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01.
arXiv (CS.LG) 2026-06-12

To GAN or Not To GAN: Segmentation Analysis on Mars DEM

arXiv:2606.13252v1 Announce Type: new Abstract: To better understand Martian Surface, which is needed to enable Rovers navigate Mars with ease, it is necessary to be able to determine the location of mounds. Detecting and studying these morphologies can also help us find evidence of extraterrestrial life, in this case, more specifically, water or signs of life conducive environments. Detection of mounds was done by manually mapping morphological parameters onto Digital Elevation Models. This paper solves the problem by automatically detecting and or predicting mounds on Mars using Neural Network based Semantic Segmentation methodologies. This is done by using supervised semantic segmentation model and generative adversarial approach. A comparison of the approaches shows that adding extra artificially generated data did not improve the result.

02.
PLOS Computational Biology 2026-06-11

A zero-parameter first-principles gate framework for full-length TP53 missense variant interpretation

by Masamichi Iizumi Missense variant interpretation often achieves useful predictive performance but remains mechanistically opaque, particularly in proteins that combine structured domains with intrinsically disordered regions (IDRs). We developed Gate & Channel, a zero-parameter, first-principles framework for full-length TP53 missense variant analysis in which each prediction is generated by explicit IF-THEN gates derived from physicochemistry, geometry, structural constraints, and polymer physics rather than fitted weights. Variants are evaluated across independent channels representing distinct physical failure modes; a variant is predicted disruptive if any gate closes. A second hierarchical layer (“Geta”) encodes physically grounded post-closure exceptions, allowing sensitivity and specificity to be improved on disjoint variant populations. The v18 framework consists of 12 channels and 2 Getas spanning structured domains and IDRs, capturing DNA-contact disruption, Zn coordination, burial-dependent packing, secondary-structure compatibility, post-translational modification chemistry, short linear motif disruption (including a multi-partner coupled-folding face), proline-directed kinase recognition, and IDR-specific proline and glycine backbone constraints. Across 1,369 TP53 missense variants, the framework achieved 84.5% sensitivity and 89.1% positive predictive value, with 90.9% sensitivity preserved in the DNA-binding core and all 9/9 hotspot mutations captured. A post hoc audit of discordant IDR calls indicated that many apparent false positives had plausible molecular rationales, consistent with a distinction between molecular mechanism disruption and clinical penetrance. Applied to KRAS, TDP-43, and BRCA1, the same channels capture the dominant pathogenic mechanisms in each protein as a proof of principle, while residual missed variants name specific gates yet to be written. The framework is distributed as the open-source Python package pathogenicity-gates (v0.5.1, MIT). These results show that a substantial fraction of full-length TP53 missense variation can be resolved through explicit, auditable physical gates that carry meaning beyond TP53, with each remaining failure naming the next rule to be written.

03.
arXiv (CS.AI) 2026-06-19

Sovereign Execution Brokers: Enforcing Certificate-Bound Authority in Agentic Control Planes

arXiv:2606.20520v1 Announce Type: cross Abstract: Autonomous agents are increasingly connected to cloud, deployment, and data-control workflows, but production mutation authority should not reside inside non-deterministic reasoning processes. Existing access-control mechanisms authorize identities, while assurance layers certify proposed actions; neither alone provides a mandatory enforcement point for certified authority at the moment of mutation. This paper introduces the Sovereign Execution Broker (SEB), a runtime enforcement boundary for certificate-bound agentic infrastructure. SEB consumes certificates issued by the Sovereign Assurance Boundary (SAB), verifies that the requested mutation matches the certified execution contract, checks validity windows, policy epochs, revocation epochs, and live-state drift, mints scoped execution identity, invokes infrastructure APIs, and records signed decision and outcome records. By separating proposal, admission, and execution, SEB turns certified authority into a short-lived, revocable, auditable runtime capability, provided that production mutation APIs reject non-broker identities. We present the SEB execution model, certificate and replay-verification predicates, scoped identity semantics, bypass-prevention deployment patterns, failure behavior, and a concrete prototype implementation. We evaluate the prototype on AWS and Kubernetes clusters, measuring latency overheads, revocation propagation, drift detection, and security under fault injection.

