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01.
arXiv (quant-ph) 2026-06-16

Complete Relational Description of Spin in a Quantum Background

arXiv:2606.15873v1 Announce Type: new Abstract: The standard description of the state of a spin in quantum mechanics presupposes externally fixed directions – a classical background. Can a spin be fully described instead in relation to other quantum mechanical systems? Poulin suggested twenty years ago group averaging over rotations the joint state of a fundamental spin and a reference spin with large angular momentum which, however, yields a classical bit in a probabilistic mixture. We revisit this idea and show that when the quantum reference system is augmented to two large spins, the standard quantum mechanical description of a spin is recovered in the limit of large quantum numbers for the reference system.

02.
arXiv (CS.AI) 2026-06-15

Distributional Biases in Post-Training: A Markovian Analysis of Reasoning Trajectories

arXiv:2511.07368v3 Announce Type: replace-cross Abstract: Foundation models exhibit broad knowledge but limited task-specific reasoning, motivating post-training strategies such as RL with verifiable rewards (RLVR) and test-time scaling (TTS). While recent work highlights the role of exploration in improving pass@K, empirical evidence points to a paradox: RLVR and ORM/PRM typically reinforce existing paths rather than expanding the reasoning scope, raising the question of why exploration helps if no new patterns emerge. To reconcile this paradox, we adopt the perspective of Kim et al. (2025), viewing easy (e.g., simplifying a fraction) versus hard (e.g., discovering the some symmetry) reasoning steps as low versus high probability Markov transitions. In this tractable model, pretraining corresponds to tree-graph discovering, while post-training corresponds to CoT reweighting. We provably show that, both RLVR and ORM/PRM would favor heavily to several high-probability paths, and thereby forget rare-but-crucial CoTs. Building on this, we further prove that exploration strategies such as rejecting easy instances and KL regularization help preserve rare CoTs. Empirical simulations corroborate our theoretical results.

03.
bioRxiv (Bioinfo) 2026-06-16

Expanding gene regulatory networks from transcriptome data through graphical modeling with heterogeneous priors

Gene regulatory network inference is widely used to reconstruct large-scale networks and identify functional genes from transcriptome data. Meanwhile, in many biological fields, core regulatory genes have been extensively studied, leading to the establishment of small-scale gene regulatory networks, and novel genes connected to these networks remain to be identified. However, methods for expanding existing gene networks by identifying novel regulatory interactions, rather than reconstructing the entire network, are not well established. Here, we propose a method for gene network expansion that incorporates known regulatory relationships and evaluates each candidate gene individually to infer its regulatory connections to the existing network. Using simulated datasets from the DREAM4 benchmark and the PRECISE-1K experimental dataset, our method outperformed conventional methods by incorporating prior knowledge. In particular, it improved the ability to distinguish true regulatory interactions from indirect associations arising from strong correlations among genes in the existing network. The method also showed strong performance for interactions involving genes with high outdegree or centrality. Furthermore, it maintained stable performance as the size of the existing network increased and was robust to noise in prior information. These results demonstrate that our method provides an effective framework for expanding existing gene regulatory networks by leveraging prior knowledge.

04.
arXiv (CS.CV) 2026-06-18

VGGHeads: 3D Multi Head Alignment with a Large-Scale Synthetic Dataset

Human head detection, keypoint estimation, and 3D head model fitting are essential tasks with many applications. However, traditional real-world datasets often suffer from bias, privacy, and ethical concerns, and they have been recorded in laboratory environments, which makes it difficult for trained models to generalize. Here, we introduce \method – a large-scale synthetic dataset generated with diffusion models for human head detection and 3D mesh estimation. Our dataset comprises over 1 million high-resolution images, each annotated with detailed 3D head meshes, facial landmarks, and bounding boxes. Using this dataset, we introduce a new model architecture capable of simultaneous head detection and head mesh reconstruction from a single image in a single step. Through extensive experimental evaluations, we demonstrate that models trained on our synthetic data achieve strong performance on real images. Furthermore, the versatility of our dataset makes it applicable across a broad spectrum of tasks, offering a general and comprehensive representation of human heads.

