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02.
arXiv (CS.CV) 2026-06-17

A Benchmark for Omni-Modal Reasoning in Long Videos

Long-form omni-modal video understanding requires integrating vision, speech, and ambient audio with coherent long-context reasoning. Existing video benchmarks often trade off temporal scale, modality coverage, open-ended interaction, and interpretable scoring. To address this gap, we introduce LongShOTBench, a long video understanding benchmark designed around three coupled goals: holistic omni-modal integration, intent-driven open-ended interaction, and rubric-level diagnosis. It builds single- and multi-turn questions from real viewing scenarios, with systematic tasks probing visual, speech, ambient-audio, temporal, and cross-modal reasoning. Each item includes a reference answer and a weighted criterion-level rubric, letting evaluation identify which perceptual facts, temporal links, modality-grounding requirements, and reasoning steps are satisfied or missed. All samples are manually verified to improve grounding, clarity, and rubric reliability. We also introduce LongShOTAgent, a training-free omni-modal evidence-seeking agent coupling full-video preprocessing with targeted retrieval, query-adaptive segment refinement, and explicit claim verification over visual, speech, and non-speech audio evidence. Its iterative search-refine-verify loop exposes intermediate evidence and lets modality-specific specialists re-analyze relevant moments before answering. We evaluate 105 video-capable models spanning open-source omni-modal models, vision-language systems, audio LLMs, agentic pipelines and closed-source APIs. Current MLLMs remain far from saturating LongShOTBench, while our LongShOTAgent is the strongest training-free system, reaching 66.64% overall. By releasing the benchmark, leaderboard, and method, we provide a shared, interpretable testbed for advancing long-form omni-modal video reasoning. Code, data, and the leaderboard are available at https://longshot.cvmbzuai.com/.

03.
Nature (Science) 2026-06-17

Confined migration induces non-lethal DNA damage in developing neurons

Migratory cells tend to have soft nuclei that deform and penetrate narrow spaces1,2. Extensive nuclear deformation during migration can cause nuclear-envelope rupture and DNA damage in cancer cells, which may contribute to malignant transformation during tumour progression3–6. However, the importance of DNA damage in physiological migration is less well understood. Here we demonstrate that the migration of neurons in developing cerebral and cerebellar cortices is accompanied by massive DNA double-stranded breaks (DSBs) due to mechanostress during passage through narrow interstitial spaces. In contrast to many other migratory cells, these DSBs occur without detectable nuclear envelope rupture. Confined migration increases topoisomerase-IIβ covalently bound DSBs, and these lesions are repaired through non-homologous end-joining during brain development without causing cell death. Genome sequencing revealed that DSBs tend to occur at transcriptionally inactive regions. The deletion of ligase IV at the onset of neuronal migration leads to persistent DSB accumulation in cerebellar neurons with moderate transcriptional changes in genes related to synaptic function, neuronal development and stress and immune responses. The mutant mouse develops mild motor deficits in later life, suggesting that the DNA damage generated during normal brain development poses a potential disease risk if left unrepaired. The migration of neurons in developing cerebral and cerebellar cortices is accompanied by massive DNA double-strand breaks due to mechanostress during passage through narrow interstitial spaces.

04.
arXiv (CS.LG) 2026-06-16

ReQAT: Achieving Full-Precision Reasoning Accuracy with 4-bit Floating-Point Quantization-Aware Training

arXiv:2606.15682v1 Announce Type: new Abstract: Large Reasoning Models (LRMs) achieve strong problem-solving through long chain-of-thought, but their deployment is constrained by the high cost of full-precision inference and growing KV cache footprints. Microscaled FP4 formats enable efficient FP4 deployment; however, fully quantizing weights, activations, and KV caches (W4A4KV4) causes severe reasoning degradation that existing PTQ and QAT fail to recover. We identify that FP4 failures concentrate on low-entropy tokens–precise symbolic commitments such as digits and operators–where quantization noise inflates sampling errors that cascade through reasoning traces. Based on this insight, we propose ReQAT, a reasoning-centric FP4 training framework with three components: (i) Trace-Aligned QAT (TAQ), which revisits identical reasoning traces to focus updates on critical low-entropy decisions; (ii) Selective Entropy Minimization (SEM), which reinforces confidence at low-entropy positions; and (iii) Q-FIT, a quantization-friendly initialization that jointly calibrates RoPE-consistent KV cache transformations to stabilize QAT. Under the same training budget, ReQAT not only recovers but surpasses BF16 fine-tuning accuracy, while delivering up to 3.9x throughput speedup on NVIDIA DGX Spark and 3.1x on B200.

