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01.
arXiv (CS.AI) 2026-06-24

LemonHarness Technical Report

arXiv:2606.24311v1 Announce Type: new Abstract: As large language model (LLM) agents are applied to longer tasks, they increasingly modify workspace state across multiple rounds of iteration. However, agents typically observe only tool outputs and log fragments, while the actual state changes occur in the file system. Without explicit workspace boundaries, state-changing operations such as file writes and temporary artifact generation may scatter changes across paths. Over time, these weakly constrained changes accumulate, making states such as modified files difficult to track. This paper presents LemonHarness, an integrated execution framework for long-horizon agents. LemonHarness establishes an explicit execution boundary by constraining state-changing operations within a clearly defined workspace and bringing model invocation, tool execution, and rule knowledge within a single controlled boundary. State-changing operations, including file writes, dependency installation, and temporary artifact creation, are executed through structured tool interfaces, with execution feedback recorded as observations available to subsequent model decisions. The system also introduces a reusable rule knowledge base, which turns recurring execution rules and acceptance criteria into runtime knowledge. LemonHarness further adds a time-aware execution mechanism that exposes elapsed and remaining budget to the model, so it can rebalance exploration, implementation, and validation effort as time pressure shifts and avoid timeouts from long waits or excessive verification. On Terminal-Bench 2.0, LemonHarness_GPT-5.3-CodeX reached 84.49% accuracy over 445 trials; pairing the same framework with the stronger GPT-5.5 backbone raised the average accuracy to 86.52% across five jobs. The results suggest that a unified runtime boundary, callable rule knowledge, and time-aware execution can improve the stability of long-horizon agent execution.

02.
Science (Express) 2026-06-11

Laser phase plate improves structure determination of small proteins by cryo-EM | Science

作者: 未知作者

Phase plates can in principle overcome the poor image contrast in electron cryo–microscopy (cryo-EM) and the resulting limits on the structural reconstruction of small proteins. However, previous designs have been unstable and compromised the high-resolution signal. They have thus been unable to surpass results achieved by standard cryo-EM. Here, we show that the laser phase plate (LPP), installed in a custom, modern Titan Krios microscope, enhances the resolution in single-particle reconstruction of small proteins by improving specimen-motion correction, recovery of information from the early frames, as well as particle visualization, 3D classification, and alignment. These advances use standard defocus ranges and reconstruction procedures, but open the door to LPP-tailored protocols offering further improvements by leveraging the LPP demonstrated here.

03.
arXiv (math.PR) 2026-06-19

An alternative approach to well-posedness of McKean-Vlasov equations arising in Consensus-Based Optimization

arXiv:2512.19446v4 Announce Type: replace-cross Abstract: In this work we study the mean-field description of Consensus-Based Optimization (CBO), a derivative-free particle optimization method. Such a description is provided by a non-local SDE of McKean-Vlasov type, whose fields lack of global Lipschitz continuity. We propose a novel approach to prove the well-posedness of the mean-field CBO equation based on a truncation argument. The latter is performed through the introduction of a cut-off function, defined on the space of probability measures, acting on the fields. This procedure allows us to study the well-posedness problem in the classical framework of Sznitman. Through this argument, we recover the established result on the existence of strong solutions, and we extend the class of solutions for which pathwise uniqueness holds.

04.
PLOS Computational Biology 2026-06-22

Beyond the canonical: The role of post-transcriptional regulation in drug-target interaction prediction