04.
arXiv (CS.CL) 2026-06-19

CogniFold: Always-On Proactive Memory via Cognitive Folding

Existing agent memory remains predominantly reactive and retrieval-based, lacking the capacity to autonomously organize experience into persistent cognitive structure. Toward genuinely autonomous agents, we introduce CogniFold, a brain-inspired "always-on" agent memory designed for the next generation of proactive assistants. CogniFold continuously folds fragmented event streams into self-emerging cognitive structures, bootstrapping progressively higher-level cognition from incoming events and accumulated knowledge. We ground this by extending Complementary Learning Systems (CLS) theory from two layers (hippocampus, neocortex) to three, adding a prefrontal intent layer. Emulating the prefrontal cortex as the locus of intentional control and decision-making, CogniFold achieves this through graph-topology self-organization: cognitive structures proactively assemble under the stream, merge when semantically similar, decay when stale, relink through associative recall, and surface intents when concept-cluster density crosses a threshold. We evaluate structural formation using CogEval-Bench, demonstrating that CogniFold uniquely produces memory structures that match cognitive expectations and concept emergence. Furthermore, across eight downstream benchmarks – two probing long-term conversational memory (LoCoMo, LongMemEval) and six spanning other cognitive domains – we validate that CogniFold simultaneously performs robustly on conventional memory tasks. Our code is available at https://github.com/OpenNorve/CogniFold.

05.
arXiv (CS.AI) 2026-06-11

Runtime Enforcement of Hybrid System Properties

arXiv:2606.12022v1 Announce Type: cross Abstract: Runtime enforcement has emerged as a promising approach for ensuring the safety of autonomous and cyber-physical systems operating in uncertain and dynamic environments. Unlike traditional runtime verification, runtime enforcement actively intervenes during execution to prevent property violations by modifying unsafe system behaviors. Existing enforcement frameworks primarily focus on untimed or discrete-time specifications and are often limited to delaying or suppressing events, making them inadequate for reactive systems exhibiting complex continuous dynamics. In this paper, we propose a runtime enforcement framework where safety requirements are modeled using Hybrid Automata (HA). The framework combines discrete-event editing with continuous-time monitoring to support enforcement actions such as suppression, delay, and insertion of events at arbitrary time instants. Upon observing environmental inputs, the automaton is initialized, and runtime reachability analysis is used to synthesize safe corrective actions. We formally define the enforcement problem for safety hybrid automata, establish enforceability conditions, and present an online enforcement algorithm for reactive systems. A detailed case study on an Adaptive Cruise Control (ACC) system demonstrates the effectiveness of the proposed approach in maintaining safety properties under unsafe controller behaviors. Experimental results show that the framework introduces minimal computational overhead while ensuring continuous compliance with safety requirements in real time.

06.
arXiv (math.PR) 2026-06-18

Denoising Distances in Metric Measure Spaces

arXiv:2606.18301v1 Announce Type: cross Abstract: Recent work studied the problem of finding clusters and denoising pairwise distances from noisy distances of points sampled on a manifold. We study the same problems in more general metric measure spaces under \lowerphiregularity{}. We give an algorithm that extracts large localized clusters around every sampled point and uses them to denoise distances to any fixed accuracy, with near-linear running time in the dense fixed-accuracy regime. We also show how to achieve much higher accuracy with a non-efficient algorithm. This suggests that unlike the Riemannian case, denoising to higher accuracy in more general metric spaces has a statistical-computational gap.

07.
arXiv (quant-ph) 2026-06-16

Improved Cryogenic Photodiode Optical Biasing for Low-Noise and Low-Jitter Superconducting Nanowire Single-Photon Detectors

arXiv:2606.07140v2 Announce Type: replace Abstract: We experimentally demonstrate an improved optical biasing scheme for superconducting nanowire single-photon detectors (SNSPDs), which employs a cryogenic InGaAs-InP photodiode (PD) as a local bias source. It is found that, under illumination from a stable external light source, this PD generates a stable photocurrent in a cryogenic environment (~2.3 K), with fluctuations in the photocurrent primarily attributed to fluctuations in the incident optical power. Furthermore, by screening and effectively blocking stray photons leaking from the PD, which give rise to background dark counts, we have achieved an SNSPD exhibiting an ultra-low intrinsic dark count rate of 1e-4 cps. Utilizing this improved optical biasing technique, our SNSPD achieved performance comparable to that obtained under conventional electrical biasing: a system detection efficiency of 80.7%, a background dark count rate of 32.6 cps, and a minimum timing jitter of 57.5 ps. These results indicate that cryogenic-PD-based optical biasing serves as a viable, low-noise, and low-jitter alternative to traditional electrical biasing. Moreover, this work offers useful design guidance for the future development of PD-based low-noise bias sources and for the construction of all-photonic SNSPD systems tailored for high-precision quantum photonics applications.