05.
arXiv (CS.AI) 2026-06-17

CausalT5k: Diagnosing Refusal and Failure Modes in Trustworthy Causal Reasoning Across Causal Rungs

arXiv:2602.08939v2 Announce Type: replace Abstract: Large language models increasingly produce fluent causal explanations, yet they often fail in ways aggregate accuracy cannot diagnose: confusing association with intervention, abandoning correct judgments under pressure, over-refusing valid claims, or answering when evidence is underdetermined. We introduce CTK, a diagnostic benchmark of 5,147 cases and growing, across 10 domains and all three levels of Pearl's Ladder of Causation. Unlike benchmarks that only score correctness, CTK reveals why a model failed by annotating causal rung, trap type, pressure sensitivity, refusal quality, and Utility-Safety tradeoffs. Its Sheep/Wolf taxonomy separates valid causal designs from inferential traps; paired neutral/pressure variants measure sycophantic drift through Bad Flip Rate; and Wise Refusal fields test whether a model identifies the missing information needed before endorsing a claim. CTK exposes failure modes hidden by aggregate accuracy: the Skepticism Trap, Rung Collapse under scaling, pressure-induced drift, Detection-Correction gaps, and counterfactual error modes. Rather than prescribing a correction method, it provides the diagnostic substrate for studying causal-reasoning failure profiles.

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

Sample-Efficient Hypergradient Estimation for Decentralized Bi-Level Reinforcement Learning

arXiv:2603.14867v4 Announce Type: replace-cross Abstract: Many strategic decision-making problems, such as environment design for warehouse robots, can be naturally formulated as bi-level reinforcement learning (RL), where a leader agent optimizes its objective while a follower solves a Markov decision process (MDP) conditioned on the leader's decisions. In many situations, a fundamental challenge arises when the leader cannot intervene in the follower's optimization process; it can only observe the optimization outcome. We address this decentralized setting by deriving the hypergradient of the leader's objective, i.e., the gradient of the leader's strategy that accounts for changes in the follower's optimal policy. Unlike prior hypergradient-based methods that require extensive data for repeated state visits or rely on gradient estimators whose complexity can increase substantially with the high-dimensional leader's decision space, we leverage the Boltzmann covariance trick to derive an alternative hypergradient formulation. This enables efficient hypergradient estimation solely from interaction samples, even when the leader's decision space is high-dimensional. Additionally, to our knowledge, this is the first method that enables hypergradient-based optimization for 2-player Markov games in decentralized settings. Experiments highlight the impact of hypergradient updates and demonstrate our method's effectiveness in both discrete and continuous state tasks.

08.
arXiv (CS.CL) 2026-06-16

Spectro-Temporal Interference Confounds Phase Encoding in Spatial Audio Foundation Models

Recent spatial self supervised audio models achieve high performance on localization tasks, raising questions about their encoding of microsecond interaural phase fine structures. We propose a psychoacoustic benchmark based on the binaural masking level difference to evaluate this. Using an equalization cancellation baseline and a GCC PHAT positive control we evaluate nine frozen audio models spanning binaural SSL, monaural SSL, and neural audio codecs. Four monaural negative controls yield zero BMLD confirming binaural specificity. Two general purpose binaural SSL models exhibit minimal phase sensitivity while dedicated binaural spatial SSL models achieve BMLD comparable to the analytical baseline. Progressive physical ablations show that general purpose binaural SSL models rely on spectro temporal interference textures rather than cross channel phase computation. High detection rates in speech reflect a confounding reliance on broadband envelopes rather than genuine phase encoding.

09.
arXiv (CS.LG) 2026-06-16

Acoustic Prompting via Stage-wise Modulation for Few-Shot Learning in Audio Language Models

arXiv:2606.15751v1 Announce Type: cross Abstract: Audio-Language Models (ALMs) have shown remarkable success in zero-shot audio classification by aligning audio waveforms with text. Recent efforts to improve downstream performance focus on learning optimal text prompts. However, previous approaches focus on the text encoder, leaving the potential of learnable prompts within the audio encoder unexplored. In this paper, we propose a novel framework that introduces trainable prompts into the audio encoder to capture task-specific acoustic features. We demonstrate that integrating audio-side prompt learning with existing text-side approaches enhances few-shot adaptation. Through extensive experiments across 11 datasets show that integrating our method as a plug-and-play module alongside existing text prompt tuning generally leads to performance improvements. These findings suggest that explicitly modulating the audio representation space effectively complements text-only prompting approaches. The code is available at https://github.com/hyebin-c/aspl.