by Md Istiaq Ansari, Khandakar Tanvir Ahmed, Debby D. Wang, Kirill Medvedev, Wei Zhang Protein isoforms produced from the same gene through post-transcriptional regulatory mechanisms, such as alternative splicing, can substantially alter protein structure and function, including drug-binding properties. However, most existing drug-target interaction (DTI) and drug-target affinity (DTA) prediction models rely exclusively on a single representative protein sequence per gene, typically the canonical or longest isoform, thereby overlooking the functional diversity introduced by alternative isoforms. This assumption can introduce bias, limit generalizability, and compromise the biological validity of model predictions. In this study, we systematically investigate the impact of protein isoform variation on DTI prediction accuracy. Our results show that substituting the canonical sequence with an alternative isoform often leads to substantial declines in predictive performance. Structural and binding affinity analyses further reveal that these discrepancies are frequently associated with changes in predicted binding-site configurations, which we further examine through controlled perturbations of binding-site residues. These experiments suggest that even subtle alterations in binding regions can lead to inconsistent DTI predictions. Overall, our findings uncover a critical limitation in current DTI modeling frameworks and underscore the importance of incorporating isoform-specific information to better reflect biological reality and improve therapeutic relevance. The codes and datasets are available at https://github.com/compbiolabucf/DTIVariant.

05.
PLOS Computational Biology 2026-06-01

On real-time calibrated prediction for complex model-based decision support in pandemics: Part 2

by Trevelyan J. McKinley, Daniel B. Williamson, Xiaoyu Xiong, James M. Salter, Robert Challen, Leon Danon, Ben Youngman, Doug McNeall Calibration of complex stochastic infectious disease models is challenging. These often have high-dimensional input and output spaces, with the models exhibiting complex, non-linear dynamics. Coupled with a paucity of necessary data, this results in a large number of non-ignorable hidden states that must be handled by the inference routine. Likelihood-based approaches to this missing data problem are very flexible, but challenging to scale, due to having to monitor and update these hidden states. Methods based on simulating the hidden states directly from the model-of-interest have an advantage that they are often more straightforward to code, and thus are easier to implement and adapt in real-time. However, these often require evaluating very large numbers of simulations, rendering them infeasible for many large-scale problems. We present a framework for using emulation-based methods to calibrate a large-scale, stochastic, age-structured, spatial meta-population model of COVID-19 transmission in England and Wales. By embedding a model discrepancy process into the simulation model, and combining this with particle filtering, we show that it is possible to calibrate complex models to high-dimensional data by emulating the log-likelihood surface instead of individual data points. The use of embedded model discrepancy also helps to alleviate other key challenges, such as the introduction of infection across space and time. We conclude with a discussion of major challenges remaining and key areas for future work.

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

Neither Parallel Nor Sequential: How DiffusionGemma Actually Commits Tokens

arXiv:2606.14620v1 Announce Type: new Abstract: Open diffusion language models are marketed as parallel, non-autoregressive decoders, yet the order in which a shipped checkpoint actually commits its tokens is almost never measured. We instrument DiffusionGemma 26B, a masked discrete-diffusion mixture-of-experts model built on Gemma 4, hooking its sampler's accept step to record which canvas positions commit, when, and at what confidence. Across a 686-prompt, six-regime probe suite we find that its decoding is neither parallel nor block-autoregressive: it follows a partial left-to-right commit bias whose apparent strength depends almost entirely on the granularity at which you look. Order is weak token by token and strengthens smoothly as the analysis is coarsened, so the model's "block size" turns out to be an artifact of the measuring ruler rather than the architecture. The model commits in large simultaneous batches, leaving much of the within-batch order genuinely undefined rather than merely unobserved. The behaviour is regime-dependent: structured JSON is committed in essentially arbitrary order, and a position's commit confidence tracks correctness on mathematical reasoning but carries no signal on factual recall. Commitment is aggressive, finishing in a short late burst well inside the step budget, while task accuracy matches the model's autoregressive Gemma-4 sibling. Beyond these findings, our central contribution is methodological: measuring decoding order honestly demands handling trailing-EOS padding, within-regime confounding, commit non-monotonicity, block-size sensitivity, and large commit-batch ties, each of which can otherwise manufacture a decoding-order result that is not really there.