08.
arXiv (quant-ph) 2026-06-11

Quantum thermodynamics, quantum correlations and quantum coherence in accelerating Unruh-DeWitt detectors in both steady and dynamical state

arXiv:2512.18123v2 Announce Type: replace Abstract: We investigate the interplay between quantum thermodynamics, quantum correlations, and quantum coherence within the framework of the Unruh-DeWitt (UdW) detector model. By analyzing both the steady and dynamical states of various quantum resources (including steerability, entanglement, quantum discord, and coherence), we study how these resources evolve under Markovian and non-Markovian environments. Furthermore, we investigate the impact of both the Unruh temperature and the energy levels on three key quantum phenomena: thermodynamic evolution, quantum correlations, and quantum coherence, considering different initial state preparations. The hierarchical structure relating quantum correlations and quantum coherence is determined. We further examine the thermodynamic performance of a quantum heat engine, highlighting the influence of memory effects and classical correlations on heat exchange, work extraction, and efficiency. Our results reveal that non-Markovian dynamics can enhance the preservation of quantum correlations and improve the engine's efficiency compared to purely Markovian regime. These findings provide insights into the role of quantum correlations and quantum coherence in quantum thermodynamic processes and open avenues for optimizing quantum devices operating in relativistic or open-system settings.

09.
arXiv (CS.LG) 2026-06-17

Towards Fast GNN Surrogates for CO2 Migration in Complex Geological Formations

arXiv:2606.17180v1 Announce Type: new Abstract: This chapter discusses how a data-driven machine learning approach can reproduce key aspects of the physical behavior of multiphase flows in complex geological formations. We propose an end-to-end graph neural surrogate tailored to CO$_2$ plume migration forecasting in geological storage. The method is evaluated on the SPE11A benchmark, a well-known industry test case designed to assess CO$_2$ storage scenarios and characterized by sharp gas-water interfaces, strong advective transport, and rapid convective mixing with fingering development. The benchmark is reformulated as a graph in which nodes represent computational cells and edges encode transmissibility-based interactions enriched with geometric attributes. Directional transport arising from grid geometry, permeability contrasts, and geological heterogeneity is captured through an anisotropic message-passing mechanism, where interaction weights are computed via geometry-conditioned edge embeddings, biasing message aggregation toward physically relevant transport directions. Temporal evolution is modeled in latent space using an autoregressive residual formulation trained with multi-step supervision. The proposed model produces competitive forecasts of gas saturation and liquid-phase density, which are key indicators for CO$_2$ storage monitoring, with cumulative errors that remain moderate over extended forecasting horizons.

10.
arXiv (CS.AI) 2026-06-16

Shachi: A Modular, Controllable Framework for LLM-Based Agent-Based Modeling of Emergent Collective Behavior

arXiv:2509.21862v3 Announce Type: replace Abstract: How collective behaviors emerge from the interactions of individual LLM-driven agents is a central question in artificial life, yet controlled study of these emergent dynamics has been hindered by the lack of a principled simulation framework for systematic experimentation. To address this, we introduce Shachi, a principled methodology and modular framework that decomposes an agent's cognition into core components: Configuration for intrinsic identity, Memory for contextual continuity, and Tools for extended capabilities, all orchestrated by an LLM reasoning engine. This decomposition treats each cognitive component as an independently controllable variable, enabling perturbation studies that trace how micro-level cognitive traits propagate into population-level dynamics. We investigate behavioral patterns across a 10-task benchmark spanning three levels of collective complexity. Shachi enables memory transfer across environment transitions, producing history-dependent behavioral shifts, and allows agents to simultaneously inhabit multiple environments, revealing cross-environment interference invisible in single-environment studies. Furthermore, in a real-world U.S. tariff shock case study, locally interacting agents with individually controlled cognitive components produce macro-level market dynamics directionally consistent with observed real-world outcomes. Our work provides a rigorous, open-source simulation framework for LLM-based ABM, aimed at fostering cumulative scientific inquiry into the emergent collective behaviors of interacting artificial agents.