05.
Nature (Science) 2026-06-09

How ice forms is a mystery — now scientists are cracking the case

Theories about how ice crystals grow in cooling liquids are wildly inaccurate when compared with experimental data, but studies are starting to illuminate the earliest moments in freezing. Theories about how ice crystals grow in cooling liquids are wildly inaccurate when compared with experimental data, but studies are starting to illuminate the earliest moments in freezing.

06.
arXiv (quant-ph) 2026-06-17

Frequency-Division Multiplexed CV-QKD System

arXiv:2603.20718v2 Announce Type: replace Abstract: We propose a frequency-division multiplexed (FDM) continuous-variable quantum key distribution (CV-QKD) system with enhanced spectral efficiency through optimized channel spacing of low-symbol-rate signals. A four-channel 10-Mbaud FDM-CV-QKD system was experimentally demonstrated using Gaussian modulation, a transmitted local oscillator, and homodyne detection. Despite the inter-channel interference, under a finite-size scenario (m=1.25x10^6), the system achieved a 3.6-fold back-to-back secret key rate gain and outperformed the single-channel frequency-upconverted signal up to 26.8 km.

07.
arXiv (CS.CV) 2026-06-11

Scene-Adaptive Nonlinear Tone Curves for Pseudo Ground-Truth Generation in Low-Light 3D Gaussian Splatting

Low-light novel view synthesis is challenging because dark multi-view images contain noise, weak structural detail, and compressed dynamic range. Recent 3D Gaussian Splatting (3DGS) methods address these challenges by generating pseudo ground-truth (pseudo-GT) images as supervision targets when paired normal-light references are unavailable. Existing pseudo-GT methods apply a uniform linear gain to all pixels, which clips bright regions while providing insufficient enhancement in dark regions, limiting reconstruction quality. We observe that nonlinear tone mappings, long established in 2D low-light enhancement, have not been explored for pseudo-GT generation in 3D reconstruction. Accordingly, we propose a scene-adaptive nonlinear tone-curve framework that replaces linear pseudo-GT with nonlinear alternatives. The framework introduces percentile-based normalisation for scene-agnostic curve application, a scene-adaptive offset for automatic black-level adjustment, and two complementary curves: Adaptive SoftExp (ASE), a bounded exponential curve, and Adaptive Poly3 (AP3), a data-driven cubic polynomial. The module changes only the pseudo-GT computation and leaves the 3DGS backbone unchanged. Experiments on three benchmarks covering 21 scenes show that both curves consistently outperform the linear baseline with PSNR improvements up to +4.34 dB on LOM and +3.25 dB on RealX3D. Both curves achieve similar performance despite their different mathematical forms, suggesting the improvement is curve-agnostic. Code is available at https://github.com/lvmingzhe/adaptiveToneCurve

08.
arXiv (CS.LG) 2026-06-12

BrainPro: Towards Large-scale Brain State-aware EEG Representation Learning

arXiv:2509.22050v2 Announce Type: replace Abstract: Electroencephalography (EEG) reflects underlying brain states, whose activities are distributed across brain regions and manifest as spatial patterns on the scalp. Learning these spatially structured, state-related patterns requires consistent spatial representations across datasets. However, existing EEG foundation models are typically based on self-attention, which does not preserve location-specific information and struggles to align signals recorded with different channel configurations. Moreover, brain states contain both shared and state-specific regional activity, suggesting that learning neurophysiologically plausible, state-aware representations can complement the shared representations targeted by current models and improve downstream decoding. To address these limitations, we propose BrainPro, a large EEG model that combines a retrieval-based spatial learning mechanism for cross-layout spatial alignment with a brain state-decoupling module that learns both shared and state-specific representations through parallel encoders and region-aware reconstruction. Pre-trained on a large EEG corpus, BrainPro achieves state-of-the-art performance across nine public BCI datasets spanning emotion, motor, speech, stress, mental disease, and attention tasks. Analyses of spatial filters, channel-drop robustness, and encoder contributions further validate the effectiveness of its spatial alignment and state-aware pathways. These results show that BrainPro achieves improved interpretability of learned spatial patterns and produces representations that benefit diverse EEG decoding tasks.