07.
arXiv (math.PR) 2026-06-11

Convergence of a Critical Multitype Bellman–Harris Process with One Infinite-Mean Lifetime

arXiv:2606.11511v1 Announce Type: new Abstract: We study a critical multitype Bellman–Harris branching particle system in $\mathbb R^N$ with a finite type space $\mathbb K=\{1,\dots,K\}$. Particles of type $i$ move according to a symmetric $\alpha_i$-stable process and reproduce according to a critical offspring law whose mean matrix is irreducible and stochastic. The lifetime distribution of type $1$ is assumed to have infinite mean with regularly varying tail $$ 1-F_1(t)\sim c_1t^{-\gamma},\, 0 \frac{\gamma}{\beta}, $$ and a local increment condition on the heavy lifetime distribution, we prove convergence of the system to a Poisson random measure concentrated on the infinite-mean type.

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

Dynamically Optimal Unraveling Schemes for Simulating Lindblad Equations

arXiv:2509.19887v2 Announce Type: replace Abstract: Stochastic unraveling schemes are powerful computational tools for simulating Lindblad equations, offering significant reductions in memory requirements. However, this advantage is accompanied by increased stochastic uncertainty, and the question of optimal unraveling remains open. In this work, we investigate unraveling schemes driven by Brownian motion or Poisson processes and present a comprehensive parametric characterization of these approaches. For the case of a single Lindblad operator and one noise term, this parametric family provides a complete description for unraveling scheme with pathwise norm-preservation. We further analytically derive dynamically optimal quantum state diffusion (DO-QSD) and dynamically optimal quantum jump process (DO-QJP) that minimize the growth rate of the variance of an observable locally in time. Compared to jump process ansatz, DO-QSD offers two notable advantages: firstly, the variance for DO-QSD can be rigorously shown not to exceed that of any jump-process ansatz locally in time; secondly, it has very simple expressions. Numerical results demonstrate that the proposed DO-QSD scheme may achieve substantial reductions in the variance of observables and the resulting simulation error.

09.
arXiv (CS.CV) 2026-06-11

DIRECT: When and Where Should You Allocate Test-Time Compute in Embodied Planners?

Vision-Language Models (VLMs) are increasingly deployed as high-level planners for embodied agents, with an emerging strategy of scaling test-time compute to improve capability. However, we observe that doing so increases latency, token usage, and FLOPs while yielding uneven, often diminishing gains in downstream success, limiting where embodied agents can be deployed. We argue that choosing when and where to spend test-time compute is central to bringing frontier performance to the real world. We introduce DIRECT, a routing framework that uses multimodal scene context to allocate compute per prompt, improving the success–cost Pareto frontier over fixed model selection. Across three dominant scaling axes, namely chain-of-thought depth, model size, and memory history, our experiments on VLABench and RoboMME show that test-time compute is not a uniform lever: different axes yield qualitatively distinct capability gains. We validate these insights on a physical Franka arm in a DROID setup spanning zero-shot manipulation and long-horizon chaining, where our router matches or exceeds a stronger model's success rate at up to 65% lower average latency. Ultimately, our results show that naively scaling test-time compute is wasteful, and that DIRECT can provide frontier-level embodied planning in robotic systems at a fraction of the cost. Project page can be found at jadee-dao.github.io/direct/.

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

Gen-VCoT: Generative Visual Chain-of-Thought Reasoning via Diffusion-Based RGB Intermediate Representations

Multimodal large language models (MLLMs) excel at visual reasoning but rely on text-based chain-of-thought (CoT), lacking interpretable visual intermediates. Existing methods use opaque tokens or external tools, missing key properties. We propose Gen-VCoT, a framework using expert vision models to generate RGB images as reasoning intermediates. It has three stages: visual grounding (SAM segmentation), geometric reasoning (Marigold depth maps), and semantic reasoning (Qwen2-VL integration). An adaptive router selects reasoning depth. Evaluations show Gen-VCoT improves spatial (25% better) and depth (50% better) questions, but may hurt simple factual queries. Text CoT outperforms visual intermediates on CLEVR (91.2% vs 62.5%), showing task-dependent optimal representations. Gen-VCoT establishes a new paradigm for interpretable multimodal reasoning.

