points and places 95.1% of predictions within +3/-3 percentage points of the true score. These accurate continuous predictions support practical go/no-go screening policies that can reduce unnecessary full fine-tuning while retaining most promising runs.