09.
arXiv (CS.AI) 2026-06-25

FBOS-RL: Feedback-Driven Bi-Objective Synergistic Reinforcement Learning

arXiv:2605.20256v2 Announce Type: replace-cross Abstract: Reinforcement learning has become a cornerstone for aligning and unlocking the reasoning capabilities of large-scale models. At its core, the training loop of GRPO and its variants alternates between rollout sampling and policy update: the policy first samples rollouts from its action space, and then updates its parameters according to the advantages computed over them. Unlike supervised learning, where each gradient step is anchored to an explicit ground-truth target, the optimal gradient direction for updating model parameters in this setting is not known a priori; the high-quality rollouts drawn during the sampling stage therefore act as the implicit "teacher" that guides every parameter update. However, mainstream RL algorithms such as GRPO adopt a simple sampling scheme that conditions all rollouts on the same original prompt. When a task lies beyond the policy model's current capability, this sampling scheme rarely yields a high-quality rollout, leaving the policy model without a meaningful gradient direction when updating its parameters, which causes training to stall. To address this issue, we propose FBOS-RL. Specifically, we let the model perform Feedback-Guided Exploration Enhancement based on the feedback provided by the environment, and on top of this we design two mutually reinforcing training objectives: EPA and ECC. Extensive experiments demonstrate that EPA and ECC can mutually reinforce each other, forming a positive flywheel effect that significantly improves both the training efficiency and the final performance ceiling of reinforcement learning. Specifically, under both an identical number of rollouts and the same number of training steps, FBOS-RL learns substantially faster than GRPO and feedback-based baselines and ultimately attains a higher performance ceiling, while exhibiting higher policy entropy and lower gradient norms throughout training.

10.
Nature Biotechnology 2026-06-11

Large-scale, spatially resolved panoramic CRISPR screening in native tissue environments using Perturb-DBiT

作者:

Spatially resolved CRISPR screening in vivo has been limited to small perturbation panels and subsets of protein-coding RNAs. We present Perturb-DBiT, a method for co-sequencing of spatial total RNA whole transcriptomes and single guide RNAs (sgRNAs) on the same tissue section in situ. In a human cancer metastatic colonization model, we applied large (80,000+) sgRNA panels across tumor colonies in multiple consecutive tissue sections alongside their corresponding total RNA transcriptomes. We linked perturbations affecting long noncoding RNA covariation, microRNA–mRNA interactions and distinct amino acid-specific tRNA alterations to tumor migration and growth. By integrating transcriptional pseudotime trajectories, we further observed the impact of perturbations on clonal dynamics and cooperation. In an immune-competent syngeneic mouse model, investigation of the tumor immune microenvironment indicated distinct, synergistic effects on immune infiltration and suppression. Perturb-DBiT provides a spatially resolved comprehensive view of perturbation responses in complex tissues, including small and large RNA regulation, tumor proliferation, migration, metastasis and immune interactions. In vivo CRISPR genetic perturbations are spatially mapped at scale.