11.
PLOS Computational Biology 2026-06-23

A novel biclustering algorithm for mining m<sup>6</sup>A co-methylation patterns based on beta-binomial distribution and data screening strategy

作者:

by Zhaoyang Liu, Yuteng Xiao, Dao Xiang, Hao Shi, Kaijian Xia Studies have shown that m6A plays a key role in different life processes such as RNA metabolism, physiology and pathology. However, due to the complexity of life processes, its specific regulatory details are still not revealed. The computational approach based on co-methylation pattern mining of m6A sequencing data can assist in revealing its mechanism and save time and economic cost, however, the current algorithms suffer from the problems of insufficient robustness to low signal-to-noise data and unreliable performance. Based on this, this paper proposes an enhanced beta-binomial distribution biclustering algorithm (EBBM) based on data screening strategy. This algorithm is based on the framework of Bayesian, adopts Gibbs sampling method for parameter inference, and introduces the data screening strategy in the process of parameter inference, which effectively removes the problem that the low signal-to-noise data in the original sequencing data of m6A affects the reliability of the clustering results. The simulation experiment results show that this algorithm can effectively deal with the interference of low signal-to-noise data and accurately mine the co-methylation patterns pre-planted in the data, which is significantly better than the current mainstream biclustering algorithm. In real human m6A sequencing data with 32 samples, this algorithm mined two effective co-methylation patterns, which were enriched to different biological processes, such as negative regulation of phosphorylation and peptidyl lysine methylation, etc. The scoring results of GEO_Score indicate that the results of this algorithm are more biologically meaningful than the clustering results of current mainstream m6A co-methylation pattern mining algorithms.

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

Theorem-Grounded Execution Ontologies for Interpretable Machine Reasoning

arXiv:2606.16010v1 Announce Type: cross Abstract: Large language models have achieved impressive performance on reasoning tasks spanning mathematics, science, programming, and commonsense inference. Despite these advances, their reasoning processes remain largely latent, making them difficult to interpret, verify, replay, debug, and transfer across domains. Existing approaches such as chain-of-thought, tree-of-thoughts, graph-of-thoughts, and tool-augmented reasoning expose intermediate reasoning artifacts but typically lack explicit execution semantics, formal state representations, and verifiable reasoning structures. We introduce Theorem-Grounded Execution Ontologies (TGEO), a framework that models reasoning as an executable state-transition process rather than a sequence of generated tokens. Given an input problem, TGEO identifies relevant theorem families, binds the problem to a domain ontology, discovers semantic objects, instantiates states and operators, constructs predicates and contracts, and synthesizes an executable reasoning graph. The resulting graph provides an interpretable, replayable, and auditable representation of reasoning in which every state transition, operator application, and validation step is explicitly represented. TGEO integrates five architectural components: (1) theorem-grounded reasoning priors, (2) executable ontologies, (3) operator-mediated state transitions, (4) predicate and contract-based execution validation, and (5) architectural auditing and failure localization. We evaluate TGEO on theorem-intensive reasoning tasks derived from mathematical benchmark domains and a curated Golden Execution Suite. Our findings demonstrate the value of executable reasoning representations for interpretable, verifiable, and reproducible AI reasoning systems.

13.
arXiv (CS.CV) 2026-06-16

Shift-and-Sum Quantization for Visual Autoregressive Models

Post-training quantization (PTQ) enables efficient deployment of deep networks using a small set of data. Its application to visual autoregressive models (VAR), however, remains relatively unexplored. We identify two key challenges for applying PTQ to VAR: (i) large reconstruction errors in attention-value products, especially at coarse scales where high attention scores occur more frequently; and (ii) a discrepancy between the sampling frequencies of codebook entries and their predicted probabilities due to limited calibration data. To address these challenges, we propose a PTQ framework tailored for VAR. First, we introduce a shift-and-sum quantization method that reduces reconstruction errors by aggregating quantized results from symmetrically shifted duplicates of value tokens. Second, we present a resampling strategy for calibration data that aligns sampling frequencies of codebook entries with their predicted probabilities. Experiments on class-conditional image generation, inpainting, outpainting, and class-conditional editing show consistent improvements across VAR architectures, establishing a new state of the art in PTQ for VAR.

