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01.
arXiv (quant-ph) 2026-06-15

Quantum codes and optimal pure quantum $(r,\delta)$-LRCs via the MP construction

arXiv:2606.14253v1 Announce Type: new Abstract: In this paper, we employ MP codes whose defining matrices are $\tau$-optimal defining ($\tau$-OD) matrices to construct new quantum codes and quantum $(r,\delta)$-LRCs. Specifically, we report the following results: We establish a unified $\tau$-monomial decomposition theorem for invertible self-adjoint matrices over finite fields of arbitrary characteristic, which generalizes the result in "Quantum codes using the $\tau$-OD MP construction" where the characteristic was required to be odd. Based on this theorem, we prove the existence of $\tau$-OD matrices over $\mathbb{F}_{q^2}$ for any characteristic and demonstrate that there exist several new infinite families of $\tau$-OD matrices over $\mathbb{F}_{q^2}$ of characteristic $2$. As an application of MP codes involving $\tau$-OD matrices, we construct several infinite families of quantum codes with flexible parameters. Within this framework, we present $222$ record-breaking quantum codes that surpass the best-known records maintained in Grassl's database. We propose two effective schemes for constructing optimal pure quantum $(r,\delta)$-LRCs via MP codes. Accordingly, we construct four new infinite families of optimal pure quantum $(r,\delta)$-LRCs with flexible parameters. Notably, we report an interesting phenomenon by exhibiting $30$ optimal pure quantum $(r,\delta)$-LRCs derived from our framework; that is, there exist quantum codes that are not only optimal pure quantum $(r,\delta)$-LRCs but also, according to Grassl's database, best-known, optimal, or record-breaking quantum codes. To the best of our knowledge, the new discovery that quantum codes are simultaneously optimal pure quantum $(r,\delta)$-LRCs and record-breaking quantum codes has not been previously reported in the literature.

02.
arXiv (CS.CV) 2026-06-16

DifFRACT: Diffusion Feature Reconstruction and Attribution for Circuit Tracing

Mechanistic interpretability seeks to explain neural network behavior by decomposing model computations into interpretable features and circuits. While transcoder-based circuit tracing has recently enabled detailed causal analyses of large language models, multimodal diffusion transformers for image generation remain comparatively opaque. We still lack tools for understanding how semantic information propagates across denoising steps and how text and image representations interact within double-stream MM-DiT architectures. Existing methods provide only partial insight: attention maps expose a limited view of token interactions, while sparse autoencoders can discover interpretable features but do not directly reveal how these features are transformed and composed through nonlinear MLP layers. In this work, we extend transcoder-based circuit tracing to multimodal diffusion transformers. We train timestep-conditioned transcoders that faithfully approximate the input-output behavior of MLP sublayers in FLUX.1[schnell]. By replacing MLPs with transcoders and linearizing the remaining computation, we obtain exact feature-to-feature attribution and recover compact, interpretable circuits. Empirically, our transcoders match or slightly outperform sparse autoencoders on the sparsity-faithfulness tradeoff. The resulting circuits reveal mechanisms underlying attribute binding and cross-stream semantic propagation, and provide causal explanations for systematic generation errors. Moreover, circuit-guided interventions are substantially more precise and effective than standard SAE-based steering. Our results demonstrate that transcoder-based circuit analysis is feasible for state-of-the-art diffusion transformers and provides a powerful framework for understanding and controlling multimodal generative models. The code is available at https://github.com/Artalmaz31/DifFRACT

03.
arXiv (CS.CV) 2026-06-24

VistaRef: Boosting Visual Spatial Orientation Awareness for Pointing-to-Object Detection

Grounding deictic gestures in natural images is fundamental to AR and human-robot collaboration, providing a basis for seamless spatial interaction. While Transformer-based visual models have achieved significant progress in general object detection, their global attention mechanisms often neglect micro-geometric relationships, degrading orientation accuracy. In pointing tasks, this deficiency manifests as an inability to accurately capture the pointing ray implied by finger poses, which results in pointing drift and localization ambiguity when dealing with distant or densely packed objects. To address this, we propose VistaRef, a framework designed to explicitly enhance spatial orientation awareness. First, we develop the Local Hand Entity Modeling (LHEM) module, which incorporates hand-pose embeddings to strengthen the model's capability to capture subtle finger deviations. Second, drawing inspiration from multi-view geometry, we construct the Geometric Ray Modeling (GRM) module to transform implicit orientation information into explicit spatial geometric features, guiding feature aggregation and deep fusion via attention mechanisms. Furthermore, we introduce a novel Orientation-Consistent Alignment Loss (OCAL) to synergistically supervise hand presence and pointing consistency, ensuring that all architectural improvements collectively serve the core objective of spatial localization. Experimental results demonstrate that VistaRef significantly outperforms the baseline, achieving a 14-point absolute gain in grounding accuracy. Qualitative analysis further confirms that VistaRef effectively models the geometric correlation from hand to target, bridging the spatial perception gap inherent in traditional Transformers for complex scenarios. Code: https://github.com/lingli1724/VistaRef.