11.
arXiv (math.PR) 2026-06-11

Mean-field theory via dissociated arrays for particle systems interacting through noisy weights

arXiv:2606.12135v1 Announce Type: new Abstract: We study a mean-field limit for a $N$-particle system in which each particle follows a diffusion and interacts with other particles through a weight on each directed edge. Each weight evolves according to its own nonlinear SDE driven by a Brownian motion, with coefficients involving the states of the two endpoint particles of the edge. The initial vertex and edge variables are assumed to have a dissociated Aldous–Hoover form. We construct the limiting nonlinear SDE by averaging the interaction over an independent neighbor and an edge input, prove its well-posedness, and show that the dissociated vertex-edge structure is propagated by the dynamics. This propagation property is an analogue of propagation of chaos in the case where the weight of each edge may remain correlated with the states of the two endpoint particles. Under either a bounded-observable assumption or a sub-Gaussian edge-input condition, the finite system converges to this limit through quantitative coupling estimates for a typical particle and a typical edge. We also prove the convergence of the empirical measure of particle's state pairs and their interaction weights.

12.
arXiv (quant-ph) 2026-06-16

Light-induced nonadiabatic dissipative quantum dynamics of the Na2 molecule

arXiv:2606.15292v1 Announce Type: new Abstract: Strong light-matter coupling between molecules and optical or plasmonic cavity modes has emerged as a promising platform for advancing photonics, materials science, and chemistry. However, optical cavities and plasmonic resonators in particular are inherently lossy systems characterized by finite photon lifetimes. Accurate theoretical descriptions of molecular dynamics under strong coupling therefore require a proper treatment of cavity losses. In this work, we compare three theoretical approaches for modeling dissipative molecule-cavity dynamics within a realistic parameter regime: the Lindblad master equation, the stochastic Schrödinger equation, and the non-Hermitian Schrödinger equation. As an example, we consider the two lowest energy state of Na2 molecule coupled to a cavity mode and analyze the time evolution of the excited-state population and the mean photon number. Our results demonstrate that the stochastic Schrödinger equation provides an accurate and computationally efficient alternative to the Lindblad master equation, while the non-Hermitian Schrödinger approach is found to be applicable only within a limited range of conditions. Furthermore, we show that inclusion of molecular rotation leads to rotational-vibrational-photonic coupling and gives rise to pronounced nonadiabatic dynamics through light-induced conical intersections. These findings highlight the importance of both dissipation and rotational degrees of freedom for a realistic description of molecular dynamics in strongly coupled molecule-cavity systems.

13.
arXiv (CS.CL) 2026-06-12

LabVLA: Grounding Vision-Language-Action Models in Scientific Laboratories

Scientific laboratories increasingly rely on AI systems to reason about experiments, but the physical act of doing science remains largely outside their reach. AI can help read literature, generate hypotheses, and plan protocols, yet the execution of those protocols at the bench still requires a human operator. Vision-Language-Action (VLA) models provide one possible interface between written protocols and robot execution, but existing policies are trained mostly on household and tabletop demonstrations and rarely encounter the instruments, transparent liquids, or fixed protocol workflows found in scientific laboratories. Closing this gap requires both laboratory-specific supervision and a unified learning framework that can accommodate the diverse robot embodiments used to execute experimental protocols. We therefore identify data and embodiment as central bottlenecks alongside model design. To address the data side, we build RoboGenesis, a simulation-based workflow and data engine that composes configured laboratory workflows from atomic skills, validates and filters rollouts, and exports structured demonstrations across supported robot profiles. On the policy side, we present LabVLA, trained with a two-stage recipe: FAST action token pretraining first makes the Qwen3-VL-4B-Instruct backbone action aware before any continuous control is learned, and flow matching posttraining then attaches a DiT action expert under knowledge insulation. On the LabUtopia benchmark, LabVLA achieves the highest average success rate among all evaluated baselines under both in-distribution and out-of-distribution settings.

14.
arXiv (CS.LG) 2026-06-17

Searching Neural Architectures for Sensor Nodes on IoT Gateways

arXiv:2505.23939v2 Announce Type: replace Abstract: This paper presents an automatic method for the design of Neural Networks (NNs) at the edge, enabling Machine Learning (ML) access even in privacy-sensitive Internet of Things (IoT) applications. The proposed method runs on IoT gateways and designs NNs for connected sensor nodes without sharing the collected data outside the local network, keeping the data in the site of collection. This approach has the potential to enable ML for Healthcare Internet of Things (HIoT) and Industrial Internet of Things (IIoT), designing hardware-friendly and custom NNs at the edge for personalized healthcare and advanced industrial services such as quality control, predictive maintenance, or fault diagnosis. By preventing data from being disclosed to cloud services, this method safeguards sensitive information, including industrial secrets and personal data. The outcomes of a thorough experimental session confirm that – on the Visual Wake Words dataset – the proposed approach can achieve state-of-the-art results by exploiting a search procedure that runs in less than 10 hours on the Raspberry Pi Zero 2.