14.
arXiv (CS.CV) 2026-06-12

MoVerse: Real-Time Video World Modeling with Panoramic Gaussian Scaffold

We present MoVerse, a real-time video world model that creates an interactively navigable scene from a single narrow-field-of-view image. This setting is challenging because the input observes only a small fraction of the environment, while interactive roaming requires a complete surrounding world, persistent geometry, controllable camera motion, and temporally coherent high-fidelity observations. MoVerse addresses this problem by separating world construction from observation rendering. It first expands the input into a gravity-aligned 360$^\circ$ panorama with topology-aware diffusion, closing the missing field of view before 3D reasoning. It then lifts the panorama into a persistent 3D Gaussian scaffold using panoramic geometry-aware residual prediction, yielding a dense and directly renderable spatial memory. Finally, a Gaussian-conditioned video renderer translates scaffold renderings along user-specified camera trajectories into photorealistic video. To make this renderer practical for interaction, we train a bidirectional diffusion teacher for high-quality conditional rendering and distill it into a causal autoregressive student for bounded-latency streaming. This design combines the controllability and long-range consistency of explicit 3D representations with the perceptual quality of generative video models. MoVerse supports real-time scene roaming at 8~FPS on a single NVIDIA RTX~4090 GPU, demonstrating a practical path toward single-image world creation with interactive video output.

15.
Nature (Science) 2026-06-10

Improved quantum processor logical error rates via correction and detection

作者:

Performing quantum algorithms for critical problems in physics and chemistry requires substantially lower error rates than the physical error rates of present quantum computers. Achieving such low logical error rates requires quantum error correction1,2 and physical error rates below a critical threshold value3–8. We experimentally demonstrate on a trapped-ion quantum charge-coupled device (QCCD)9,10 improvements in logical error rates ranging from 11× to 800× compared with several physical circuit baselines, including quantum computation on multiple qubits. Our results hinge on two quantum error correction code constructions optimized for an ion-trap processor: a 12-qubit code encoding two qubits inspired by Knill11 and a 16-qubit tesseract colour code encoding four qubits12,13. These constructions are combined with a scalable method of error detection and post-selection to achieve reduced logical error rates. Our results show that state-of-the-art quantum devices are already able to make use of fault tolerance and error correction to strongly suppress errors in non-trivial quantum circuit computations. Experimental demonstration of quantum error-correcting codes combined with error detection and post-selection applied to a trapped-ion quantum processor shows improvements in logical error rates ranging from 11× to 800× compared with several physical circuit baselines.

16.
arXiv (CS.AI) 2026-06-19

Interpretable Sperm Morphology Classification via Attention-Guided Deep Learning

arXiv:2606.20438v1 Announce Type: new Abstract: Male infertility is a major cause of couple infertility, often linked to abnormal sperm morphology. While deep learning models offer automated analysis, most lack interpretability, limiting their clinical adoption. This study proposes an attention-guided deep learning framework for sperm morphology classification. We combine a pretrained EfficientNet-B0 with a Convolutional Block Attention Module (CBAM) to focus on key areas of the sperm head, improving both accuracy and interpretability. Evaluated on the SMIDS and HuSHem public datasets, our model achieves accuracies of 90.2% and 93.9% (macro F1 scores of 0.913 and 0.948), outperforming SimpleCNN and standard EfficientNet-B0. Furthermore, we use Grad-CAM++ visualizations to highlight features influencing the model's decisions. The results demonstrate that this accurate and transparent framework is a practical tool for automated sperm analysis in fertility clinics.