04.
arXiv (CS.CV) 2026-06-24

AerialFusionMapNet: Online HD Map Construction with Aerial-Onboard BEV Fusion

High-resolution aerial imagery has recently emerged as a complementary modality for automated driving perception and has shown potential to improve birds-eye-view (BEV) scene understanding when fused with onboard sensors. Prior work demonstrated performance gains for online high-definition (HD) map construction through aerial-onboard fusion; however, conventional end-to-end fusion does not fully exploit the structural information contained in aerial representations. In this work, we introduce AerialFusionMapNet, a fusion-based mapping framework with a structured two-stage training strategy that explicitly enhances the contribution of aerial features within a unified pipeline. The proposed training scheme enables more effective integration of structural aerial priors. On the nuScenes geographic split, AerialFusionMapNet achieves up to 54.7 mAP, improving over prior aerial-onboard fusion baselines from 48.8 mAP by +5.9 absolute and +12.1% relative. The results suggest that structured training design, rather than increased architectural complexity, plays a more decisive role in unlocking the full potential of aerial imagery for online HD map construction. Code and trained models are available at https://github.com/DriverlessMobility/AerialFusionMapNet.

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

Descriptive versus Regulatory Uncertainty in Bounded Predictive Systems

arXiv:2605.18909v2 Announce Type: replace Abstract: Any system that models the world under finite representational capacity must compress; any compression entails a prior; and the prior is the system's bias. What has not been established is whether uncertainty participates in the dynamics governing future behavior, or merely describes the output distribution without consequence. We introduce a structural distinction between descriptive uncertainty, which does not recursively modulate the system's policy, and regulatory uncertainty, which directly enters the optimization landscape and drives persistent adaptive restructuring. We prove formally that current transformer architectures are confined to descriptive uncertainty at inference. We ground this in thermodynamics via Landauer's principle: for uncertainty to be regulatory, epistemic error must cost real energy; in a decoupled system, hallucinations and correct derivations dissipate identical energy. We test this empirically across three locally-deployed language models (3B, 8B, 70B parameters). Token-level Shannon entropy is statistically invariant across tasks spanning pattern retrieval, causal operator application, and out-of-distribution causal generalization in all three models (all pairwise p >= 0.568; within-model ranges 0.011-0.028 nats), while task accuracy varies substantially across the same conditions (0%-100%). Entropy and accuracy are orthogonal. The decoupling is scale-invariant: larger models achieve higher accuracy but identical entropy flatness. This structural incapacity is not resolvable by additional parameters or training data. Genuine epistemic grounding requires physical coupling between thermodynamic substrate state and information processing cost.

06.
medRxiv (Medicine) 2026-06-15

VarEx: A Large Language Model Pipeline for Automated Extraction of Exposures, Outcomes, and Covariates from Epidemiologic Studies

Objective: Observational studies are essential for investigating risk factors for Alzheimer's disease and related dementias (ADRD), but inconsistent reporting and selection of covariates can contribute to residual confounding, omitted-variable bias, and reduced reproducibility. We developed and evaluated VAREX (Variable Extraction), a large language model (LLM)-based information extraction framework designed to automatically identify exposures, outcomes, and covariates from epidemiologic studies and populate structured evidence repositories. Materials and Methods: VAREX combines retrieval-augmented generation, biomedical language-model embeddings, semantic chunking, cross-encoder reranking, and prompt-engineered LLM workflows to extract epidemiologic variables from full-text biomedical articles. The framework was evaluated using a reference-standard corpus of observational studies examining blood pressure variability (BPV) and Alzheimer's disease-related dementias (ADRD), together with external validation datasets involving other exposure-outcome relationships. Extracted variables were compared with independently curated human reference standards using semantic matching and one-to-one assignment procedures. Covariates were additionally classified into ten epidemiologically relevant semantic categories. Results: In the primary BPV[->]ADRD corpus (10 studies), VAREX achieved a precision of 0.91, recall of 0.84, and F1-score of 0.87 for variable extraction. Covariate classification accuracy was 0.90, yielding a strict extraction-and-classification F1-score of 0.78. External validation datasets demonstrated comparable performance across diverse epidemiologic domains, with extraction F1-scores ranging from 0.73 to 0.85. Category-level performance was strongest for health behaviors (F1=0.96), sociodemographic variables (F1=0.90), and medication exposures (F1=0.89). Compared with published estimates of manual systematic-review effort, VAREX reduced processing time from approximately 61 minutes to 9 minutes per article, representing an 85.7% reduction in review time. Discussion: These findings demonstrate that LLM-based information extraction can accurately identify and classify epidemiologic variables across heterogeneous observational-study designs. Automated extraction enables scalable construction of structured repositories of exposures, outcomes, and covariates while substantially reducing the labor required for evidence synthesis and systematic reviews. Conclusion: VAREX provides an effective framework for automated extraction and classification of epidemiologic variables from the biomedical literature. By supporting large-scale evidence synthesis and structured knowledge resource development, VAREX may facilitate more rigorous observational research, improved confounder identification, and enhanced reproducibility in epidemiology.