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

Mask-Proof: An LLM-based Automated Data Curation Pipeline on Mathematical Proofs

arXiv:2606.15258v1 Announce Type: new Abstract: Large language models (LLMs) are increasingly capable of mathematical problem solving and can even assist with research-level proofs, yet we still lack a scalable and reproducible way to measure step-level reasoning in long proofs across diverse sources. This evaluation gap limits trustworthy AI assistance in proof-certified scientific progress. Existing evaluations often emphasize final answers or rely on costly expert grading, while end-to-end proof generation remains open-ended and hard to verify automatically. We introduce Mask-Proof, a pipeline that turns real proofs into automatically checkable masked-step tasks. It masks key formula steps, provides the necessary surrounding context, and evaluates model reconstructions with an LLM-based equivalence judge using repeated votes for stability. The resulting Mask-ProofBench contains 292 curated problems across diverse research areas. Experiments with 17 models show that reasoning-enhanced models outperform standard models by 12% to 27%. Our evaluator achieves 96.8% agreement with expert annotators, enabling faithful, reproducible, and comparable measurement of step-level mathematical reasoning. Benchmark, annotations, and code are available at https://github.com/weating/Mask-Proof.

11.
arXiv (CS.CL) 2026-06-17

Evidence of Layered Positional and Directional Constraints in the Voynich Manuscript: Implications for Cipher-Like Structure

The Voynich Manuscript (VMS) exhibits a script of uncertain origin whose grapheme sequences have resisted linguistic analysis. We present a systematic analysis of its grapheme sequences, revealing two complementary structural layers: a character-level right-to-left optimization in word-internal sequences and a left-to-right dependency at word boundaries, a directional dissociation not observed in any of our four comparison languages (English, French, Hebrew, Arabic). We further evaluate two classes of structured generator against a four-signature joint criterion: a parametric slot-based generator and a Cardan grille implementing Rugg's (2004) gibberish hypothesis. Across their full tested parameter spaces, neither class reproduces all four signatures simultaneously. While these results do not rule out generator classes we have not tested, they provide the first quantitative benchmarks against which any future generative or cryptanalytic model of the VMS can be evaluated, and they suggest that the VMS exhibits cipher-like structural constraints that are difficult to reproduce from simple positional or frequency-based mechanisms alone.

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

Speaking the Language of Science: Toward a General-Purpose Generative Foundation Model for the Natural Sciences

In this report, we present LOGOS (Language Of Generative Objects in Science), a scientific generative language model that unifies heterogeneous tasks across the natural sciences within a single autoregressive framework based on a shared scientific grammar. It encodes diverse scientific objects and their spatial interactions as token sequences over a common vocabulary. By representing spatial contact and constraint patterns as discrete tokens, the model captures complex structural interactions in a purely sequential manner, without relying on explicit coordinates or geometric neural networks. This unified representation enables a wide range of downstream tasks to be formulated consistently as next-token prediction in the same grammar space, creating strong alignment between continued multi-domain pre-training and downstream objectives. Across diverse tasks, LOGOS consistently matches or outperforms domain-specific baselines, providing preliminary evidence for the feasibility of "one model fits all" in the natural sciences. We train LOGOS models at different scales (1B, 3B, and 8B parameters) and find a consistent positive correlation between model size and performance. This suggests that the future of AI for Science (AI4S) may not lie in building an independent technical stack that is separated from large language models (LLMs). Instead, it may depend on deeply aligning scientific foundation models with LLMs through shared architectures, shared training paradigms, and shared inference infrastructure, so that LLMs can truly become a new entry point for AI4S. We release the model weights and associated resources to facilitate further research.