15.
arXiv (CS.AI) 2026-06-19

Repurposing a Speech Classifier for Guided Diffusion-Based Speech Generation

arXiv:2606.20457v1 Announce Type: cross Abstract: Classifier guidance is a way to control diffusion generation by using a noise-conditioned classifier to steer the sampling process toward a target class. One drawback of classifier guidance is that it requires two separately trained models: a classifier and a diffusion model. We therefore study a more compact alternative in which a conventionally trained speech classifier is repurposed as the backbone for diffusion generation. Starting from a frozen noise-conditioned classifier in log-Mel space, we attach a lightweight subnetwork that reuses intermediate classifier representations and train only this subnetwork under a Denoising Score Matching objective. Our work shows that a pretrained classifier can be repurposed for conditional generation, providing an appealing bridge between discriminative modeling and conditional speech synthesis resulting in high speech quality within a single-backbone model, with reduced memory footprint and computational cost.

16.
arXiv (quant-ph) 2026-06-15

Universal Crossovers of Stabilizer Entropy Beyond Criticality

arXiv:2606.13810v1 Announce Type: new Abstract: Stabilizer Rényi entropy has emerged as a probe of nonstabilizerness in quantum many-body systems, but its scaling structure beyond critical points remains poorly understood compared with entanglement entropy. Recent field-theory approaches indicate that stabilizer entropy contains universal critical data and boundary-sensitive terms, raising the question of how these structures extend into massive and crossover regimes. We address this problem for a broad class of finite-range spin chains at Rényi index one-half. We derive exact finite-size formulas for both full periodic chains and finite intervals of the infinite chain, making the universal crossover from critical to noncritical behavior analytically accessible. In periodic geometry, the entropy obeys a volume law away from criticality and exhibits a universal finite-size crossover controlled by the competition between system size and correlation length. We also show that the large-scale SRE density develops a cusp across the field-tuned critical line, while the XX endpoint is governed by a distinct scaling regime associated with the saturation point. In the subsystem geometry, the interval entropy separates bulk critical behavior from boundary contributions generated by the way the finite region cuts the infinite chain. The crossover from critical to massive behavior is then encoded in boundary constants and universal functions controlled by the correlation length. Through exact stabilizer-entropy correspondences, the scaling theory extends to internal XY reductions, Finite-range spin chains, and Cluster–Ising representatives. Our results provide an exact lattice benchmark for the emerging QFT description of stabilizer entropy beyond isolated conformal points.

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

Combining Retrieval-Augmented Text Generation with LLMs for Reading Content Recommendations

arXiv:2606.14817v1 Announce Type: cross Abstract: This work presents the design, implementation, and evaluation of a system for generating personalized reading content using Large Language Models (LLMs) combined with Retrieval-Augmented Generation (RAG). The proposed architecture consists of four modules: Input, RAG, Generation, and Judging and enables users to specify both a question and a target reading content complexity. RAG is employed to retrieve relevant information from the Internet, enriching and grounding the content produced by three modern LLMs: Meta LLaMA 4 Scout, LLaMA 3.1 8B Instant, and Google Gemma2 9B. Reading materials are generated using three prompting strategies (Chain-of-Thought, zero-shot, and few-shot), and the LLM-as-a-Judge module automatically evaluates answer quality and alignment with the desired readability level. Experimental results show that RAG consistently improves system performance across all models and prompting techniques, increasing relevance and particularly groundedness by up to 26-35 percentage points. Overall, the findings demonstrate that the RAG-augmented architecture effectively produces reading content tailored to user queries and desired textual complexity.

