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01.
arXiv (CS.LG) 2026-06-19

We Need to Rethink Benchmarking in Anomaly Detection

arXiv:2507.15584v2 Announce Type: replace Abstract: Despite the continuous proposal of new anomaly detection algorithms and extensive benchmarking efforts, progress seems to stagnate, with only minor performance differences between established baselines and new algorithms. In this position paper, we argue that this stagnation is due to limitations in how we evaluate anomaly detection algorithms. In current benchmarks, a trivial algorithm that only checks for extreme values in individual features performs competitively with state-of-the-art deep learning methods, despite failing on simple cases such as anomalies within an annulus of normal points. Moreover, existing benchmarks do not adequately reflect the diversity of anomaly detection applications, making it difficult for practitioners to reliably select algorithms for their applications. Consequently, we need to rethink benchmarking in anomaly detection. In our opinion, anomaly detection should be studied using scenarios that group applications sharing relevant characteristics, defined through a common taxonomy. Benchmarking within scenarios enables scenario-specific choices for preprocessing, metrics, and model selection, clarifying which advances transfer across similar applications and providing practitioners with reliable guidance for their specific contexts.

02.
bioRxiv (Bioinfo) 2026-06-13

ADMETron: An AI-driven SaaS platform for comprehensive ADMET prediction and compound prioritisation

ONTOSIGHT(R) ADMETron is an AI-driven platform designed for rapid prediction and visualization of Absorption, Distribution, Metabolism, Excretion, and Toxicity (ADMET) properties to support modern drug discovery. The platform integrates an interactive web interface with a scalable predictive engine, enabling high-throughput virtual screening and batch analysis of chemical compounds. Its core architecture combines recurrent neural network (RNN)-derived molecular embeddings from SMILES representations with physicochemical descriptors, which are subsequently modeled using gradient boosting machines (GBMs). This framework provides predictions across 34 ADMET endpoints, including physicochemical properties, absorption, CYP450 interactions, hERG liability, and mutagenicity. The predictive performance of ADMETron was evaluated using benchmark datasets from the Therapeutics Data Commons (TDC), demonstrating strong performance and generalizability across both classification and regression tasks. Beyond predictive modeling, the platform introduces an interactive radar graph-based structure-activity relationship (SAR) visualization framework that enables real-time comparison of multiple compounds and reference drugs across selected ADMET parameters. This feature facilitates intuitive interpretation of multidimensional molecular profiles and supports lead optimization and compound prioritization. Comparative assessment against widely used online ADMET tools further demonstrated broad endpoint coverage spanning pharmacokinetic, physicochemical, toxicity, and medicinal chemistry properties within a unified environment. Together, these capabilities establish ADMETron as a comprehensive platform for ADMET assessment and data-driven decision-making in drug discovery. (https://admetron.partex.ai/).

03.
arXiv (CS.CL) 2026-06-17

The Critical Role of Model Selection in Causal Inference: A Comparative Analysis of Classification Models within the InferBERT Framework for Pharmacovigilance

Distinguishing causal adverse drug events (ADEs) from spurious correlations remains a central challenge in pharmacovigilance. The InferBERT framework integrates transformer models with Do-calculus, but its success hinges on the underlying classification model. This study evaluates the impact of model choice in InferBERT, assessing whether simpler models suffice, if domain-specific pre-training helps, whether scaling to LLMs improves causal detection, and the effect of post-hoc calibration. We performed a comparative study on two benchmarks: Analgesics-induced Acute Liver Failure (AILF) and Tramadol-related Mortalities (TRAM). Four models were evaluated-XGBoost (baseline), ALBERT (original InferBERT), BioBERT (biomedical transformer), and Med-LLaMA (medical LLM)-using 5-fold cross-validation repeated over 20 runs. We measured accuracy, Expected Calibration Error (ECE) pre- and post-isotonic regression, and Jaccard concordance of causal terms with PRR, ROR, and EBGM; significance was tested with paired t-tests. BioBERT achieved the highest accuracy on both datasets, while Med-LLaMA underperformed despite its size and parameter-efficient fine-tuning. Domain-specific pre-training was decisive. Calibration improved ECE but had mixed effects on accuracy and causal discovery. BioBERT's superiority also yielded the strongest concordance with traditional pharmacovigilance signals. These results show that domain-specific pre-training provides a clear advantage over simpler baselines and larger LLMs. Investing in manageable, domain-aware models is more effective for computational pharmacovigilance than simply scaling model size.