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

V-JEPA 2.1: Unlocking Dense Features in Video Self-Supervised Learning

We present V-JEPA 2.1, a family of self-supervised models that learn dense, high-quality visual representations for both images and videos while retaining strong global scene understanding. The approach combines four key components. First, a dense predictive loss uses a masking-based objective in which both visible and masked tokens contribute to the training signal, encouraging explicit spatial and temporal grounding. Second, deep self-supervision applies the self-supervised objective hierarchically across multiple intermediate encoder layers to improve representation quality. Third, multi-modal tokenizers enable unified training across images and videos. Finally, the model benefits from effective scaling in both model capacity and training data. Together, these design choices produce representations that are spatially structured, semantically coherent, and temporally consistent. Empirically, V-JEPA 2.1 achieves state-of-the-art performance on several challenging benchmarks, including 7.71 mAP on Ego4D for short-term object-interaction anticipation and 40.8 Recall@5 on EPIC-KITCHENS for high-level action anticipation, as well as a 20-point improvement in real-robot grasping success rate over V-JEPA-2 AC. The model also demonstrates strong performance in robotic navigation (5.687 ATE on TartanDrive), depth estimation (0.307 RMSE on NYUv2 with a linear probe), and global recognition (77.7 on Something-Something-V2). These results show that V-JEPA 2.1 significantly advances the state of the art in dense visual understanding and world modeling.

14.
arXiv (math.PR) 2026-06-15

Sectional Curvature for Kantorovich-Wasserstein and Hellinger-Kantorovich Geometries

arXiv:2606.14318v1 Announce Type: cross Abstract: We derive an explicit formula for the sectional curvature of the space ${\cal M}(M)$ of finite measures on a Riemannian manifold M. The space ${\cal M}(M)$ is equipped with the Hellinger-Kantorovich metric $HK$. Even in the case M=R^n, the curvature is comprised of two parts: the `lifted part' is negative, and the `twisted part' is positive. It will be analyzed in detail for the multidimensional torus. Our general approach to sectional curvature in geodesic spaces also leads to new insights into the curvature of the space $P_2(M)$ of probability measures on M equipped with the Kantorovich-Wasserstein metric $W_2$.

15.
arXiv (CS.AI) 2026-06-18

Domain-Shift Aware Neural Networks for Unbalance Characterization in Rotating Systems

arXiv:2606.18882v1 Announce Type: cross Abstract: This work investigates the application of a domain-shift aware neural network for regression tasks aimed at estimating unbalance masses in rotating shafts under varying operating conditions. Experimental data were collected from a test rig in which a primary shaft, equipped with a flange carrying unbalanced masses, was driven at different rotational speeds, while a secondary shaft could be optionally activated to introduce domain discrepancy. The unbalance masses were positioned at a fixed radial distance, and the dynamic response of the system was recorded using triaxial accelerometers. The inverse problem of mass estimation is formulated within a domain adaptation framework, where the network is trained with a maximum mean discrepancy strategy to align feature representations across source and target distributions. The results demonstrate the effectiveness of explicitly addressing domain shift in improving prediction accuracy, especially when the system's physical behavior and sources of domain discrepancy are not fully known and fall outside the training conditions. These findings highlight the potential of domain-shift aware models for regression tasks in Structural Health Monitoring.

16.
bioRxiv (Bioinfo) 2026-06-15

DAQplugin: Deep Learning based Real-time Model Evaluation Plugin for ChimeraX

Although an increasing number of protein structures are determined by cryogenic electron microscopy (cryo-EM), protein structure modeling frequently suffers from residue misassignments and sequence register shifts, particularly in regions with ambiguous density. Here, we present DAQplugin, a ChimeraX plugin that performs real-time evaluation of protein models against cryo-EM density maps using the deep-learning-based residue-wise model quality (DAQ) score. Unlike existing validation tools that are typically applied after model construction, DAQplugin enables real-time deep-learning-based validation during model building and refinement. To our knowledge, DAQplugin is the first tool that provides real-time deep-learning based validation of protein models for cryo-EM map within an interactive modeling environment. In addition to identifying potential modeling errors, DAQplugin also provides guidance for correcting sequence register shifts by suggesting alternative residue placements along the backbone. The computation in this plugin is designed to run efficiently on general CPUs without requiring GPU hardware. Using DAQplugin, users can perform deep-learning-based validation on standard laptops during interactive model building, model-map fitting, and refinement. DAQplugin is able to facilitate more accurate interpretation of cryo-EM density maps and improve the reliability assessment of protein structure models.