07.
arXiv (quant-ph) 2026-06-11

Fast Adiabatic Quantum Gates via Hyperfine Intermediate States

arXiv:2606.11655v1 Announce Type: new Abstract: The appeal of adiabatic quantum computing lies in its intrinsic robustness against various technical imperfections, making it attractive for many quantum information applications. However, it faces a fundamental challenge: accelerating the adiabatic operations while preserving adiabaticity within the qubit coherence time. In this article, we propose an electromagnetically induced transparency-based adiabatic CNOT gate protocol which harnesses atomic hyperfine intermediate states (HISs) to speed up the adiabatic evolution. The HISs, naturally-existed in two-photon transitions, often need to be suppressed due to their significant decay errors. In contrast, this paper introduces a novel method that utilizes appropriately chosen HISs not only to enhance the adiabaticity in STAY pathway but also to accelerate the population transfer in TRANSFER pathway. Through pulse optimization, we achieve adiabatic gate fidelities exceeding 0.9991 within 0.3903 {\mu}s in realistic Cs atomic setups. To demonstrate the generality of protocol we further assess the impact of decays from multiple HIS and extend our model to arbitrary number of states, providing a practical route toward fast and robust adiabatic quantum gates in Rydberg-atom platforms.

08.
arXiv (quant-ph) 2026-06-19

Topological Quantum Interferometry

arXiv:2606.19730v1 Announce Type: new Abstract: Structured light provides high-dimensional Hilbert spaces holding tremendous potential for fundamental quantum optics and quantum technologies. However, existing characterization methods, like Hong-Ou-Mandel (HOM) interference, typically assume perfectly tuned conditions, overlooking the geometric physics governing spatial mode evolution. Here, we establish topological quantum interferometry driven by an interaction-based geometric phase, the exchange Berry phase (BPX). Our formalism generalizes $q$-plate state generation and characterization to arbitrary topological charges and (de)tuning conditions, demonstrating that BPX acts as a geometric marker governing spatial interference. We show BPX serves as a deterministic control parameter, decomposing two-photon spatial patterns into geometry-dictated fundamental modes. This mapping reveals topological invariants and phase singularities that function as a non-tomographic witness for state dimensionality estimation, circumventing full-state reconstruction. Being device-independent and highly scalable, this approach enables scalable high-dimensional characterization and topologically protected state selection, with direct applicability to quantum metrology and high-capacity quantum networks.

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

Variational Learning for Insertion-based Generation

arXiv:2606.02133v3 Announce Type: replace-cross Abstract: Non-monotonic sequence generation methods, such as masked diffusion models, provide a flexible alternative to left-to-right autoregressive modeling by allowing tokens to be generated in non-fixed and prescribed orders. Despite their practical advantages, most existing non-monotonic models are order-agnostic and rely on a fixed-length grid, limiting their ability to support variable-length generation and adaptive insertion order. In this work, we introduce a probabilistic framework for learning insertion order in variable-length insertion models. We formalize a bijective correspondence between insertion trajectories and permutations, which enables an exact reparameterization of the data likelihood as a sum over permutations. Building on this result, we propose the Insertion Process (IP), a stochastic generative model that jointly learns where to insert, what to insert, and when to terminate, trained via permutation-based variational inference. Unlike prior fixed-canvas approaches, IP natively supports variable-length generation and learns data-driven preferences over insertion orders. Experiments on goal-conditioned planning and molecular string generation demonstrate that learning insertion order improves both modeling quality and generalization in domains without a canonical left-to-right structure.