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

Does the Question Really Matter? Training-Free Data Selection for Vision-Language SFT

arXiv:2603.09715v2 Announce Type: replace Abstract: Visual instruction tuning is crucial for improving vision-language large models (VLLMs). However, many samples can be solved via linguistic patterns or common-sense shortcuts, without genuine cross-modal reasoning, limiting the effectiveness of multimodal learning. Prior data selection methods often rely on costly proxy model training and focus on difficulty or diversity, failing to capture a sample's true contribution to vision-language joint reasoning. In this paper, we propose CVS, a training-free data selection method based on the insight that, for high-quality multimodal samples, introducing the question should substantially alter the model's assessment of answer validity given an image. CVS leverages a frozen VLLM as an evaluator and measures the discrepancy in answer validity with and without conditioning on the question, enabling the identification of samples that require vision-language joint reasoning while filtering semantic-conflict noise. Experiments on Vision-Flan and The Cauldron show that CVS achieves solid performance across datasets. On Vision-Flan, CVS outperforms full-data training by 3.5% and 4.8% using only 10% and 15% of the data, respectively, and remains robust on the highly heterogeneous Cauldron dataset. Moreover, CVS reduces computational cost by 17.3% and 44.4% compared to COINCIDE and XMAS.

05.
arXiv (CS.CV) 2026-06-12

An Improved Generative Adversarial Network for Micro-Resistivity Imaging Logging Restoration

An improved GAN-based imaging logging image restoration method is presented in this paper for solving the problem of partially missing micro-resistivity imaging logging images. The method uses FCN as the generative network infrastructure and adds a depth-separable convolutional residual block to learn and retain more effective pixel and semantic information; an Inception module is added to increase the multi-scale perceptual field of the network and reduce the number of parameters in the network; and a multi-scale feature extraction module and a spatial attention residual block are added to combine the channel attention. The multi-scale module adds a multi-scale feature extraction module and a spatial attention residual block, which combine the channel attention mechanism and the residual block to achieve multi-scale feature extraction. The global discriminative network and the local discriminative network are designed to gradually improve the content and semantic structure coherence between the restored parts and the whole image by playing off each other and the generative network. According to the experimental results, the average structural similarity measure of the five sets of imaged logging images with different sizes of missing regions in the test set is 0.903, which is an improvement of about 0.3 compared with other similar methods. It is shown that the method in this study can be used for the restoration of micro-resistivity imaging log images with good improvement in semantic structural coherence and texture details, thus providing a new deep learning method to ensure the smooth advancement of the subsequent interpretation of micro-resistivity imaging log images.

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

ANSR-DT: A Neuro-Symbolic Framework for Adaptive and Explainable Digital Twins

arXiv:2501.08561v4 Announce Type: replace Abstract: Digital twins are increasingly used to monitor and optimize industrial systems, yet many existing frameworks remain difficult to interpret, slow to adapt, and limited in their ability to incorporate explicit domain knowledge. This paper presents ANSR-DT, an adaptive neuro-symbolic framework that unifies temporal anomaly detection, symbolic reasoning, and reinforcement-learning-based decision support within a single digital twin pipeline. ANSR-DT combines a CNN-LSTM model for multivariate pattern recognition with Prolog-based reasoning that converts learned signals into explicit rules, enabling transparent diagnoses and traceable decision paths. A PPO-based adaptation layer further refines operational responses under changing conditions while preserving interpretability. Experiments against 8 baselines show that ANSR-DT delivers competitive predictive performance together with stable rule extraction, scalable symbolic reasoning, and actionable explanations. Additional validation on the Skoltech Anomaly Benchmark (SKAB) further indicates that the framework transfers beyond synthetic settings. These findings position ANSR-DT as a practical foundation for trustworthy, adaptive, and explainable industrial digital twins.