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

Food4All: An Agentic Framework and Benchmark for Food Resource Navigation with Adaptive User Understanding

Food assistance referral requires conversational agents to translate underspecified, often noisy help-seeking dialogues into locally valid resource recommendations. We present Food4All, an agentic food-resource referral framework and benchmark grounded in 686 structured Indiana food resources. Food4All couples a food-specific search tool with 300 multi-turn evaluation tasks spanning single food needs, composite cases with access or document constraints, and five non-ideal user interaction traits: unreasonable demands, rambling responses, impatience, incomplete answers, and inconsistent information. We evaluate six Large Language Models (LLMs) on requirement grounding, resource retrieval, final referral correctness, and interaction efficiency. Although the strongest model achieves 96.33% referral accuracy, our diagnostics reveal persistent failures in grounding schedule, eligibility, intake, and document constraints, as well as failures to preserve valid retrieved resources in the final recommendation. Trait-level analysis further shows that different non-ideal behaviors stress different parts of the referral pipeline. Food4All provides a controlled testbed for studying tool-calling agents in constraint-sensitive food assistance referral under realistic user interaction challenges.

12.
medRxiv (Medicine) 2026-06-15

Population-scale genomics reveals divergent pathogenicity of variant classes across paralogous collagen IV genes

Monoallelic pathogenic or likely pathogenic variants in COL4A3 and COL4A4 occur in approximately 1 in 106 individuals, yet whether these paralogous genes confer equivalent pathogenicity for the same variant classes has not been tested at population scale. Using whole-genome sequencing data from the UK Biobank (UKB; n = 500,000), with replication in the All of Us Research Program (n = 414,000), we performed per-variant association testing, gene-based collapsing analyses and phenome-wide association studies (PheWAS) across haematuria, proteinuria and chronic kidney disease. We identified 64 COL4A3 and 92 COL4A4 rare variants significantly associated with haematuria or proteinuria, generating a quantitative allelic series for clinical variant interpretation. Glycine substitutions within collagenous domains conferred similar risks in both genes. In contrast, truncating and non-collagenous domain (NC1) missense variants were strongly associated with haematuria and proteinuria in COL4A4 carriers but showed substantially attenuated or absent associations in COL4A3 carriers despite comparable carrier frequencies and predicted pathogenicity scores. These findings were independently replicated in All of Us. Genome-wide association analysis identified the COL4A3/COL4A4 locus as the dominant genetic determinant of haematuria, with the signal attributable to the aggregate effects of rare coding variants and no evidence of independent common variant or trans-acting modifier effects. These findings demonstrate substantial gene-specific differences in tolerance to truncating and NC1 variants between COL4A3 and COL4A4, challenging assumptions of equivalent pathogenicity across paralogous collagen IV genes. Gene identity and not variant class alone, should inform risk stratification, variant interpretation and genetic counselling in individuals carrying collagen IV risk genotypes.

13.
arXiv (CS.LG) 2026-06-15

NeST: Neuron Selective Tuning for LLM Safety

arXiv:2602.16835v2 Announce Type: replace-cross Abstract: Safety alignment is essential for the responsible deployment of Large Language Models (LLMs). Yet, existing approaches often rely on heavyweight fine-tuning that is costly to update, audit, and maintain across model families. Full fine-tuning incurs substantial computational and storage overhead, while parameter-efficient methods, e.g., Low-Rank Adaptation (LoRA), trade efficiency for inconsistent safety gains and sensitivity to design choices. Safety intervention mechanisms reduce unsafe outputs without modifying model weights, but do not directly shape or preserve the internal representations that govern safety behavior. We present NeST, a Neuron-Selective Tuning framework for efficient post-hoc safety alignment. NeST identifies safety-relevant feed-forward neurons via activation probing on vanilla harmful and benign prompts, clusters neurons with similar activation profiles, and trains shared cluster-level updates while freezing the rest of the model. Importantly, NeST is trained only on vanilla malicious prompts, without using jailbreak-specific attack data, yet generalizes robustly to diverse jailbreaks. The learned updates are then folded into the original weights, incurring no inference-time overhead. Evaluated on 14 open-weight language and multimodal models, NeST outperforms lightweight baselines and approaches full fine-tuning robustness with significantly fewer trainable parameters. On text-only models, NeST reduces average jailbreak attack success rate from 44.5% to 1.1% while training only 0.4M parameters on average. Across multimodal settings, it reduces ASR from 55.3% to 1.1%, and for downstream fine-tuned variants, it restores safety by reducing ASR from 53.8% to 0.8%. These results show that robust, maintainable safety alignment can be achieved by concentrating adaptation on localized, functionally coherent safety structures.