17.
arXiv (CS.AI) 2026-06-18

EffiNav: Fusing Depth and Vision-Language for Efficient Object Goal Navigation

arXiv:2606.18634v1 Announce Type: cross Abstract: To locate a target object while exploring the unknown environment is a fundamental capability for autonomous agents, with applications ranging from search-and-rescue to field robots. A simplified version of such task is Object Goal Navigation (ObjNav). In ObjNav, successful arrival at the target object provides a basic measure of performance; however, the efficiency of the navigation trajectory is equally important, as it indicates how intelligently the agent explores and how much time remains for subsequent tasks. In unknown environments, the key to efficient navigation lies in deciding where to explore next. While many prior works aim to address this core challenge and achieved promising performance in certain settings, recent training-based models and non-training frameworks still suffer from generalization and efficiency issues respectively, which in the worst cases can lead to excessive exploration of already-visited areas or redundant back-and-forth motion. We evaluate EffiNav on two widely used simulation benchmarks Habitat Matterport 3D (HM3D) and Open-Vocabulary Object goal Navigation (OVON), and further validate its effectiveness on physical robots in real-world settings. We conduct failure analysis on massive simulation episodes. With minimal modification, we also extend EffiNav to a memory-augmented ObjNav task on the GOAT-BENCH dataset, demonstrating its adaptability beyond standard ObjNav settings. Across two standard metrics–Success Rate (SR) and Success weighted by Path Length (SPL), EffiNav matches or outperforms recent baselines, reflecting its efficiency, robustness, and practical applicability. Recognizing the different emphases of the two datasets, the performances reveals this framework is more balanced and generalizable for efficient ObjNav.

18.
PLOS Medicine 2026-06-12

Comparison of count-based and clustering definitions of multimorbidity and their association with prevalence of multimorbidity, health profiles, and mortality: A cohort study of UK Biobank participants

by Gabriella C. Silva, Aurore Fayosse, Louis Jacob, Séverine Sabia, Archana Singh-Manoux, Benjamin Landré Background Multimorbidity, the presence of several chronic conditions, is linked to higher mortality and healthcare use and thus poses a major challenge for aging populations. While most studies rely on simple counts of conditions, clustering approaches have been proposed to describe patterns of co-occurring diseases. We aimed to evaluate the extent to which these methodological choices influence prevalence and association with health profiles and mortality. Methods and findings Using UK Biobank baseline data (n = 474,397), collected between 2006 and 2010, we compared six count-based definitions of multimorbidity based on different condition lists (extended, most prevalent, or body systems) and thresholds (≥2 versus ≥3 conditions). We also applied a clustering analysis to characterize subtypes of multimorbidity among participants with at least two chronic conditions. We compared prevalence and associations with concurrent health outcomes (polypharmacy, self-rated health, frailty, falls, surgery, chronic pain), blood-based measures (C-reactive protein, Cystatin-C, HDL, LDL Cholesterol, IGF-1), and 3- and 10-year mortality risks. Analyses were undertaken separately in men and women using multivariable regression models adjusted for sociodemographic characteristics and body mass index. Multimorbidity prevalence ranged from 1.0% (cluster-based) to 35.3% (count-based). Count-based definitions using lists with more conditions yielded higher prevalence. Higher thresholds identified more severe health profiles on all measured health outcomes, blood-based measures, but not higher mortality risks. Associations with blood-based measures were more pronounced using clustering, with the highest differences from the standard definition distributed across clusters. Odds ratios for 3-year mortality ranged from 1.44 [1.26; 1.64] to 4.60 [3.73; 5.62] for men and 1.35 [1.07; 1.69] to 3.83 [2.78; 5.14] for women. For 10-year mortality, they ranged from 1.42 [1.34; 1.50] to 3.86 [3.46; 4.30] in men and 1.29 [1.21; 1.39] to 3.33 [2.93; 3.77] for women, with clustering identifying groups with low prevalence and high mortality risks. Findings should be interpreted in light of the selected nature of the UK Biobank cohort and the cross-sectional assessment of several health indicators. Conclusion Operational definitions of multimorbidity substantially influence prevalence estimates, while associations with mortality appear more robust across count-based approaches. Clustering analyses provide complementary insights into heterogeneity within multimorbid populations. Future translational studies are warranted to determine how multimorbidity definitions can be optimized to ultimately improve clinical management and health outcomes in practice.