07.
arXiv (CS.LG) 2026-06-16

Multi-Fidelity SINDy: Sparse Discovery of Nonlinear Dynamical Systems with Fidelity-Weighted Measurements

arXiv:2606.15690v1 Announce Type: new Abstract: Data from simulations and experiments are rarely noise-free and often exhibit heterogeneous levels of fidelity. Measurement uncertainty may vary across repeated observations, sensing devices, or even within a single experiment. This work addresses the problem of discovering nonlinear dynamical systems from such inhomogeneous data. We extend the Sparse Identification of Nonlinear Dynamical Systems (SINDy) framework to account for variable noise levels by combining Ensemble SINDy and Weak SINDy within a weighted regression formulation derived from generalized least squares. A statistical justification for the weighting strategy is also provided. The methodology is validated on several benchmark systems, including ordinary and partial differential equations. In addition, we show the benefit of multi-fidelity integration for forecasting the dynamics of a double pendulum system. The results confirm that the proposed approach mitigates the adverse effects of heteroscedastic noise and that repeated, low-cost, low-quality measurements can improve model recovery, in some cases matching or outperforming reconstructions obtained using only high-fidelity data.

08.
arXiv (CS.LG) 2026-06-19

Indexed Bellman Information Complexity

Authors:

arXiv:2606.11171v2 Announce Type: replace Abstract: We develop indexed Bellman information complexity, a representation-level theory of interactive decision making centered on information indices and reference histories. The representation strips away problem-specific syntax and retains only the ingredients needed for dynamic programming and information accounting, thereby unifying the earlier framework of indexed algorithmic information ratios (AIR). On the upper-bound side, regret is controlled by Bellman supersolutions or potential identities whose gradient bracket is paid for by indexed information. Upper-confidence-bound (UCB), estimation-to-decision/decision-estimation-coefficient (E2D/DEC), and adaptive-minimax-sampling or exploration-by-optimization (AMS/EBO) methods appear as three relaxations of this same identity. On the lower-bound side, the posterior-reference trajectory supplies both the information telescope and the ghost quantile of small-regret trajectories. The resulting critical radius in the lower bound is an effective-dimension-scale quantity, as in Fano and local-prior-mass lower bounds, rather than the constant radius of a two-point Le Cam argument. The examples show that DEC is best viewed as a one-step relaxation of indexed Bellman information complexity, not as a universally tight conversion mechanism. We illustrate the framework through several applications, with particular emphasis on kernel bandits. In this setting, the active action marginal provides a concrete basis for comparing UCB, E2D, and AMS/EBO.

09.
bioRxiv (Bioinfo) 2026-06-11

OCOO-T : A SIMPLE AND SCALABLE VIRTUAL CELL MODEL FOR TRANSCRIPTIONAL PERTURBATION RESPONSE PREDICTION

Predicting single-cell transcriptional responses to genetic, chemical and cytokine perturbations is a fundamental challenge in computational biology and AI Virtual Cell (AIVC) modeling, with direct implications for drug discovery and the elucidation of gene regulatory networks. Existing approaches often rely on auxiliary cell-state encoders, hierarchical variational autoencoders, dedicated Transformer encoder-decoder modules, or gene-interaction priors to compress high-dimensional expression profiles into latent representations. While effective, these designs increase architectural complexity and may limit scalability and generalizability. This paper introduces OCOO-T, a minimalist flow-matching-based AIVC model for transcriptional perturbation response prediction. OCOO-T utilizes a vanilla Transformer stack that operates directly on continuous gene expression profiles and formulates perturbation response prediction as a continuous-time denoising process. Perturbation embeddings, dosage information, and cell-line/cell-type specificity are integrated through adaptive layer normalization and in-context tokens. Comprehensive evaluations on Tahoe100M, Replogle, and PBMC benchmarks demonstrate that OCOO-T achieves state-of-the-art performance across diverse perturbations and cell types while effectively scaling to long transcriptional profiles through patching and depatching of cellular contexts. By leveraging the simplicity of Transformer-based denoising for single-cell omics, OCOO-T provides an effective and scalable framework for in-silico cellular simulation.