14.
PLOS Medicine 2026-06-23

Parental body mass index and offspring childhood body size and eating behaviour: A structural equation modelling analysis in the Norwegian Mother, Father and Child Cohort Study

作者:

by Tom A. Bond, Tom A. McAdams, Nicole M. Warrington, Laurie J. Hannigan, Espen Moen Eilertsen, Ziada Ayorech, Fartein A. Torvik, George Davey Smith, Deborah A. Lawlor, Eivind Ystrom, Alexandra Havdahl, David M. Evans Background The intergenerational transmission of obesity-related traits could propagate an accelerating cycle of obesity, if parental adiposity causally influences offspring adiposity. The extent to which intergenerational obesity associations are due to such causal effects, as opposed to genetic confounding (inheritance), is unclear. We aimed to establish whether associations between parental peri-pregnancy body mass index (BMI) and offspring birth weight (BW), BMI until 8 years of age, and 8-year-old eating behaviour are due to genetic confounding. Methods and findings Data were from the Norwegian Mother, Father and Child Cohort Study, a prospective population-based birth cohort born between 1999 and 2009 at 50 out of 52 hospital maternity units in Norway. We compared the strength of the associations of maternal pre-pregnancy BMI versus paternal BMI during pregnancy, with offspring outcomes including birth weight and BMI assessed between age 6 months and 8 years of age, and appetite-related eating behaviour traits assessed at age 8 years via the Child Eating Behaviour Questionnaire (CEBQ), adjusting for potential confounders including parity, parental/grandparental language group and parental age, smoking, education and income). We then used an extended children of twins structural equation model (SEM) to quantify the extent to which associations were due to genetic confounding. Up to 85,866 children (51.3% male) were included in linear regression models, whereas SEM models included up to 50,999 children. Maternal BMI was more strongly associated than paternal BMI with offspring BW, but the maternal-paternal difference decreased for offspring BMI after birth. Greater parental BMI was associated with obesity-related offspring eating behaviours. SEM results indicated that genetic confounding did not explain the association between parental BMI and offspring BW, but explained the majority of the association with offspring BMI from 6 months onwards. For 8-year BMI, genetic confounding explained 79% (95% CI [62, 95]; p = 1.9 × 10−12) of the covariance with maternal BMI and 94% (95% CI [72, 113]; p = 2.7 × 10−14) of the covariance with paternal BMI. Limitations of this study include selective recruitment and attrition, potential bias due to parental assortative mating, and that findings may not generalise beyond high-income country settings with high obesity prevalence. Conclusions We found strong evidence that parent–child BMI associations may primarily be due to genetic confounding. When considered alongside prior evidence, this finding may argue against a strong causal effect of maternal or paternal adiposity on childhood adiposity via intrauterine or periconceptional mechanisms.

15.
arXiv (CS.LG) 2026-06-15

Arbitrary control over multimode wave propagation for machine learning

arXiv:2402.17750v2 Announce Type: replace-cross Abstract: Controlled multimode wave propagation can enable more space-efficient photonic processors than architectures based on discrete components connected by single-mode waveguides. Instead of defining discrete elements, one can sculpt the continuous substrate of a photonic processor to perform computations through multimode interference in two dimensions. Here we designed and demonstrated a device with a refractive index that can be rapidly reprogrammed across space, allowing arbitrary control of wave propagation. The device, a two-dimensional programmable waveguide, uses parallel electro-optic modulation of the refractive index of a slab waveguide with about $10^4$ programmable spatial degrees of freedom. We implemented neural network inference on benchmark tasks with up to $49$-dimensional vectors in a single pass, without digital pre-processing or post-processing. Theoretical and numerical analyses further indicated that two-dimensional programmable waveguides may offer not only a constant-factor reduction in device area but also a scaling benefit, with the area required growing as $N^{1.5}$ rather than $N^2$.

16.
medRxiv (Medicine) 2026-06-10

Resolving Diagnostic Discordance in Group 2 Pulmonary Hypertension Through Staged Physiologic Testing: Insights From PVDOMICS