19.
arXiv (math.PR) 2026-06-18

Rigidity of infinite exchangeable sequences with Gaussian marginals

arXiv:2606.18654v1 Announce Type: new Abstract: We study infinite exchangeable sequences with Gaussian one-dimensional marginals. We formulate the conjecture that joint Gaussianity of a single pair of coordinates forces the entire sequence to be a Gaussian process. Although this conjecture remains open, we prove that joint Gaussianity of the first four coordinates is sufficient. We also establish the corresponding two-point criterion under the additional assumption that the directing measure is almost surely infinitely divisible.

20.
medRxiv (Medicine) 2026-06-16

Recurrence After Hepatic Hydatid Cyst Surgery: Scolicidal Agent Application Technique and the Effect of Cystopiliary Fistula

Objective: This study aimed to evaluate long-term outcomes in patients who underwent surgical treatment for hepatic hydatid cyst (HCC) disease and, in particular, to investigate the effect of scolicidal agent (SA) application method and the presence of cystobiliary fistula (CBF) on the development of recurrence. Materials and Methods: This single-center, retrospective study included 197 patients who underwent surgical treatment for HCC disease. Hypertonic saline was used as SA in all patients and was classified as intracystic or pericystic application according to the application method. The presence of CBF was evaluated according to intraoperative and postoperative findings. Patients were followed for 86 months, and the development of recurrence was identified by radiological methods. Comparisons were made between the groups with and without recurrence in terms of SA application method and the presence of CBF. Results: The median age of the patients was 38 years, and the median follow-up period was 86 months. SA application was performed into the cyst in 51.3% of the patients and around the cyst in 48.7%. The presence of CBF was detected in 49.7% of the patients. No statistically significant difference was found between the recurrent and non-recurrent groups in terms of SA application method (p = 0.344). Similarly, no significant relationship was found between the presence of CBF and the development of recurrence (p = 0.721). Conclusion: This study showed that the SA application method and the presence of CBF are not determinants of recurrence in HCC disease. It is thought that recurrence rates can be kept low with appropriate surgical technique and effective biliary tract management.

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

Structured Nonparametric Variational Inference for Dependent Latent Modeling

arXiv:2606.15458v1 Announce Type: cross Abstract: Variational inference (VI) is a core engine of modern AI, enabling scalable approximate Bayesian learning and uncertainty-aware training of large probabilistic and generative models. In this paper, we propose Structured Nonparametric Variational Inference (SN-VI), a novel framework for modeling complex dependencies among latent variables in posterior approximation, leveraging multivariate spline techniques. Unlike traditional methods that rely on the mean-field assumption, SN-VI preserves intricate latent variable dependencies, providing a flexible and accurate approximation of posteriors with arbitrary shapes. We establish rigorous theoretical guarantees, including the derivation of the lower bound for the variational objective and proof of asymptotic consistency in posterior estimation. To facilitate practical implementation, we develop an algorithm that automatically identifies dependent latent variables and their underlying dependence structure, without requiring manual specification. Simulation studies validate the effectiveness of SN-VI in approximating posterior distributions with bounded support and complex dependencies. The proposed method has been successfully applied to high-dimensional structured data, including computer vision datasets and spatial transcriptomics. In these applications, SN-VI demonstrates improved generative model performance and effectively uncovers coupled biological signals through the learned dependency structure.

22.
arXiv (CS.CL) 2026-06-15

Hybrid Classical-Quantum Variational Autoencoder for Neural Topic Modeling

作者:

Neural topic models enable scalable semantic discovery, but their integration with quantum hardware remains largely unexplored. We present a proof-of-concept hybrid classical-quantum variational autoencoder (VAE) for topic modeling, embedding parameterized quantum circuits within the VAE inference network while retaining a classical topic-word decoder. To address the resource constraints of quantum hardware, we propose a modified Gaussian Softmax posterior that decouples latent space dimensionality from the number of topics to be extracted, enabling the model to operate with a low-resource 10-qubit quantum device. On the AgNews dataset, the hybrid VAE outperforms state-of-the-art neural topic models (NTMs), reaching a $C_v$ coherence score of 0.71 and an NPMI score of 0.20 while preserving high topic diversity. For comparison, we also construct a fully classical variant, which also outperforms state-of-the-art models on AgNews and exhibits clear class separation in the latent space. These results demonstrate that hybrid VAEs are computationally viable even on NISQ-era devices and represent a promising direction for quantum-enhanced topic modeling.