10.
arXiv (quant-ph) 2026-06-17

Quantum Computing Algebra (QCA), the theory and implementation

arXiv:2606.17621v1 Announce Type: new Abstract: We present a real geometric algebra framework designed for the direct translation of the Dirac formalism into geometric algebra representations. Unlike previous approaches based on positive-definite signatures, QCA employs a split-signature construction that enables a natural realization of quantum states and operators while simplifying computational implementation. We further present an implementation of QCA using the GAALOP software and show how quantum gates and multi-qubit systems can be efficiently represented and generated computationally. As an application, we demonstrate the use of QCA in quantum game theory, where the real-algebraic formulation provides computational advantages for modeling entangled strategies and quantum interactions. The proposed framework establishes a practical bridge between the abstract formalism of quantum computation and efficient geometric algebra implementations.

11.
PLOS Medicine 2026-05-08

Climate change and non-communicable diseases: An invisible syndemic

by Gokul Parameswaran, Sadeer Al-Kindi, Sanjay Rajagopalan Climate change accelerates non-communicable diseases (NCDs) through cascading environmental disruptions and is attributed to driving increased NCD-related mortality. Yet this syndemic remains invisible and underfunded. We detail why addressing the climate-NCD intersection is critical for improving health. In this Perspective, Sanjay Rajagopalan and colleagues discusses how climate change accelerates non-communicable diseases (NCDs) and exacerbates NCD-related mortality, and calls for greater visibility and funding to address this syndemic and improve human health.

12.
arXiv (CS.CV) 2026-06-19

Exploring Multi-Modal Large Language Models and Two-Stage Fine-Tuning for Fashion Image Retrieval

Composed image retrieval retrieves a target image using a composed query of a reference image and a modified text description. In the fashion domain, this task requires understanding subtle attribute variations such as color, pattern, and texture. However, existing approaches face limitations due to scarce annotated data and simplistic negative sampling. We propose a novel framework that integrates a multi-modal large language model (LLaVA) to generate attribute-aware triplets and introduces a two-stage fine-tuning strategy to enhance contrastive learning. We leverage pretrained vision-language models, such as CLIP-ViT/B32, to generate and concatenate sentence-level prompts with the relative caption and to scale the number of negatives using static representations. Experimental results demonstrate enhanced compositional reasoning and improved fine-grained retrieval behavior, underscoring the feasibility and potential of the proposed framework for fashion retrieval.

13.
arXiv (CS.AI) 2026-06-18

Compute Efficiency and Serial Runtime Tradeoffs for Stochastic Momentum Methods

arXiv:2606.19179v1 Announce Type: cross Abstract: Stochastic momentum methods such as heavy ball (HB), Nesterov momentum, and variants of Accelerated SGD (ASGD) [Kidambi et al., 2018] are widely used in modern training, but their stochastic benefits depend on two distinct quantities: serial runtime, the number of iterations needed to reach a target accuracy, and compute efficiency (CE), the inverse total gradient-query or FLOP cost. Larger batches reduce serial runtime without hurting CE only when the contraction gap grows linearly with batch size. We study stochastic HB and ASGD for consistent linear regression with Gaussian covariates and prove finite-dimensional, discrete-time lower bounds on their batch-size tradeoffs. Our first result shows that HB does not improve the CE frontier over SGD for arbitrary spectra; rather, it preserves SGD-level CE over a larger batch-size window, allowing larger batches to reduce serial runtime until HB reaches its deterministic accelerated scale. This window can be a factor $\sqrt{\kappa}$ larger than the SGD critical batch size. For ASGD, the picture is more spectrum-dependent: for rapidly decaying power-law spectra, ASGD improves small-batch CE over HB/SGD, but as batch size grows it trades this CE advantage for improved serial runtime. Synthetic linear-regression experiments verify these qualitative regimes, including near-overlap of ASGD and HB for slowly decaying spectra and the predicted CE–serial tradeoff for rapidly decaying spectra.