Background World Symposium on Pulmonary Hypertension (WSPH) Group 2 pulmonary hypertension (PH) is a clinically integrated phenotype attributed to left heart disease, whereas pre- versus post-capillary classification is operationalized primarily by pulmonary capillary wedge pressure (PCWP). Although current recommendations emphasize contextual interpretation and provocative testing for intermediate PCWP values, the relationship between PCWP-based classification and underlying phenotype has not been systematically evaluated. We aim to quantify phenotype-hemodynamic discordance across the PCWP spectrum and evaluate a staged physiology-guided framework incorporating inhaled nitric oxide (iNO), ventricular geometry, and provocative testing. Methods We studied 1,032 participants from the NHLBI-sponsored PVDOMICS cohort with multidisciplinary adjudicated phenotypes integrating clinical, imaging, physiologic, and hemodynamic data. Stage-specific PCWP thresholds classified pre- versus post-capillary physiology at rest, during iNO, and during provocation (fluid challenge or invasive cardiopulmonary exercise testing [iCPET]). Echocardiographic right ventricular-to-left ventricular (RV/LV) ratio was evaluated as a marker of ventricular interdependence. Restricted cubic spline and staged concordance analyses defined certainty-based PCWP ranges and incremental diagnostic yield. Results Adjudicated Group 2 phenotype was present in 37.0% of participants. Resting PCWP demonstrated good discrimination (AUC 0.86), but substantial bidirectional phenotype-hemodynamic discordance persisted across intermediate PCWP ranges. At a resting PCWP of 12 mmHg, 25% of participants classified as pre-capillary had adjudicated Group 2 PH, whereas at 18 mmHg, 35% classified as post-capillary remained discordant non-Group 2. Concordance did not approach 90% until PCWP values were 24 mmHg. Dynamic testing incrementally improved concordance within these overlap zones. Nearly half of adjudicated Group 2 PH participants (46.5%) were not identified by resting PCWP alone; incorporation of iNO and provocative testing increased cumulative Group 2 identification by 63.4% and improved sensitivity from 79.9% to 83.7%. Model discrimination improved from an AUC of 0.863 to 0.908 (likelihood-ratio P

17.
arXiv (CS.AI) 2026-06-12

Optimizing Appliance Scheduling for Solar Energy Management Using Metaheuristic Algorithms

arXiv:2606.13407v1 Announce Type: new Abstract: Renewable energy is essential for meeting future energy demands; however, solar energy generation, which occurs only during daylight hours often does not align with household consumption patterns. Appliances such as cookers, washing machines, and dryers are typically operated according to user preferred schedules rather than solar energy availability, creating a scheduling optimization problem. The objective is to determine optimal appliance start times to maximize renewable energy utilization while minimizing user inconvenience and adhering to system constraints. This paper presents a metaheuristic approach using Iterated Local Search (ILS) and Simulated Annealing (SA) to optimize appliance start times, while considering appliance operating durations, power consumption, inverter limit, battery state of charge constraints, and solar generation forecasts. Unlike most existing work, the scheduling is extended beyond a single day to accommodate unfinished tasks from previous days (spillover), ensuring operational continuity and enabling sequential operation across multiple days. Experimental results show that the sequential multi-day scheduling framework effectively manages system constraints while ensuring user convenience under exclusive solar generation. These findings also open opportunities for future research on multi-objective trade-offs between investment in equipment of various sizes, return on that investment, and user satisfaction.

18.
bioRxiv (Bioinfo) 2026-06-11

AGZArank: Investigating epitope-conditioned antibody binder ranking with structure-derived synthetic supervision

Computational antibody design methods can generate large libraries of candidate binders for a target epitope, but prioritizing which candidates to test experimentally remains a major bottleneck. Existing scoring approaches, including physics-based affinity estimators, structure-prediction-derived confidence measures, and inverse-folding likelihood models, provide useful proxy signals but are not explicitly optimized for early enrichment of binders among many structurally similar candidates. Here we investigate epitope-conditioned antibody binder ranking as a dedicated learning problem and introduce AGZArank, a geometric deep learning framework trained with structure-derived synthetic supervision based on normalized pseudo-energy targets. On a benchmark of 45 experimentally validated antibody-antigen interfaces, AGZArank recovered the true binder within the top ten candidates in 44.4% of cases and showed stronger generalization on post-2021 structures than ProteinMPNN, ESM-IF, and PRODIGY. Ablation experiments indicate that ranking performance depends primarily on training scale and alignment between the optimization objective and retrieval-based evaluation, rather than architectural complexity alone. These results support candidate prioritization as a distinct and tractable problem in computational antibody design.