10.
arXiv (CS.LG) 2026-06-11

Spatially Masked Regression Reveals Local and Distributed Predictability in Electrophysiological Recordings

arXiv:2606.11415v1 Announce Type: cross Abstract: Neural recordings are often interpreted as local measurements, yet the signal at any one sensor can also reflect structured activity distributed across the broader network. This raises a basic question: to what extent does an electrode's signal reflect local versus distributed information in the underlying system? More specifically, how much of an electrode's activity is carried by its immediate neighborhood, and how much is embedded more broadly across the array? We address this with a Spatially Masked Regression (SMR) framework that reconstructs each electrode's timeseries from the remaining electrodes while excluding a configurable neighborhood around the target. By progressively increasing this mask, spatial locality becomes an experimental control for quantifying how much predictive information survives after nearby channels are withheld. We apply SMR to intracranial EEG with heterogeneous electrode coverage and to scalp EEG with standardized montages over sensorimotor cortex. Using distance correlation between original and reconstructed signals, we find strong within-subject reconstruction in both modalities, substantial residual predictability even when local neighbors are excluded, and markedly stronger cross-subject transfer in EEG than in iEEG. Masking shows that nearby electrodes contribute strongly to reconstruction but do not account for all of it, indicating that individual channels reflect both local redundancy and broader distributed structure. Surrogates that preserve selected marginal or spectral properties while disrupting phase structure or temporal ordering substantially reduce performance, supporting the conclusion that SMR depends on structured temporal and cross-channel organization rather than on marginal statistics alone. These results position SMR as an interpretable framework for quantifying the balance between local and distributed information in recordings.

11.
arXiv (CS.LG) 2026-06-24

Hybrid Sequence Modeling and Reinforced Verification for Controllable Target-Conditioned Decision Making

arXiv:2508.16420v3 Announce Type: replace Abstract: Target-conditioned sequence models provide a simple interface for controllable offline decision making, but the requested target return can be an unreliable control signal, especially when the target return lies in underrepresented regions of the dataset. This paper proposes Doctor, a hybrid sequence modeling and reinforced verification framework for controllable target-conditioned offline decision making. Doctor trains a shared masked trajectory Transformer with two complementary objectives: masked trajectory reconstruction for candidate generation and in-sample value learning for action-value verification. At inference time, the model samples multiple nearby target returns, generates candidate actions in parallel, and selects the action whose verified value is closest to the requested target return. We analyze this verifier-guided selection rule and show that its value-level alignment error is bounded by candidate-value coverage around the target return and verifier accuracy. Experiments on D4RL and EpiCare show that Doctor improves target-return alignment under reduced high-return coverage, remains competitive on standard offline return-maximization benchmarks, and enables a single policy to modulate between conservative and aggressive operating points in a simulated clinical decision-making task. These results suggest that reinforced verification can improve the controllability of target-conditioned policies.

12.
PLOS Medicine 2026-05-08

Optimal minimal residual disease threshold in pediatric acute myeloid leukemia: A retrospective cohort study based on the TARGET database

Authors:

by Xiong-yu Liao, Hong Zheng, Jian-pei Fang, Dun-hua Zhou, Kun-yin Qiu Background Minimal residual disease (MRD) monitoring is a cornerstone of risk stratification in pediatric acute myeloid leukemia (AML), with a threshold of 0.1% conventionally defining positivity by flow cytometry. Advances in flow cytometric technologies, enabling detection of leukemic cells with higher sensitivity and specificity, warrant a reevaluation of whether a lower threshold improves prognostic accuracy. Methods and findings We conducted a retrospective cohort study using data from the Therapeutically Applicable Research to Generate Effective Treatments (TARGET)-AML initiative. The study population comprised 1,205 pediatric patients with de novo AML treated across Children’s Oncology Group (COG) clinical trial centers. Patients were enrolled between September 1996 and December 2016, with a median follow-up of 6.2 years (range: 0.5–20.1 years). The primary objective was to compare the prognostic performance of the traditional MRD threshold (≥0.1%) with a lower threshold (≥0.05%) after induction courses 1 and 2. The main outcome measure was 5-year event-free survival (EFS). Analyses included Kaplan−Meier survival estimates, Cox proportional hazards models to calculate hazard ratios (HR) with 95% confidence intervals (CI), receiver operating characteristic (ROC) curves, and net reclassification improvement (NRI). The optimal threshold for predicting 5-year EFS, determined by ROC analysis, was 0.05% after both induction course 1 (AUC: 0.840, 95%CI[0.76,0.88]) and course 2 (AUC: 0.854, 95%CI[0.78,0.89]). The 0.05% threshold demonstrated higher HR for the first event than the 0.1% threshold (after course 1: HR = 2.8, 95%CI[2.3,3.3]; P 