18.
arXiv (quant-ph) 2026-06-11

Non-Hermitian Delocalization Realizes Random Dirac Criticality in One Dimension

arXiv:2606.12089v1 Announce Type: cross Abstract: Non-Hermitian systems can evade Anderson localization and exhibit delocalized states even in one dimension. Here, we show that such non-Hermitian delocalized states under periodic boundary conditions (PBC) are intrinsically critical, realizing the universality class of one-dimensional random Dirac fermions. By linking spectral winding to topological Anderson transitions via Hermitization, we demonstrate that the delocalized PBC states exhibit a Dirac-type criticality with universal algebraic correlations. In contrast to Hermitian systems, where this criticality occurs only at fine-tuned transition points, it emerges generically in non-Hermitian systems as a consequence of spectral topology. These results identify a universal mechanism by which non-Hermiticity promotes criticality, providing a unified description of non-Hermitian delocalization in one dimension.

19.
medRxiv (Medicine) 2026-06-10

Documented clinical genetic testing among carriers of hereditary breast and ovarian cancer variants: Ancestry and socioeconomic disparities in the All of Us research program

Importance: Hereditary breast and ovarian cancer (HBOC) variant carriers benefit from risk-reducing interventions, but only if identified. The extent to which carriers are clinically recognized, and whether recognition is equitable across diverse populations, is poorly characterized in a single large U.S. cohort. Objective: To estimate P/LP HBOC carrier prevalence across genetic ancestry groups, quantify documented clinical genetic testing among carriers, and evaluate ancestry and socioeconomic disparities in testing. Design, Setting, and Participants: Cross-sectional analysis of the All of Us Research Program Controlled Tier (Curated Data Repository v8/C2024Q3R9), comprising participants with short-read whole genome sequencing and linked electronic health record (EHR) and survey data. Carriers were ascertained from research genomic data independent of clinical testing. Exposures: Genetically inferred ancestry (African [AFR], Admixed American [AMR], East Asian [EAS], European [EUR], Middle Eastern [MID], South Asian [SAS]); self-reported household income and educational attainment. Main Outcomes and Measures: (1) Carrier prevalence with Wilson 95% CIs; (2) documented clinical genetic testing (procedure codes) among carriers; (3) adjusted odds of documented testing among women, by ancestry, before and after socioeconomic adjustment, using multivariable logistic regression. Results: Among 414,830 participants, P/LP HBOC carrier prevalence was 1.42% (95% CI, 1.38-1.45) overall and similar across ancestry groups (AFR 1.24%, AMR 1.32%, EAS 1.19%, EUR 1.52%, MID 1.68%, SAS 1.33%; overlapping CIs). Among 250,071 women in the testing analysis, documented clinical genetic testing was rare: only 74 of 5,878 carriers overall (1.3%) and 59 of 3,572 European-ancestry carriers (1.7%) had a documented test, with counts below reportable thresholds in all other ancestry groups. African-ancestry women had lower adjusted odds of documented testing than European-ancestry women (Model 1 adjusted odds ratio [aOR], 0.32; 95% CI, 0.27-0.39), an association that attenuated but persisted after adjustment for income and education (Model 2 aOR, 0.48; 95% CI, 0.40-0.58; P < 0.001); Admixed American women also had reduced adjusted odds (aOR, 0.71; 95% CI, 0.61-0.84). Lower income and lower education were independently and dose-dependently associated with lower testing odds (income

20.
arXiv (CS.AI) 2026-06-25

TopoCast: A Topological Fidelity Framework for Evaluating Transformer-Based Time Series Forecasting