23.
bioRxiv (Bioinfo) 2026-06-11

Sequence-Based Therapeutic Peptide Classification with Augmented Negative Sampling

Therapeutic peptides offer high target specificity, low toxicity, and the ability to modulate protein-protein interactions, yet experimental functional characterization remains costly and slow. Computational prediction of therapeutic function directly from sequence could accelerate peptide screening and enable generative design pipelines, but requires reliable discrimination between therapeutic and non-therapeutic peptides. Existing multi-label predictors cover few functions, rely on limited datasets, and exhibit high glspl{fpr}, limiting their practical utility. We present a lightweight CNN classifier trained on the most comprehensive therapeutic peptide database to date (54,655 peptides, 48 functional categories). A key contribution is a statistically motivated negative sampling strategy using Markov models to generate diverse synthetic decoys at multiple difficulty levels. When evaluated on this controlled decoy benchmark, the FRP is reduced from over 60% for previous models to 2.1% for our approach. Our fine-tuned five-model ensemble achieves 78.9% Micro F1 and 54.6% Macro F1 while requiring only amino acid sequences as inputs. Analysis using a sparse L1-constrained variant of our model shows that convolutional filters capture conserved functional motifs and statistically improbable non-therapeutic patterns, with downstream layers combining these signals, providing mechanistic evidence that the network learns biologically meaningful structure. In a generalization task on the TPpred-LE benchmark, our model achieves 55.3% Micro F1 and 38.6% Macro F1, comparable to TPpred-LE trained on its native dataset (57.9%/38.1%) while predicting four times more therapeutic functions with four times fewer parameters. Code and models will be made available at https://github.com/terra-quantum-public/tq-therapep-ai.

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

A T-API-Compliant ReAct Agentic Loop for Optical Networks: Generic vs. Domain-Specific Tool Abstractions

arXiv:2606.18000v1 Announce Type: cross Abstract: Optical networks need intent-driven, closed-loop agentic management, a key enabler for higher autonomy levels. We present the first T-API-compliant reasoning and act (ReAct) loop. We show that domain-specific composite tools achieve 90% oracle-validated correctness with threefold token savings compared to generic tools.

25.
arXiv (CS.CL) 2026-06-12

Marginal Alignment Does Not Guarantee Joint-Distribution Fidelity: An Official-Reference Audit of Nemotron-Personas-Korea with Cross-Locale Replication

Synthetic persona datasets cite alignment with official demographics as a basis for trust, yet downstream users consume them as joint structures across age, sex, region, occupation, education, name, and institutional status. Marginal alignment does not imply that these joints are preserved. We propose the Independence-Assumption Footprint (IAF), an audit primitive that operates on the attribute combinations a dataset card itself documents as treated independently. For each such combination, IAF compares the synthetic joint against an external official or institutional reference, using direct joint tables where available and rule-implied checks otherwise. Applied to NVIDIA Nemotron-Personas-Korea (one million Korean synthetic personas), IAF finds that NPK aligns with KOSIS marginals while three joints fail. The major-by-occupation distribution against the KEIS graduate universe carries a large conditional mismatch. The age profile of military service is institutionally inconsistent. Female representation in male-dominated occupations is substantially over-flattened toward parity, with the strict screening verdict mapping-dependent and age-robust under direct standardisation. A transferability demonstration across six further NPK locales finds locale-dependent rather than universal diagnostics, with reference-taxonomy cardinality confounding cross-locale flag counts. For synthetic personas used as silicon samples, marginal claims must therefore be paired with disclosure-anchored joint audits before reuse. The released audit artefacts (reference manifests, occupational crosswalks, derived metrics, reproducibility scripts) instantiate this protocol on the NPK family and are released for retargeting at other synthetic persona resources.