13.
arXiv (CS.AI) 2026-06-17

A Neuro-Symbolic Approach to Strategy Synthesis for Strategic Logics

arXiv:2606.17962v1 Announce Type: cross Abstract: Reasoning about what agents can achieve through strategic interaction is a core challenge in Multi-Agent Systems (MAS). Logics for strategic ability, such as ATL, provide rigorous methods, but their adoption is often hindered by the computational cost of strategy synthesis. We introduce a neuro-symbolic framework that integrates large language models (LLMs) into the model-checking pipeline for MAS. The LLM acts as a strategy-generation oracle, proposing candidate strategies that are then formally validated by a standard MAS model checker. This generate-and-certify architecture uses LLM guidance to navigate large combinatorial strategy spaces while preserving formal soundness: generated strategies are accepted only when certified by the verifier. We instantiate the framework for bounded strategic reasoning in NatATL and introduce the first NatATL strategy-synthesis dataset, consisting of 4211 instances. Experiments with an open-weight Qwen3-32B model show that our certified pipeline achieves 92\% accuracy on strategy-synthesis outcomes.

14.
arXiv (CS.LG) 2026-06-16

Closing the Approximation Gap in Simulation-free Latent SDEs

arXiv:2606.16138v1 Announce Type: cross Abstract: Recovering dynamical systems from noisy observations is a recurring challenge across scientific domains, including neuroscience and physics. Latent stochastic differential equations (SDEs) address this by modeling the system as an unobserved state that evolves according to a learnable SDE and generates the observations. Variational inference (VI) provides a tractable objective for fitting latent SDEs. Traditional VI algorithms evaluate this objective by numerical simulation over a time discretization, trading fidelity for computational cost. A recent class of algorithms, simulation-free VI, sidesteps this tradeoff by parameterizing the posterior through its instantaneous marginals rather than its drift. In this work, we show that the efficiency of existing simulation-free VI algorithms comes at a price: their parameterizations restrict the approximate posterior to a subset of the SDEs available to simulation-based methods, degrading posterior inference and parameter learning. We propose Helmholtz-SDE, a simulation-free VI algorithm that closes this gap by optimizing over path laws compatible with a prescribed collection of marginals. Helmholtz-SDE recovers dynamics more faithfully than prior simulation-free methods, with the largest gains under high posterior uncertainty. It further matches the performance of simulation-based VI at a fraction of the runtime.

15.
arXiv (CS.AI) 2026-06-12

Reducing the Complexity of Deep Learning Models for EEG Analysis on Wearable Devices

arXiv:2606.12742v1 Announce Type: new Abstract: Wearable healthcare devices are the fastest-growing Internet of Things (IoT) sector. Many automated healthcare services rely on two crucial biological signals, namely ECG and EEG, which reflect the activity of the heart and brain, respectively. Although deep neural networks are considered the primary way to process and analyze these signals, the very tight energy and computational power constraints in wearable devices are far below the computational, energy, and memory bandwidth demands of DNN models, thereby impeding the deployment of deep learning in many practical wearable services. This paper investigates the feasibility of deploying state-of-the-art DNN models in resource-constrained wearable devices. Notably, we explore the trade-off between accuracy and computational complexity of DNNs when parameter quantization and electrode reduction methods are used. Our investigation centers on several state-of-the-art DNN models designed for EEG signal analysis, specifically for detecting epileptic seizures. Our findings demonstrate that, when applied judiciously, these techniques can significantly reduce the complexity of the DNNs under consideration with minimal adverse effects on accuracy. These results reveal the explicit trade-offs between accuracy and complexity reduction encountered when adapting DNN-based online EEG analysis for wearable devices.

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

Non-invertible symmetries out of equilibrium: Eigenstate order and Floquet physics

arXiv:2508.14213v2 Announce Type: replace-cross Abstract: Through the study of the Rep($D_8$) non-invertible symmetry, we show how non-invertible symmetries manifest in dynamics. Results are presented for dynamics generated by Hamiltonians as well as Floquet unitaries. For both examples, the role of the non-invertible symmetry is studied through the appearance of non-invertible symmetry protected edge modes. In addition, the role of the non-invertible symmetry for the Hamiltonian is studied through eigenstate order. In particular, by considering the effect of symmetry preserving disorder, the non-invertible symmetry is shown to give rise to degeneracies in the spectra of the Hamiltonian that can only be completely lifted at orders of perturbation that scale with system size. The eigenstates of disordered Hamiltonians, whose ground state correspond to non-trivial symmetry protected topological (SPT) states, are shown to have either trivial or non-trivial SPT order that are detected as non-zero expectation value of string order-parameters. In contrast, non-trivial SPT order is absent in the eigenstates of trivial SPT Hamiltonians with disorder. The interface between two different SPT phases host edge modes whose dynamics is studied numerically and analytically. The edge mode is shown to oscillate at frequencies related to different effective chain lengths that are weighted by the temperature, becoming an exact zero mode in the limit of zero temperature. A Floquet model with the non-invertible symmetry is constructed whose edge mode is shown to exhibit period-doubled dynamics at low effective-temperatures. The zero and period-doubled edge modes differ from those in conventional SPTs by being symmetric under the invertible symmetry, while being charged under the non-invertible symmetry.

