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01.
arXiv (CS.AI) 2026-06-18

PosterForest: Hierarchical Multi-Agent Collaboration for Scientific Poster Generation

arXiv:2508.21720v3 Announce Type: replace Abstract: Automating scientific poster generation requires hierarchical document understanding and coherent content-layout planning. Existing methods often rely on flat summarization or optimize content and layout separately. As a result, they often suffer from information loss, weak logical flow, and poor visual balance. We present PosterForest, a training-free framework for scientific poster generation. Our method introduces the Poster Tree, a structured intermediate representation that captures document hierarchy and visual-textual semantics across multiple levels. Building on this representation, content and layout agents perform hierarchical reasoning and recursive refinement, progressively optimizing the poster from global organization to local composition. This joint optimization improves semantic coherence, logical flow, and visual harmony. Experiments show that PosterForest outperforms prior methods in both automatic and human evaluations, without additional training or domain-specific supervision.

02.
arXiv (quant-ph) 2026-06-15

Dissipation-induced superradiance in matter coupled to a self-interacting cavity

arXiv:2606.14526v1 Announce Type: new Abstract: Light-matter interactions are often modeled via the Dicke model, namely, by two-level systems coupled to a cavity mode. Alas, the threshold for superradiance is often experimentally inaccessible or hindered by light's diamagnetic term. Here, within the Dicke setting, we consider self-interacting light in a cavity, modeled by a photonic Kerr nonlinearity. We show that negative Kerr nonlinearity gives rise to a low-threshold superradiant phase with spin inversion. While unstable in a closed system, cavity dissipation stabilizes this lit phase, opening avenues for lasing and bath-engineered phases.

03.
PLOS Computational Biology 2026-06-22

CoDaLoMic: An R package for modeling microbiome compositional and longitudinal data

by Irene Creus-Martí, Andrés Moya, Francisco J. Santonja In this paper we present CoDaLoMic, an R package for analyzing longitudinal and compositional microbiome datasets. The CoDaLoMic package implements three models specifically designed for the analysis of microbiome data that are both compositional and longitudinal. Unlike many existing methods that focus solely on pairwise interactions, CoDaLoMic also captures interactions among groups of bacteria, providing a more robust methodological framework for studying microbial relationships at the community level. In addition, the package facilitates the analysis of microbiome variability in relation to host health status and allows for the identification of groups of taxa that exhibit similar temporal dynamics. Working with time series data makes it possible to understand not only the current state of a microbial community but also its dynamics over time, which is essential for identifying patterns of ecological succession, detecting events of dysbiosis or recovery, and inferring potential causal relationships between taxa. On the other hand, focusing on interactions among groups of bacteria, rather than analyzing only pairwise relationships, enables a more integrated and functionally meaningful view of the microbiome. Many key ecological functions are the result of the collective behavior of functionally related groups of taxa. Two datasets have been considered in CoDaLoMic, one real and one simulated. The real dataset contains the information of the genera present in the microbiome of the Blatella germanica cockroach at 105 time points. The simulated dataset is defined taking Lotka-Volterra structure into account. CoDaLoMic is available at CRAN.

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

Lung-R1: A Knowledge Graph-Guided LLM for Pulmonary Diagnostic Reasoning

arXiv:2606.11675v1 Announce Type: new Abstract: Diagnosing pulmonary diseases requires integrating heterogeneous evidence amid phenotypic variability and cross-disease overlap. Although large language models (LLMs) have shown progress on pulmonary knowledge question answering (QA) and information-processing tasks, reliable pulmonary diagnosis requires patient-specific, relation-aware reasoning over electronic medical record (EMR) evidence rather than isolated knowledge recall. We define this gap between pulmonary knowledge and case-level diagnostic reasoning as the Pulmonary Knowledge-to-Diagnosis Gap. To address it, we introduce LungKG, the first structured pulmonary knowledge graph for diagnostic knowledge organization and record-grounded reasoning. LungKG contains 59,038 nodes and 164,308 edges across 15 entity types and 112 relation types, serving as both a reusable pulmonary knowledge resource and the foundation for LungKG-guided model adaptation. Built on LungKG, we propose Lung-R1, a LungKG-guided pulmonary LLM trained through KG-constrained reasoning-chain construction and KG-guided reinforcement learning. In a 20-system evaluation, Lung-R1-14B achieves state-of-the-art performance across Choice, Pulmonary-QA, and EMR Diagnosis, reaching an EMR Diagnosis score of 4.3583 and surpassing the strongest non-Lung-R1 baseline by 0.1476 points. These results demonstrate the value of LungKG-guided training for EMR-based pulmonary diagnosis.