arXiv:2606.25439v1 Announce Type: cross Abstract: Deep learning-based models have achieved state-of-the-art performance in Time Series Forecasting (TSF), yet their evaluation remains dominated by pointwise error metrics such as Mean Squared Error (MSE), which quantify numerical accuracy but overlook structural properties of the forecast signal, including recurrent dynamics, oscillatory behavior, and phase alignment. As a result, forecasts exhibiting over-smoothing, phase shifts, or frequency distortions may achieve favorable error scores despite substantial structural degradation. To address this limitation, we propose TopoCast, a topology-driven framework for evaluating structural fidelity in TSF. TopoCast reconstructs phase-space representations of forecast and ground-truth sequences using Takens delay embedding and applies persistent homology to characterize their intrinsic dynamics. We derive four complementary topological fidelity measures from persistence diagrams and aggregate them into a Topological Fidelity Score (TFS). We further introduce dominant cycle overlap, a novel metric that maps persistent topological features to the temporal domain to assess whether dominant oscillatory patterns occur at the correct time points. Combined with TFS, this yields the Localized Topological Fidelity Score (LTFS), a phase-aware measure that captures temporal localization errors invisible to existing evaluation metrics. Experiments on five Transformer architectures across three real-world benchmark datasets demonstrate that models with similar forecasting errors can exhibit markedly different structural fidelity profiles, revealing failure modes overlooked by conventional evaluation and highlighting the value of topology-aware forecast assessment.

21.
arXiv (CS.AI) 2026-06-24

BioMedArena: An Open-source Toolkit for Building and Evaluating Biomedical Deep Research Agents

arXiv:2605.06177v2 Announce Type: replace Abstract: Reproducing and comparing deep research agents today is hard: the same backbone evaluated on the same benchmark can report different accuracies across papers because the harness and tool registry differ, and integrating a new model into a comparable evaluation surface costs weeks of model-specific engineering. These are symptoms of a broader reproducibility problem in deep research agent research. Here, we introduce BioMedArena, an open-source toolkit that addresses this reproducibility gap and provides an arena for comparing deep research agents under a shared evaluation environment. BioMedArena decouples six layers of biomedical agent evaluation – benchmark loading, tool exposure, tool selection, harness mode, context management, and scoring – and exposes 166 biomedical benchmarks and 75 biomedical tools across 9 functional families. Adding a new model, benchmark, or tool can be accomplished with a few-line provider adapter. Beyond evaluation infrastructure, BioMedArena ships a library of high-quality reference components: 6 agent harnesses (including our proposed Mutual-Evolve) and 6 context-management strategies, any of which can be equipped on any backbone. Equipping these components substantially improves all 12 backbones; on each of 8 representative biomedical benchmarks, the best equipped backbone surpasses prior state-of-the-art (SOTA), by 15.01 percentage points on average. The toolkit, configurations, and per-task traces are available at https://github.com/AI-in-Health/BioMedArena.

22.
medRxiv (Medicine) 2026-06-18

Avidity of anti-pertussis toxin antibodies is associated with symptomatic Bordetella pertussis infection in a novel controlled human infection model

Background The association between functional antibody responses following Bordetella pertussis infection and symptomatic disease remains unclear. We characterized the maturation of anti-pertussis toxin (PT) IgG avidity after human challenge with B. pertussis and determined its association with symptomatic infection. Methods Healthy adults were intranasally inoculated with live B. pertussis organisms in a controlled human infection model and monitored for development of pertussis symptoms (NCT05136599). Serum samples were collected one day before inoculation and at 14, 28, 56, 180, and 365 days post challenge. Anti PT IgG avidity was tested using a titration of ammonium isothiocyanate (the bond breaking agent) to quantify a wide range of antibody avidities from low to very-high. Associations between covariates and avidity were examined using linear regression models, and high dimensional analyses were used to integrate all data. Findings Anti PT IgG avidity increased in both symptomatic (n=20) and asymptomatic (n=10) participants after the challenge, reached maximum levels at day 56, and then declined through day 365. Symptomatic participants developed significantly higher levels of high- and very high-avidity anti-PT antibodies at 28, 56, 180, and 365 days post-challenge compared with those who remained asymptomatic. In multivariate analyses, symptomatic infection was associated with higher levels of high and very high avidity anti-PT IgG at day180 and365 after challenge. Distinct avidity profiles in symptomatic vs asymptomatic participants emerged at day28 onwards, with the former group having higher levels of antibodies with higher avidities. However, levels of medium-high, high and very high avidity antibodies in symptomatic participants were lower at day 365 after challenge compared to their peak levels. Interpretation Anti-PT IgG avidity was associated with symptomatic B. pertussis infection and thus may serve as a surrogate of clinical disease outcome. These results highlight that antibody avidity provides an additional functional assay besides antibody quantitation to dissect immune responses to pertussis. Further investigation of anti PT IgG avidity should be pursued in natural pertussis outbreaks to determine whether it might be used to differentiate symptomatic from asymptomatic infections for epidemiologic purposes.