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

Mixtures Closest to a Given Measure: A Semidefinite Programming Approach

arXiv:2509.22879v2 Announce Type: replace-cross Abstract: Mixture models, such as Gaussian mixture models, are widely used in machine learning to represent complex data distributions. A key challenge, especially in high-dimensional settings, is to determine the mixture order and estimate the mixture parameters. We study the problem of approximating a target measure, available only through finitely many of its moments, by a mixture of distributions from a parametric family (e.g., Gaussian, exponential, Poisson), with approximation quality measured by the 2-Wasserstein or the total variation distance. Unlike many existing approaches, the parameter set is not assumed to be finite; it is modeled as a compact basic semi-algebraic set. We introduce a hierarchy of semidefinite relaxations with asymptotic convergence to the desired optimal value. In addition, when a certain rank condition is satisfied, the convergence is even finite and recovery of an optimal mixing measure is obtained. We also present an application to clustering, where our framework serves either as a stand-alone method or as a preprocessing step that yields both the number of clusters and strong initial parameter estimates, thereby accelerating convergence of standard (local) clustering algorithms.

18.
arXiv (CS.CV) 2026-06-16

Landmark-free Assessment of Lower-limb Alignment with Implicit Neural Shape Functions from Knee Radiographs

Radiographic assessment of lower-limb alignment (LLA) is important for predicting joint health and surgical outcomes in total knee arthroplasty. Traditional measurement methods are manual and time-consuming, while recent machine learning approaches typically rely on locating a fixed set of anatomical landmarks. This dependence limits flexibility and may require re-annotation when clinical definitions change. To address this, we propose an automated workflow using Implicit Neural Shape Functions (INSF). Rather than relying on explicit landmark coordinates, we encode the anatomy into a compact latent space and regress clinical alignment measurements directly from these latent codes. This architecture allows for rapid extendability to new tasks without altering the backbone representation. We trained our method on an internal dataset of 566 knee radiographs, each annotated with the outline of the femur and tibia. We evaluated it on both an internal test dataset of 50 patients and a separate external set of 402 preoperative cases from the MRKR dataset. Manual clinical measurements are available for these data, and the MRKR measurements will be made publicly accessible. Performance was comparable to state-of-the-art landmark-based methods and manual agreement, while offering a flexible shape representation that can be extended to additional measurement tasks.

19.
arXiv (CS.AI) 2026-06-17

Temporal Preference Optimization for Unsupervised Retrieval

arXiv:2606.17664v1 Announce Type: cross Abstract: Unsupervised dense retrievers offer scalability by learning semantic similarity from unlabeled documents via contrastive learning, but they struggle to capture the temporal relevance, retrieving semantically related but temporally misaligned documents-an important aspect when a document collection spans multiple time periods (e.g., retrieving documents from 2018-2025 for "Who is the president in 2019?" introduces temporal ambiguity). Existing methods rely on supervised training with explicit timestamps, which are not always feasible. We propose TPOUR (Temporal Preference Optimization for Unsupervised Retriever), which uses our novel training method Temporal Retrieval Preference Optimization (TRPO). TRPO reinterprets preference learning in the temporal dimension, guiding the retriever to favor temporally aligned documents. TPOUR further generalizes to unseen time periods via interpolation in a learned time embedding, enabling continuous temporal alignment. Experiments on temporal information retrieval (T-IR), TPOUR outperforms both unsupervised and supervised baselines. Compared to Qwen-Embedding-8B, despite being about 72.7x smaller, TPOUR Contriever improves average nDCG@5 by +4.04 (+12.15%) on explicit and +4.98 (+15.21%) on implicit queries. We provide our code at https://github.com/agwaBom/TPOUR.