19.
medRxiv (Medicine) 2026-06-24

Beyond Nodal Status: Interactions Between Molecular Subtype, Tumor Burden, and Survival in 12,225 Patients with Breast Cancer

Background Lymph node status and molecular subtype are among the most established prognostic factors in breast cancer. However, the extent to which their prognostic effects vary across different tumor size categories and clinical subgroups remains incompletely understood. We investigated the interplay between nodal status, molecular subtype, and tumor size in a large real world breast cancer cohort and developed a prognostic nomogram for individualized survival prediction. Methods A total of 12,225 women with invasive breast cancer from the Shiraz Breast Cancer Registry were analyzed. Patients were stratified according to tumor size, lymph node status, and molecular subtype. Overall survival (OS) and disease free survival (DFS) were evaluated using Kaplan Meier analyses and subgroup comparisons. Logistic regression was performed to identify predictors of lymph node involvement, while Cox regression was used to determine independent prognostic factors. A nomogram was subsequently developed and internally validated for prediction of 3-year and 5-year OS. Results Of 12,225 patients, 41.7% had lymph node positive disease. Across nearly all tumor size categories and molecular subtypes, nodal involvement was associated with significantly worse OS and DFS. Notably, the survival disadvantage associated with nodal positivity was more pronounced among patients with larger tumors and among those with HER2 positive and triple negative breast cancer (TNBC). Although TNBC demonstrated the lowest rate of lymph node involvement among molecular subtypes (adjusted OR 0.54, 95% CI 0.46-0.63), it appeared to show one of the largest survival gaps between node positive and node negative disease. In the overall cohort, survival outcomes generally ranked from best to worst as Luminal A, Luminal B, HER2 positive, and TNBC. However, survival differences among molecular subtypes were not consistently observed across all tumor size and nodal status subgroups. When significant differences were present, Luminal A and Luminal B tumors consistently showed superior outcomes compared with HER2 positive and TNBC tumors. Multivariable analysis identified lymph node status, tumor size, molecular subtype, lymphovascular invasion, tumor necrosis, type of surgery, radiotherapy, hormone therapy, and adjuvant chemotherapy as independent prognostic factors. A nomogram integrating clinicopathological and treatment variables demonstrated good predictive performance, with time dependent AUCs of 0.749 and 0.751 for 3 year and 5 year OS, respectively, and showed good calibration. Conclusions The prognostic impact of lymph node status is not uniform across breast cancer subgroups and appears particularly pronounced in larger tumors and biologically aggressive subtypes. Despite a lower likelihood of nodal involvement, TNBC showed substantial outcome deterioration when nodal metastasis was present. These findings highlight the importance of jointly considering nodal status, molecular subtype, and tumor burden in prognostic assessment.

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

BioVid: Autoregressive Video Generation with Biological Behavior Semantic Comprehension

Video generation for biological behavior requires more than visually plausible motion: the duration of an action is itself a semantic property. Existing models usually rely on fixed temporal windows, external continuation, or prompt-driven stories, so length is specified externally rather than learned from behavior. To address this gap, we propose BioVid, a data-driven autoregressive framework for adaptive-length biological behavior generation. BioVid uses a 2D-encode/3D-decode tokenizer: a two-dimensional FSQ-R3GAN encoder converts each frame into discrete visual tokens, preserving single-frame information suited for next-token prediction and EOS-based termination, while a temporally inflated and video-finetuned three-dimensional decoder reconstructs generated tokens with temporal context to reduce flickering. A causal Transformer then models the frame-wise token sequence and, conditioned only on the first frame, stops generation when it emits an End-of-Sequence token, allowing duration to emerge from the learned behavior distribution. We evaluate BioVid on the A001 drinking action from NTU RGB+D. On 94 held-out clips, BioVid achieves a Wasserstein-1 distance of 1.24 frames from the real duration distribution. In comparison, fixed-length baselines yield distances of approximately 6-7 frames even when configured to the available length closest to the dataset mean, and approximately 15 frames when using the conventional 16-frame generation length. These results demonstrate the ability of BioVid to learn and reproduce the intrinsic duration distribution of biological behavior.

21.
arXiv (CS.AI) 2026-06-16

Artificial Intelligence Index Report 2026

arXiv:2606.15708v1 Announce Type: new Abstract: Welcome to the ninth edition of the AI Index report. As AI continues to advance rapidly, the question becomes whether the systems built around it can keep up. Governance frameworks, evaluation methods, education systems, and the data infrastructure needed to track AI's impact are struggling to match the pace of the technology itself. That gap between what AI can do and how prepared we are to manage it runs through every chapter of this year's report. New in this edition, the report tracks how AI is being tested more ambitiously across reasoning, safety, and real-world task execution, and why those measurements are increasingly difficult to rely on. It also features new estimates of generative AI's economic value alongside emerging evidence of its labor market effects, an analytical framework on AI sovereignty, and a science chapter developed in collaboration with Schmidt Sciences. For the first time, the report features standalone chapters on AI in science and AI in medicine, reflecting AI's growing impact across these two domains.