14.
medRxiv (Medicine) 2026-06-22

Regional Service-System Conditions Associated with Facility-Linked Home-Based Specialist Care in Japan: A Claims-Based Ecological Study of Home Dialysis

Authors:

Background Complex chronic care is increasingly delivered in patients' homes while remaining linked to specialist facilities for training, monitoring, and backup care. Home dialysis provides a useful case because peritoneal dialysis (PD) and home hemodialysis (HHD) share a home-facility delivery structure but differ in technical and operational requirements. This study examined regional service-system conditions associated with the presence and scale of PD and HHD in Japan. Methods This ecological study used publicly available claims, administrative, census, and geospatial data harmonized to 334 Secondary Medical Areas. Regional indicators were organized into four domains: dialysis service delivery, implementation support for home-based care, hospital backup capacity, and living and sociodemographic context. Diffusion was examined using claims-based indicators of regional presence and post-presence scale, analyzed separately for PD and HHD with Firth penalized logistic regression and zero-truncated negative binomial regression, respectively. Results PD was observed in 271 regions and HHD in 109. Patterns of associated regional conditions differed by modality and stage. PD was associated mainly with existing dialysis-service organization, whereas HHD was associated with broader regional supports, including home-care delivery, living infrastructure, transition support, and hospital-system indicators. Conditions associated with presence differed from those associated with scale. Cross-modality associations suggested that shared regional factors may shape the distribution of both modalities. Conclusions Regional conditions for home dialysis diffusion in Japan differed by modality and stage. PD was linked mainly to existing dialysis-service organization, whereas HHD was linked to multi-domain regional support for technically demanding home treatment. Under standardized reimbursement, local service-system capacity may remain important for modality- and stage-specific diffusion of home dialysis.

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

Beyond the Current Observation: Evaluating Multimodal Large Language Models in Controllable Non-Markov Games

Deploying multimodal foundation models as closed-loop policies increasingly requires conditioning actions on observations that are no longer visible. However, existing benchmarks either expose the full state, conflate hidden-state reconstruction with other agent skills, or test recall only after an episode has ended. We introduce RNG-Bench (Reconstructive Non-Markov Games), a benchmark suite designed to isolate a base model's ability to reconstruct past observations and act on them during multi-step interaction. RNG-Bench includes two complementary games: Matching Pairs, where card identities briefly revealed at specific locations must later be recalled, and 3D Maze, where egocentric views must be integrated into a spatial map. Both games are evaluated under a unified harness with three controlled difficulty axes: grid size, visual pattern, and observation modality. The benchmark further introduces a head-to-head duel protocol to control for instance-level variance and a Memory Gap metric that disentangles forgetting from poor action selection. The hardest configurations require contexts of roughly 128K tokens and 350 image inputs per episode, and remain far from saturated by frontier MLLMs. Memory Gap analysis shows that most residual errors stem from forgetting earlier observations rather than from suboptimal decision making. Finally, fine-tuning Qwen3.5-9B on optimal-policy rollouts and filtered model demonstrations improves performance on RNG-Bench and transfers to existing benchmarks without degrading general multimodal capability.

16.
arXiv (math.PR) 2026-06-11

The Geometry of Admissible Short Selling in Discrete-Time Stochastic Portfolio Theory

arXiv:2606.11191v1 Announce Type: cross Abstract: While discrete-time Stochastic Portfolio Theory (SPT) provides a robust framework for market analysis, existing work on functional generation has predominantly focused on long-only portfolios defined on the entire unit simplex. This paper extends the geometric framework of functional generation to the broader class of bankruptcy-proof long-short portfolios defined on local market state spaces. We establish that, within this admissible setting, pseudo-arbitrage is fully characterized by the concavity of the generating function on the market state space, thereby relaxing the usual global domain requirement. A central contribution of this work is a geometric characterization of the short-selling mechanism. We prove that the presence of short selling is equivalent to the negativity of the maximal concave extension of the generating potential. This phenomenon is linked to the steepness of the logarithmic gradient as the market approaches a zero boundary nested inside the simplex. To systematically exploit this mechanism, we introduce the barycentric scaling transformation, a constructive methodology that maps classical long-only generating functions onto restricted domains to engineer admissible strategies with controlled short-selling exposure. Finally, through the analysis of specific shrunken portfolios, we identify a geometric phase transition: under suitable boundary conditions, admissible strategies exhibit a long-only core and a short-selling region in a qualitative sense (without asserting an exact partition of the state space). This provides a unified geometric perspective on relative arbitrage beyond the long-only constraint.