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

Co-occurring associated retained concepts in Diffusion Unlearning

Unlearning has emerged as a key technique to mitigate harmful content generation in diffusion models. However, existing methods often remove not only the target concept, but also benign co-occurring concepts. As illustrated in Fig.1, unlearning nudity can unintentionally suppress the concept of person, preventing a model from generating images with person. We define these undesirably suppressed co-occurring concepts that must be preserved CARE (Co-occurring Associated REtained concepts). Then, we introduce the CARE score, a general metric that directly quantifies their preservation across unlearning tasks. With this foundation, we propose ReCARE (Robust erasure for CARE), a framework that explicitly safeguards CARE while erasing only the target concept. ReCARE automatically constructs the CARE-set, a curated vocabulary of benign co-occurring tokens extracted from target images, and leverages this vocabulary during training for stable unlearning. Extensive experiments across various target concepts (Nudity, Van Gogh style, and Tench object) demonstrate that ReCARE achieves overall state-of-the-art performance in balancing robust concept erasure, overall utility, and CARE preservation.

18.
arXiv (CS.CL) 2026-06-24

L3Cube-MahaPOS: A Marathi Part-of-Speech Tagging Dataset and BERT Models

Part-of-Speech (POS) tagging is a foundational NLP task underpinning machine translation, information extraction, and syntactic parsing. Despite Marathi being spoken by over 83 million people and ranking among the top twenty most spoken languages worldwide, it remains severely under-resourced in annotated corpora and standardised evaluation benchmarks. Marathi presents unique challenges for computational modelling owing to its rich morphology, relatively free word order, lack of capitalisation conventions, and pervasive code-mixing with Hindi and English. We introduce L3Cube-MahaPOS, a gold-standard POS tagging dataset for Marathi comprising 32,354 manually annotated sentences drawn from news text. Annotation was performed entirely manually by a team of Marathi-proficient annotators following a 16-tag Universal Dependencies-aligned scheme. A structured preprocessing pipeline covering Unicode normalisation, Devanagari-aware tokenisation, and noise filtering ensures label consistency across all splits. We benchmark the dataset across six model families spanning HMM, CRF, BiLSTM, BiLSTM+CharCNN, MuRIL, and the Marathi-specific transformer MahaBERT-v2. The best system achieves 88.67\% token-level accuracy and a macro-F1 of 81.67% over 15 evaluated tag classes. We release the dataset, annotation guidelines, and trained model checkpoints to foster further research in Marathi NLP.

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

Lyapunov-Based Sample Complexity Analysis for Weakly-Coupled MDPs

arXiv:2606.14095v1 Announce Type: new Abstract: We study the sample complexity of learning in average-reward weakly-coupled Markov decision processes (WCMDPs) and Restless Bandits (RBs) under a generative model. Naive reduction to a tabular MDP leads to high complexity bounds as the state-action space is exponentially large in the number of arms $N$. By exploiting the weakly coupled structure, we show that near-optimal policies can be learned with sample and computational complexities that are polynomial in $N$. Specifically, we analyze the plug-in approach, which applies an efficient planning algorithm to an empirical model estimated from data. For fully heterogeneous WCMDPs, we establish the first finite-sample PAC guarantee with polynomial complexity and an $O(1/\sqrt{N})$ optimality gap. For homogeneous RBs, we further prove that a smaller optimality gap is achievable under mild structural assumptions. A primary technical contribution of our work is a novel Lyapunov-based analysis framework. Unlike classical approaches that rely on the difficult-to-control bias function, our framework uses an explicitly constructed Lyapunov function along with a drift transfer technique between the true and empirical models. A key step of independent interest in our framework is a fine-grained perturbation analysis for the underlying linear programming (LP) relaxation, which provides a general tool for analyzing LP-based policies and weakly-coupled systems.