22.
arXiv (CS.LG) 2026-06-19

Variational Consensus Monte Carlo for Bayesian Mixture

arXiv:2606.19643v1 Announce Type: cross Abstract: Motivated by the privacy, sensitivity and sharing limitations of health data, we present a comprehensive pipeline for inference of Bayesian mixture models within a federated learning setting, i.e. when data cannot be fully shared or pooled across compute nodes. We adopt a Consensus Monte Carlo (CMC) approach, in which an MCMC algorithm is run independently within each data silo to estimate local posterior distributions, which are then aggregated to approximate the posterior over the full data. The variational CMC approach of Rabinovich, Angelino and Jordan (2015) [1] frames the aggregation step as a variational inference problem, but their application to mixtures assumes the number of clusters and key mixture parameters to be known. Our main methodological contributions are: (i) an extension of variational CMC to over-fitted Bayesian mixture models that infer the number of clusters and all model parameters, without requiring conjugacy; (ii) novel cluster-matching algorithms suitable for cross-silo settings in which not every cluster appears in each local dataset; (iii) a number of inference strategies for the aggregation step, matched to different federated learning constraints; and (iv) guidelines for choosing among these in practice. A comprehensive simulation study validates the framework and allows us to compare to state-of-the-art federated learning alternatives. Notably, we show that when the composition of local datasets reflects the underlying clustering structure in the data, our approach can recover small clusters with greater accuracy than standard MCMC applied to the pooled data. We illustrate the framework on large-scale electronic health record data, identifying multi-morbidity patterns in a British geriatric population.

23.
arXiv (CS.AI) 2026-06-19

TerraMind: Large-Scale Generative Multimodality for Earth Observation

arXiv:2504.11171v5 Announce Type: replace-cross Abstract: We present TerraMind, the first any-to-any generative, multimodal foundation model for Earth observation (EO). Unlike other multimodal models, TerraMind is pretrained on dual-scale representations combining both token-level and pixel-level data across modalities. On a token level, TerraMind encodes high-level contextual information to learn cross-modal relationships, while on a pixel level, TerraMind leverages fine-grained representations to capture critical spatial nuances. We pretrained TerraMind on nine geospatial modalities of a global, large-scale dataset. In this paper, we demonstrate that (i) TerraMind's dual-scale early fusion approach unlocks a range of zero-shot and few-shot applications for Earth observation, (ii) TerraMind introduces "Thinking-in-Modalities" (TiM) – the capability of generating additional artificial data during finetuning and inference to improve the model output – and (iii) TerraMind achieves beyond state-of-the-art performance in community-standard benchmarks for EO like PANGAEA. The pretraining dataset, the model weights, and our code are open-sourced under a permissive license.

25.
arXiv (CS.AI) 2026-06-19

DF3DV-1K: A Large-Scale Dataset and Benchmark for Distractor-Free Novel View Synthesis

arXiv:2604.13416v2 Announce Type: replace-cross Abstract: Advances in radiance fields have enabled photorealistic novel view synthesis. In several domains, large-scale real-world datasets have been developed to support comprehensive benchmarking and to facilitate progress beyond scene-specific reconstruction. However, for distractor-free radiance fields, a large-scale dataset with clean and cluttered images per scene remains lacking, limiting the development. To address this gap, we introduce DF3DV-1K, a large-scale real-world dataset comprising 1,048 scenes, each providing clean and cluttered image sets for benchmarking. In total, the dataset contains 89,924 images captured using consumer cameras to mimic casual capture, spanning 128 distractor types and 161 scene themes across indoor and outdoor environments. A curated subset of 41 scenes, DF3DV-41, is systematically designed to evaluate the robustness of distractor-free radiance field methods under challenging scenarios. Using DF3DV-1K, we benchmark nine recent distractor-free radiance field methods and 3D Gaussian Splatting, identifying the most robust methods and the most challenging scenarios. Beyond benchmarking, we demonstrate an application of DF3DV-1K by fine-tuning a diffusion-based 2D enhancer to improve radiance field methods, achieving average improvements of 0.96 dB PSNR and 0.057 LPIPS on the held-out set (e.g., DF3DV-41) and the On-the-go dataset. We hope DF3DV-1K facilitates the development of distractor-free vision and promotes progress beyond scene-specific approaches. The dataset and leaderboard are available at https://johnnylu305.github.io/df3dv1k_web/.