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

The Faithfulness Gap: Certifying Semantic Equivalence Between Natural-Language and Formal Mathematical Statements

arXiv:2606.16541v1 Announce Type: new Abstract: Autoformalization, translating natural-language mathematics into formal proof assistants, is bottlenecked not by translation fluency but by faithfulness: a formal statement can typecheck and be provable, yet still encode a different theorem than the source intended. We introduce Bidirectional Provability Fingerprinting (\bpf{}), a framework that certifies faithfulness by characterizing each candidate through its forward and backward consequence neighborhoods in the ambient theory and matching these against probes derived from the natural-language statement. We further introduce four novel components: (i) Counterfactual Probe Generation (\cpg{}), a contrastive procedure that synthesizes probes targeting specific drift directions; (ii) the Equivalence Spectrum, a continuous faithfulness score that replaces brittle binary verdicts; (iii) Adaptive Probe Budget Allocation (\apba{}), an information-theoretic budget router; and (iv) Faithfulness-Guided Decoding (\fgd{}), which uses \bpf{} signals as a reward during autoformalization. We prove a drift detection theorem and a PAC-faithfulness result establishing that the equivalence class of a natural language statement is learnable from $\mathcal{O}(\log(1/\delta)/\varepsilon)$ probes under mild assumptions. We release \driftbench{}, a benchmark of $2{,}183$ NL/Lean~4 pairs with controlled drift labels across six subfields of mathlib4. \bpf{}\,+\,\cpg{} detects $89.6\%$ of drifted formalizations at a $3.0\%$ false-positive rate-against $41.2\%$ for typecheck and $63.3\%$ for LLM-judge baselines, and \fgd{} reduces the rate at which a state-of-the-art autoformalizer emits drifted statements by $47\%$. https://pmlrbd.github.io/BPF/

18.
arXiv (CS.CV) 2026-06-19

GenTrack: A New Generation of Multi-Object Tracking

This paper introduces a novel multi-object tracking (MOT) method, dubbed GenTrack, whose main contributions include: first-a hybrid tracking approach employing both stochastic and deterministic manners to robustly handle unknown and time-varying numbers of targets, particularly in maintaining target identity (ID) consistency and managing nonlinear dynamics, second-leveraging particle swarm optimization (PSO) with some proposed fitness measures to guide stochastic particles toward their target distribution modes, enabling effective tracking even with weak and noisy object detectors, third-integration of social interactions among targets to enhance PSO-guided particles as well as improve continuous updates of both strong (matched) and weak (unmatched) tracks, thereby reducing ID switches and track loss, especially during occlusions, fourth-a GenTrack-based redefined visual MOT baseline incorporating a comprehensive state and observation model based on space consistency, appearance, detection confidence, track penalties, and social scores for systematic and efficient target updates, and five-the first ever publicly available source-code reference implementation with minimal dependencies, featuring three variants, including GenTrack Simple, Strengthen, and Super, facilitating flexible reimplementation. Experimental results have shown that GenTrack provides superior performance on standard benchmarks and real-world scenarios compared to state-of-the-art trackers, with integrated implementations of baselines for fair comparison. Potential directions for future work are also discussed. The source-code reference implementations of both the proposed method and compared-trackers are provided on GitHub: https://github.com/SDU-VelKoTek/GenTrack

19.
arXiv (CS.AI) 2026-06-11

Human-Enhanced Loop Modeling (HELM): Agent-Based Finite Element Modeling of Concrete Bridge Barriers

arXiv:2606.12025v1 Announce Type: new Abstract: Finite element (FE) modeling of safety-critical infrastructure such as bridge barriers requires high-fidelity nonlinear dynamic analysis, yet the current FE modeling process remains labor-intensive and lacks automation. This paper presents the Human-Enhanced Loop Modeling (HELM) framework, a collaborative human-agent protocol that decomposes long-sequence finite element modeling into discrete, visually verifiable checkpoints across geometry generation, boundary condition definition, and material assignment. The framework is demonstrated through a 20-case matrix of reinforced concrete bridge barriers under MASH TL-4 and TL-5 lateral loading conditions, interfacing specialized agents with two widely used commercial FE softwares, i.e., ANSYS and LS-PrePost. Experimental results show that HELM improves the baseline autonomous modeling success rate from 20% to 75%, with agent-level pass rates for geometry and boundary condition tasks approximately doubling. Error analysis reveals that spatial reasoning and algebraic logic limitations constitute the primary failure modes, underscoring the value of structured human-in-the-loop intervention for modeling automation. The complete agent design code and prompts are open-sourced and can be accessed at: https://github.com/SimAgentDev/Ansys-LSPP-AgentKit.