20.
arXiv (math.PR) 2026-06-19

A Cycle Walk for Sampling Measures on Spanning Forests for Redistricting

arXiv:2509.08629v2 Announce Type: replace-cross Abstract: We introduce the Cycle Walk, a new Markov chain Monte Carlo method for sampling distributions on balanced graph partitions, motivated by applications in political redistricting. The method operates on spanning forests and combines two types of updates: local "cycle" moves within districts and global moves that exchange population between adjacent districts while preserving balance constraints. This construction enables efficient Metropolis–Hastings correction while allowing proposals at multiple spatial scales. We show that the Cycle Walk naturally interpolates between existing approaches based on local updates and a class of global update methods derived from recombination (RECOM). Through a range of numerical experiments on synthetic graphs and real-world precinct data, we demonstrate that the Cycle Walk exhibits improved empirical convergence diagnostics for distributions that place weaker weight on spanning-tree counts, a regime that is challenging for existing methods. In particular, the algorithm remains effective when incorporating alternative compactness measures that more closely reflect policy-relevant criteria. These results suggest that the Cycle Walk provides a flexible and computationally efficient framework for sampling from a broader class of redistricting distributions than previously accessible with MCMC techniques.

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

Automated ultrasound doppler angle estimation using deep learning

arXiv:2508.04243v2 Announce Type: replace-cross Abstract: Angle estimation is an important step in the Doppler ultrasound clinical workflow to measure blood velocity. It is widely recognized that incorrect angle estimation is a leading cause of error in Doppler-based blood velocity measurements. In this paper, we propose a deep learning-based approach for automated Doppler angle estimation. The approach was developed using 2100 human carotid ultrasound images including image augmentation. Five pre-trained models were used to extract images features, and these features were passed to a custom shallow network for Doppler angle estimation. Independently, measurements were obtained by a human observer reviewing the images for comparison. The mean absolute error (MAE) between the automated and manual angle estimates ranged from 3.9{\deg} to 9.4{\deg} for the models evaluated. Furthermore, the MAE for the best performing model was less than the acceptable clinical Doppler angle error threshold thus avoiding misclassification of normal velocity values as a stenosis. The results demonstrate potential for applying a deep-learning based technique for automated ultrasound Doppler angle estimation. Such a technique could potentially be implemented within the imaging software on commercial ultrasound scanners.

22.
arXiv (CS.CV) 2026-06-16

Towards Global AI-Driven Cervical Cancer Screening

The global elimination of cervical cancer is a key public health goal set by the World Health Organization (WHO), with screening programs reducing mortality by up to 80%. However, access to experts and biopsy services is limited in low- to middle-income countries (LMICs). Deep learning (DL)-based algorithms offer promising support for screening, but most existing approaches have been developed and validated on private datasets from single countries. We present the first DL-based approach to cervical cancer screening validated on data from multiple countries. Technically, we phrase the problem of detecting and classifying lesions in colposcopy images as a multi-task learning problem, in which we simultaneously perform image-level classification and lesion segmentation. Our model was trained on a private data set of acid stain colposcopy images with manually generated lesion segmentation masks and corresponding histopathological results, employing extensive data augmentation to address image variability. In an in-distribution validation with pathology results serving as ground truth, our algorithm outperformed medical experts (Balanced Accuracy: 0.68 vs 0.64) in CIN1- (Cervical intraepithelial neoplasia grade 1 or lower) versus CIN2+ (grade 2 or higher) classification. External validation on four colposcopy data sets from four countries featuring radical differences in prevalence and patient characteristics yielded superior performance of our method compared to baseline methods. Performance variability across countries was high with AUC values ranging from 0.54 - 0.80. Overall, algorithm performance varied with age, transformation zone (cervical area most prone to lesion development), presence of comorbidities and pathognomonic signs, with comorbidities having by far the largest negative effect. Future work should focus on improving model robustness and generalizability.