20.
medRxiv (Medicine) 2026-06-11

Dissecting the functional landscape of rare diseases through genomic variation in a heterogeneous cohort of 11,000 patients

Rare diseases (RDs) remain a major diagnostic challenge. Genetic and phenotypic heterogeneity, incomplete knowledge of disease mechanisms, and limitations in variant clinical interpretation leave many patients without a molecular diagnosis. Meanwhile, the growing volume of genomic data generated in clinical practice offers an opportunity to develop data-driven methodologies for exploring disease mechanisms and improving the reanalysis of unsolved cases. We aggregated real-world genomic data from 11,084 unrelated patients with suspected RD. Patients were clinically classified into 122 diseases. We built a multi-disease genomic variant frequency database (FJD-DB), which enabled the development of variant and gene-disease association scores by means of case-control subcohort comparisons across 32 disease groups. Functional enrichment analyses were then used to highlight disease-associated protein domains, pathways, biological processes, and phenotypes. Finally, the resulting knowledge was integrated into a data-driven framework for the guided reanalysis of unsolved RD patients applied to Inherited Retinal Dystrophies (IRD) patients as first use case. FJD-DB contained more than 45 million unique variants, including ~185,000 potentially pathogenic variants. Disease-specific analyses identified disease-associated pathogenic variants and highlighted both established and candidate disease genes. We detected 179 significantly enriched protein domains across 23 diseases, 124 Human Phenotype Ontology terms across 13 diseases, 79 Reactome pathways across 10 diseases, and 72 Gene Ontology biological processes across 8 diseases, revealing highly disease-specific functional signatures. Integration of disease-specific variant, gene, and functional association signals enabled the development of a data-driven framework for guided reanalysis of unsolved RD cases. Applied to more than 1,100 unsolved IRD cases, the framework generated clinically relevant findings in 26 patients, including four molecular diagnoses, seven candidate diagnoses, and 15 cases upgraded from non-informative findings to variants of uncertain significance. Aggregated real-world genomic data can be leveraged to identify disease-associated molecular signals generating novel biological hypotheses. A unified analytical framework provides a scalable strategy for knowledge discovery and guided reanalysis, facilitating the identification of overlooked and potentially novel genetic causes of RDs.

21.
arXiv (CS.AI) 2026-06-18

Detecting High-Potential SMEs with Heterogeneous Graph Neural Networks

arXiv:2602.19591v3 Announce Type: replace-cross Abstract: Small and Medium Enterprises (SMEs) constitute 99.9% of U.S. businesses and generate 44% of economic activity, yet systematically identifying high-potential SMEs remains an open challenge. We introduce SME-HGT, a Heterogeneous Graph Transformer framework that predicts which SBIR Phase I awardees will advance to Phase II funding using exclusively public data. We construct a heterogeneous graph with 32,268 company nodes, 124 research topic nodes, and 13 government agency nodes connected by approximately 99,000 edges across three semantic relation types. SME-HGT achieves an AUPRC of 0.621 0.003 on a temporally-split test set, outperforming an MLP baseline (0.590 0.002) and R-GCN (0.608 0.013) across five random seeds. At a screening depth of 100 companies, SME-HGT attains 89.6% precision with a 2.14 lift over random selection. Our temporal evaluation protocol prevents information leakage, and our reliance on public data ensures reproducibility. These results demonstrate that relational structure among firms, research topics, and funding agencies provides meaningful signal for SME potential assessment, with implications for policymakers and early-stage investors.

22.
medRxiv (Medicine) 2026-06-22

Artificial Intelligence-Enabled Cardiac Function Estimation from Phone Videos of Echocardiograms

Importance: Mobile phone-recorded echocardiogram videos are commonly used in point of care, telemedicine, and resource-limited workflows, but artificial intelligence models for left ventricular ejection fraction (LVEF) estimation have primarily been evaluated on native Digital Imaging and Communications in Medicine (DICOM) videos. Objective: To evaluate whether previously described artificial intelligence models for LVEF estimation retain performance when applied to mobile phone-recorded echocardiographic videos. Design: Multicenter model validation study comparing model-estimated LVEF with clinician reported LVEF. Setting: Three medical centers: Kaiser Permanente Northern California, Beth Israel Deaconess Medical Center through MIMIC-IV-ECHO, and Cedars-Sinai Medical Center. Participants: Source studies with clinician reported LVEF and apical 4-chamber or apical 2-chamber views, yielding 6209 phone-recorded videos from 2648 studies and 2611 patients. Exposures: Mobile phone recording of native echocardiographic videos and fine-tuning of pretrained models using mobile phone-recorded videos from the Kaiser Permanente Northern California training cohort. Main Outcomes and Measures: Mean absolute error in ejection fraction percentage points, R^2 for continuous estimation, and area under the receiver operating characteristic curve for identifying ejection fraction greater than 50%. Results: The study included 6209 mobile phone recorded echocardiographic videos from 2648 studies and 2611 patients; the weighted mean age was 68.4 years, and 1031 patients were male (39.5%). Without phone-video fine-tuning, the primary model achieved a mean absolute error of 7.00 percentage points, coefficient of determination of 0.49, and area under the receiver operating characteristic curve of 0.91 on phone-recorded videos; corresponding native DICOM performance was 6.08 percentage points, 0.60, and 0.93, respectively. On the 2396-video fine-tuning evaluation cohort, fine-tuning improved primary model performance to a mean absolute error of 6.96 percentage points, coefficient of determination of 0.61, and area under the receiver operating characteristic curve of 0.93. Fine-tuning the public EchoNet-Dynamic model improved performance from 9.36 percentage points, 0.37, and 0.84 to 7.86 percentage points, 0.50, and 0.89, respectively. Progressive central zoom preprocessing degraded model performance. Conclusions and Relevance: These findings suggest that artificial intelligence assisted left ventricular ejection fraction estimation from mobile phone-recorded echocardiograms may be feasible when native image export is unavailable, although prospective evaluation is needed before clinical deployment.