23.
PLOS Computational Biology 2026-06-18

Ten simple rules for turning your qualifying exam into an NIH-style fellowship proposal: A guide for graduate students

by Courtney Peña-Lima, Cameron S. Bader, Brendan K. Ball, Troy C. Dildine, Mekhala V. Dissanayake, Iris van ‘t Erve, Albina Ibrayeva, Amy Nippert, M.K. Quinn, Chelse Spinner, Samuel Thompson, Antonio Tomasso, Crystal M. Botham Qualifying exams, often referred to as “quals” or candidacy exams, are an important milestone in doctoral programs. Although the style of quals varies greatly by program and institution, it is usually a proposal that requires students to develop research ideas as well as their scientific writing skills. Many quals are modeled after funding mechanisms that graduate students can apply to and on a topic that the student will pursue in their dissertation. This paper offers graduate students a step-by-step guide on how to turn their quals into a fellowship-style research proposal, using National Institutes of Health (NIH) mechanisms as a benchmark, as this is the norm within US research institutions. This paper will be most useful for students who have completed or are in the process of completing proposal-based qualifying exams, usually in the second year of a doctoral program.

24.
arXiv (CS.CL) 2026-06-15

FineDialFact: A benchmark for Fine-grained Dialogue Fact Verification

Large language models are known to produce hallucinations - factually incorrect or fabricated information - which poses significant challenges for many natural language processing applications, such as dialogue systems. As a result, detecting hallucinations has become a critical area of research. Current approaches to hallucination detection in dialogue systems primarily focus on verifying the factual consistency of generated responses. However, these responses often contain a mix of accurate, inaccurate or non-verifiable facts, making the use of a single factual label overly simplistic and coarse-grained. In this paper, we introduce a benchmark, FineDialFact, for fine-grained dialogue fact verification, which involves verifying atomic facts extracted from dialogue responses. To support this, we construct a dataset based on publicly available dialogue datasets and evaluate it using various baseline methods. Experimental results demonstrate that methods incorporating Chain-of-Thought reasoning can enhance performance in dialogue fact verification. Despite this, the best F1-score achieved on the HybriDialogue, an open-domain dialogue dataset, is only 0.74, indicating that the benchmark remains a challenging task for future research. We release our dataset and code at https://github.com/XiangyanChen/FineDialFact.

25.
arXiv (CS.AI) 2026-06-16

Minimalist Genetic Programming

arXiv:2606.10237v2 Announce Type: replace Abstract: Genetic programming (GP) is based on two important insights. First, that any learning task can fundamentally be posed as a program induction problem, where the goal is to construct a symbolic hierarchical model that is expressed as a syntax tree. Second, to pose this task as a search problem, and use evolution to locate the desired model. Since it was proposed, GP has produced notable results in a wide range of tasks and problem domains. This work presents an alternative view by modifying the second core insight of GP, posing the problem as a syntactic derivation task instead. In particular, this paper presents Minimalist Genetic Programming (MGP), an algorithm that like GP is biologically inspired, but instead of evolution it takes inspiration from the Minimalist Program to human language, in which syntax is understood as an optimal solution to the problem of linking two other mental systems. In minimalism, the core computational process is a binary set formation operator called $MERGE$, than can be used to incrementally construct complex syntactic structures using a simple Markovian process. MGP is able to discover the core building blocks of the symbolic expressions, and to incrementally combined them using $MERGE$. The proposed system is benchmarked on symbolic regression tasks that are known to be difficult to solve with standard GP systems because of the propensity for bloat. Results show that when a proper lexicon of atomic syntactic objects are chosen, MGP is able to consistently produce the exact ground truth model on a set of symbolic regression tasks where standard GP struggles to do the same. The insights provided by minimalism are shown to be relevant to the problem of program induction, and should be explored further based on the potential exhibited by MGP in this work.