20.
bioRxiv (Bioinfo) 2026-06-11

OMIO: A policy-driven Python library for reproducible microscopy image I/O

Modern fluorescence and multiphoton microscopy workflows operate within a heterogeneous ecosystem of file formats, partially overlapping metadata standards, and reader-specific conventions. In practice, this frequently leads to silent axis misinterpretations, loss or corruption of physical voxel size information, and laboratory-specific glue code that is fragile, poorly documented, and difficult to reproduce. OMIO, short for Open Microscopy Image I/O, addresses these issues by providing a lightweight, policy-driven image I/O layer for Python that enforces a canonical, OME-compatible data representation at the API boundary. The central contribution of OMIO is the explicit separation of low-level format access from semantic normalization. Existing reader libraries are used as interchangeable backends for extracting pixel data and available metadata, while OMIO enforces axis conventions, metadata interpretation, and fallback decisions in a centralized and auditable policy layer. This design allows heterogeneous microscopy inputs to be converted into a stable representation without propagating backend-specific assumptions into downstream analysis code. The core design principles of OMIO include canonical axis semantics (TZCYX), robust metadata normalization with explicit and auditable fallbacks, memory-aware operation via optional Zarr-based backends, and workflow-level semantics that extend beyond individual files to folder stacks and BIDS-like project structures. This architecture allows OMIO to orchestrate existing reader libraries into a coherent and reproducible I/O pipeline without replacing or duplicating their functionality. OMIO is implemented as an open-source and community-oriented system in which support for additional file formats and metadata conventions can be added incrementally through modular reader backends. By encouraging the contribution of example datasets, backend extensions, and feature requests, OMIO is designed to evolve alongside emerging acquisition systems while preserving strict semantic guarantees at the interface level. The resulting standardized OME-TIFF outputs are immediately suitable for downstream quantitative analysis and interactive inspection in scientific Python workflows, including workflows based on ImageJ and Napari.

21.
arXiv (CS.CL) 2026-06-19

MiqraBERT: Regression-Based Sentence-BERT Finetuning for Biblical Hebrew Parallel Detection

Textual reuse pervades the Hebrew Bible, yet the computational methods used to detect it still rest largely on lexical overlap, and they falter once a parallel involves paraphrase, lexical substitution, or syntactic reworking. This paper introduces MiqraBERT, a Sentence-BERT model finetuned from AlephBERT (a Modern Hebrew encoder) for verse-level semantic similarity in Biblical Hebrew. The training set comprises 1,650 labeled verse and half-verse pairs: 825 true parallels drawn from the Chronicles synoptic material and from foundational studies of poetic parallelism, balanced against 825 randomly sampled negatives. Through cosine-similarity regression, the model learns an embedding space in which parallel verses cluster together and unrelated verses move apart. We evaluate separation with distribution-based metrics, Wasserstein distance and the overlap coefficient, across ten random seeds. MiqraBERT improves distributional separation 2.7-fold over the pre-trained baseline and reduces the ambiguous overlap region from roughly 24% to about 6%. Narrative synoptic parallels reach a recall@10 of 87.1%; poetic parallels remain difficult, below 9%. This genre-dependent asymmetry confines the model's reliable scope to narrative textual reuse. MiqraBERT is publicly available at https://huggingface.co/davidmsmiley/MiqraBERT

22.
Nature (Science) 2026-06-17

Optical fibre gripper for high-performance 3D micromanipulation

Authors:

Optical tweezers offer precise, non-contact control, but operate in a limited force regime and impose strict requirements on the characteristics of the targets as well as the environmental conditions1–4. Millimetre-scale mechanical tweezers can offer higher gripping force but are not suitable for precise manipulations5–11. Integrating microgrippers directly at the optical fibres provides a new approach for precise micromanipulation. However, existing fibre-integrated tweezers still face challenges in achieving high-performance manipulation of micro-objects (for example, single cells) within narrow spaces, mainly due to simplified architectures, constrained designs and millimetre-scale footprints12–14. Here we report a three-dimensional (3D) optical fibre gripper (OFG), which is fabricated by two-step, two-photon polymerization. The OFG consists of rigid photoresist microclaws and soft thermoresponsive hydrogel muscle doped with silver nanoparticles, and its size is only 38 × 38 × 61 μm3. The OFG exhibits a force-to-mass ratio of about 340 μN mg−1, outperforming previously reported fibre-integrated tweezers by one to two orders of magnitude. The OFG can manipulate opaque particles, irregular micromechanical components and diverse single-cell types. We further demonstrated its potential in 3D microassembly of complex microdevices (bearings, shafts and gearboxes) and biomimetic sampling in the narrow environment (<300 μm). These results position the OFG as a compact fibre-tip manipulator for 3D micromanipulation, offering reversible and tunable gripping in an intermediate force regime between optical field trapping and millimetre-scale mechanical tweezers. A miniature three-dimensional optical fibre gripper enables powerful, precise micromanipulation of particles and single cells in confined spaces, bridging the gap between optical and mechanical tweezers.

23.
arXiv (math.PR) 2026-06-12

Storage and Transport Capacity Design for a Self-Reliable Two-Node Stochastic Resource System

arXiv:2606.12707v1 Announce Type: cross Abstract: We study a two-node stochastic resource system operating over a finite horizon. Each node experiences uncertain supply and demand and is equipped with finite storage. The objective is to ensure that resource levels remain within prescribed limits with high probability. To this end, we formulate a chance-constrained capacity-design problem in which resources can be exchanged through a capacity-limited transport link. We characterize the minimum storage required at each node, derive the optimal transport policy, and quantify the trade-off between storage and transport capacities. Our results show the existence of a critical transport-capacity threshold that enables full risk pooling between the nodes. Moreover, this threshold decreases with the operating horizon, implying that full-pooling performance can be achieved with progressively smaller transport capacity over longer horizons.

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

EChO-Agent: Evidence Chain Orchestration Agent for Audio Reasoning

arXiv:2606.15141v1 Announce Type: cross Abstract: While LALMs show promise on audio question answering, they fail to focus on question-relevant segments of audio and provide a clear, checkable reasoning process when dealing with complex audio reasoning. Reinforcement learning and tool-augmented prompting can help models better relate questions to audio but lack a reliable way to understand, integrate, and self-verify audio segments. To address this gap, we present EChO-Agent, a modular agent framework that reformulates complex audio QA as a planning, tool execution, evidence integration, and answer verification workflow. Experiments on MMAR benchmark show EChO-Agent improves both accuracy and rubric scores over baseline and ablation studies show evidence integration is the key factor.

25.
arXiv (CS.LG) 2026-06-18

RouteJudge: An Open Platform for Reproducible and Preference-Aware LLM Routing

arXiv:2606.18774v1 Announce Type: new Abstract: We present RouteJudge, an online pairwise preference evaluation framework for LLM routing systems, with a public platform available at https://routejudge.cn. Different from model-level response evaluation, RouteJudge focuses on router-level decision quality. For each user query, multiple routing strategies independently recommend candidate models under the same model pool and budget constraints. The selected model responses are then presented to users through anonymous pairwise comparisons, and the resulting user preferences are attributed back to the routing strategies behind the compared responses. Each evaluation record stores the query, routing decisions, model responses, preference labels, cost, latency, and task metadata, enabling preference-aware, cost-aware, and task-conditioned analysis of LLM routers. To support the continuous expansion of routing methods in RouteJudge, we further release ORBIT (Optimal Routing and Budgeted Inference Toolbox), a modular and extensible toolbox that standardizes the end-to-end workflow of LLM routing. ORBIT provides unified interfaces for benchmark loading, query representation, router implementation, budget-aware evaluation, and method comparison, allowing researchers to develop and evaluate routing algorithms under consistent protocols. It also serves as the submission and integration layer for RouteJudge: researchers can implement routing methods within ORBIT, validate them on existing routing benchmarks, and submit compatible routers for online preference-based evaluation. The code of ORBIT is available at https://github.com/AIGNLAI/LAMDA-ORBIT.