23.
bioRxiv (Bioinfo) 2026-06-12

Evaluating cell type annotations in single-cell omics in the absence of ground truth

Accurate cell type annotation is essential for single-cell transcriptomics, directly shaping downstream analyses and biological interpretations. Yet, objective evaluation of annotation quality remains a major challenge. Here, we argue that a cell type or cell state label has practical utility only if it captures a molecular pattern that is reproducible across biological replicates. Based on this principle, we introduce inter-sample consistency (ISC), a quantitative framework to assess annotation quality in single-cell RNA-seq datasets. Unlike existing cluster validation approaches, ISC distinguishes annotations that generalize across samples and individuals from those driven by technical or unwanted variation, thereby providing principled criteria for annotation quality and transferability. When applied to published single-cell atlases, ISC reveals widespread reproducibility gaps and provides actionable guidance for repairing inconsistent annotations. Notably, ISC enables benchmarking of automated cell type annotation tools even when ground-truth labels are unavailable, providing interpretable metrics to guide their development and evaluation. Implemented as the scTypeEval Bioconductor package, this framework offers a broadly applicable resource for evaluating and improving cell type annotations in single-cell RNA-seq experiments.

24.
arXiv (CS.CL) 2026-06-16

SAMark: A Self-Anchored Text Watermarking with Paragraph-Level Paraphrase Robustness

Semantic-level watermarking (SWM) improves robustness against text modifications by treating sentences as the basic unit. However, robustness to paragraph-level paraphrasing remains difficult because such attacks globally disrupt watermark signals by changing sentence order. In this work, we propose SAMark, a self-anchored watermarking framework that removes the dependency on sentence order by establishing a step-independent green region in semantic space. To improve detectability, we introduce a multi-channel hyperbolic scoring mechanism that amplifies watermark signals while suppressing noise from weakly aligned candidates. We further propose a diversity-aware filtering strategy that combines hard filtering with soft regularization, extending beyond simple n-gram repetition filters to address semantic redundancy. Experimental results show that SAMark achieves up to 90.2% TP@FP1% under typical paragraph-level paraphrasing attacks, outperforming the strongest prior baseline by more than 30% on average, while maintaining generation quality competitive with unwatermarked text and breaking the robustness-quality trade-off that limits prior methods.

25.
bioRxiv (Bioinfo) 2026-06-22

Few-Shot Classification of C. elegans Developmental Stages via Explainable Hierarchical Hyperbolic Graph Embeddings

Automated, accurate, and fast developmental-stage classification of C. elegans from microscopy-based morphological images is essential for aging research, drug screening, and disease modeling. However, it remains challenging due to morphological similarities between stages and the limited annotated data. In this work, we propose HyperDev, a hyperbolic few-shot learning framework that addresses these limitations by directly encoding developmental hierarchies in the embedding space, unlike conventional Euclidean approaches that treat stages as independent classes. HyperDev uses Poincare ball geometry, combined with a biologically informed developmental prior, to naturally represent stage relationships. We introduce our selfcurated C. elegans dataset spanning seven developmental stages (Egg, L1-L4, Adult, Dauer) with extreme class imbalance (6-8 samples per minority class). HyperDev achieves competitive classification accuracy (76.9-88.3%) while providing intrinsic explainability across nine 7-way few-shot evaluation settings. The learned embeddings exhibited strong biological alignment (Pearson r = 0.669, p < 0.001), while significantly outperforming ProtoNet (r = 0.187), MatchingNet (r = 0.235), and RelationNet (r = 0.464). These results establish hyperbolic geometry as a principled approach to explainable few-shot learning in biological imaging, where understanding learned representations is as critical as predictive performance. Clinical Relevance–By enabling explainable, data-efficient developmental staging from scarce samples, HyperDev supports improved phenotype quantification for aging research, disease modeling, and drug screening. Index Terms–Hyperbolic learning, few-shot classification, developmental staging, Caenorhabditis elegans, interpretability, explainability.