23.
arXiv (CS.LG) 2026-06-24

Project Ariadne: Prompt-Conditioned Route Generation for Synthesis Planning

arXiv:2606.24184v1 Announce Type: new Abstract: Retrosynthetic planning seeks to connect a target molecule to commercially available starting materials through a multistep route. Classical planners construct such routes by iteratively applying single-step reaction models within a search procedure; constrained variants often require specialized algorithms or architectural changes. Direct route generation reframes retrosynthesis as sequence generation, but existing direct-generation methods still train separate models for different planning specifications. We introduce Ariadne, a decoder-only route generator that represents the target, optional constraints, and route in one prompt-completion sequence. On the RetroCast/PaRoutes mkt-cnv-160 benchmark family, one 24-layer checkpoint follows route-depth and required-starting-material prompts: adding the corresponding prompt fields raises Solv-0 by 13.7 points for depth constraints and 31.2 points for required-leaf constraints. Ariadne also improves over DESP, a bidirectional search planner, on required-leaf Top-10 and Solv-0 in 24 GPU-minutes versus 6.8 GPU-hours. On standard reconstruction, Ariadne is comparable to DMS Explorer XL at about half the reported inference time. Across additional target-only benchmarks, Ariadne's clearest gains are on route-holdout reconstruction, whereas AiZynthFinder MCTS remains stronger on several Solv-0 comparisons. These results extend sequence generation from specialist retrosynthesis models to prompt-conditioned structural route generation. We release the codebase and training scripts to support further work, but do not introduce Tier-1–3 route checkers; those remain the main bottleneck before models of this kind can become useful to experimental chemists.

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

VeriGeo: Controllable Geometry Question Generation with Numerical and Analytical Verification

arXiv:2606.14176v1 Announce Type: new Abstract: Geometry problem generation is useful for AI-assisted education and multimodal mathematical reasoning, but reliable synthesis remains difficult because the problem statement, diagram, constraints, and solution should be mutually consistent. Existing methods often trade off controllability and reliability: seed-based rewriting is flexible but weakly verifiable, whereas diagram-first construction improves validity but is less suited to arbitrary user-specified constraints. We introduce VeriGeo, a controllable geometry generation framework grounded in executable reasoning traces. Given user constraints such as target concepts and difficulty, an Author agent generates a problem and diagram, and a Solver agent produces a proof-aligned solution. Both agents use a shared action sequence that connects natural language, diagrams, geometric constraints, and proof steps into a verifiable representation. A three-stage pipeline checks numerical consistency, analytical realizability, and global consistency, using verification-guided reflection to repair recoverable failures and reject unrecoverable ones. Across five LLM backbones, raw generations frequently fail these checks, while VeriGeo repairs a substantial fraction of the invalid attempts. Supervised fine-tuning on 8.7k examples generated by VeriGeo achieves the best reported GeoQA performance among end-to-end multimodal LLM-based solvers, and obtains strong results on PGPS9K and MathVista-GPS, demonstrating the effectiveness of verified synthetic data for improving multimodal geometry reasoning.

25.
arXiv (CS.AI) 2026-06-15

Patcher: Post-Hoc Patching of Backdoored Large Language Models

arXiv:2606.02995v2 Announce Type: replace-cross Abstract: Large language models remain vulnerable to jailbreak backdoor attacks, where adversaries poison safety alignment data to embed hidden triggers that bypass safety mechanisms. Existing defenses often require comprehensive attack information or multiple triggered examples, making them impractical when defenders only observe a single reported failure case without knowing whether it stems from a backdoor attack or a natural alignment bug. This paper presents Patcher, a post-hoc defense framework that repairs backdoored language models using only a single reported failure case and the model parameters. Patcher operates in two stages. First, it localizes backdoor triggers by computing response-conditioned gradient-based saliency scores and applying adaptive clustering to separate triggers from benign context. Second, it patches the model through a constrained fine-tuning objective that breaks the trigger-response association while preserving benign-task utility and robustness to non-triggered jailbreak attacks through KL-divergence constraints. We conduct extensive evaluations across multiple backdoor attack strategies and demonstrate that Patcher successfully localizes triggers and neutralizes backdoors while maintaining model utility. We further show robustness against adaptive attacks designed to evade our defense. This work represents a significant step toward practical defenses against training-time attacks in deployed language models.