05.
medRxiv (Medicine) 2026-06-22

COVID-19 containment policies and hyperglycemia in pregnancy: correlation with the Stringency Index in a nationwide Belgian cohort

Background During the COVID-19 pandemic, gestational diabetes (GD) prevalence showed variable changes across regions, with most reporting increases and others decreases; however, its association with perinatal outcomes in Belgium remains unknown. We aimed to compare the prevalence of hyperglycemia in pregnancy (HIP) in 2020 versus 2019 and examined the correlation between HIP prevalence and pandemic-related restrictions measured by the Stringency Index (SI) and evaluate neonatal weight percentiles changes. Methods: We included all singleton live births in Belgium in 2019 and 2020 from Belgian birth registry data. We compared monthly proportions of HIP prevalence and Small for gestational age (SGA) and Large for gestional age (LGA) newborns in 2019 and 2020. Crude and adjusted odds ratios (ORs, aORs) were estimated with logistic and multinomial regression. The Spearman correlation coefficient was used to assess the correlation between the monthly average SI and the monthly aORs of HIP. Results: For deliveries from January to June 2020, no significant differences in HIP prevalence were observed compared with 2019. From July to December 2020, there was a significant increase in HIP, with peaks in July (GD screening in April) (aOR 1.41, 1.26-1.58) and November (GD screening in August) (aOR 1.33, 95% CI 1.18-1.49). There was no significant change in neonatal weight percentiles. The Spearman correlation coefficient between the SI and HIP aORs was 0.86 (p = 0.02). Conclusion During the pandemic, we observed an increase in the prevalence of HIP, compared to 2019, without a measurable impact on LGA or SGA newborns. The aOR of HIP in a given month was strongly correlated with the corresponding SI.

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

Tight Bounds for Logistic Regression with Large Stepsize Gradient Descent in Low Dimension

arXiv:2602.12471v2 Announce Type: replace Abstract: We consider the optimization problem of minimizing the logistic loss with gradient descent to train a linear model for binary classification with separable data. With a budget of $T$ iterations, it was recently shown that an accelerated $1/T^2$ rate is possible by choosing a large stepsize $\eta = \Theta(\gamma^2 T)$ (where $\gamma$ is the dataset's margin) despite the resulting non-monotonicity of the loss. In this paper, we provide a tighter analysis of gradient descent for this problem when the data is two-dimensional: we show that GD with a sufficiently large learning rate $\eta$ finds a point with loss smaller than $\mathcal{O}(1/(\eta \gamma^2 T))$, as long as $T \geq \Omega(n/\gamma + 1/\gamma^2)$, where $n$ is the dataset size. Our improved rate comes from a tighter bound on the time $\tau$ that it takes for GD to transition from unstable (non-monotonic loss) to stable (monotonic loss), via a fine-grained analysis of the oscillatory dynamics of GD in the subspace orthogonal to the max-margin classifier. We also provide a lower bound of $\tau$ matching our upper bound up to logarithmic factors, showing that our analysis is tight.

07.
arXiv (CS.AI) 2026-06-12

A Zero-shot Generalized Graph Anomaly Detection Framework via Node Reconstruction

arXiv:2606.12673v1 Announce Type: cross Abstract: Cross-domain graph anomaly detection (GAD) aims to identify abnormal nodes in unseen target graphs, showing strong potential in real-world applications with heterogeneous graph data. However, existing methods often depend on dataset-specific feature semantics and structural patterns, which limits their ability to generalize across different domains. To address this challenge, we propose AlignGAD, a zero-shot generalized graph anomaly detection framework. Our framework is built upon three key components: a Global Unification Module that aligns heterogeneous node features and normalizes graph signals in the spectral domain; a Clustering Module that constructs cluster-aware graph views to capture group-level abnormal patterns; and a Node Discrepancy Scoring Module that measures reconstruction discrepancy and aggregates anomaly evidence from different graph views. Experiments on multiple real-world datasets demonstrate the effectiveness of AlignGAD under the zero-shot GAD setting.

08.
arXiv (CS.CV) 2026-06-17

Edit3DGS: Unified Framework for Dynamic Head Editing via 2D Instruction-Guided Diffusion and 3D Gaussian Splatting

We present Edit3DGS, a unified framework for dynamic 3D head editing that integrates 2D instruction-guided diffusion with 3D Gaussian splatting. Unlike prior approaches that separately address frame-based edits or static 3D reconstruction, our method couples semantic controllability in the image domain with photorealistic, temporally consistent 3D representations. Given an input video, editable facial regions are masked and modified using a text-conditioned diffusion model to support fine-grained operations such as expression transformation, attribute modification, and appearance refinement. The edited frames are then aggregated through 3D Gaussian splatting to produce a coherent, high-fidelity avatar that preserves both identity and motion dynamics. To enforce consistency, Edit3DGS incorporates multi-view batch editing and lightweight inpainting strategies that recover lost expressions across timesteps. Experimental results demonstrate that our framework enables controllable, artifact-free head editing with smooth temporal transitions, offering practical applications in virtual avatars, immersive communication, film production, and interactive media.

09.
arXiv (quant-ph) 2026-06-19

Impossibility of superluminal signalling rules out causal loops in conical spacetimes

arXiv:2606.20476v1 Announce Type: cross Abstract: In PRL 129, 110401 it was shown that it is theoretically possible to have operationally detectable causal loops without violating the principle of no superluminal signalling (NSS) in (1+1)-Minkowski spacetime. Whether or not such causal loops are also possible in $d > 1$ spatial dimensions, has remained a key open question. We resolve this question by showing that in a wide class of "conical" spacetimes, including Minkowski with d > 1, NSS does rule out all operationally detectable causal loops, in classical, quantum and post-quantum theories. This establishes that the relationship between the relativistic principles of NSS and no causal loops depends inherently on the geometry of spacetime.

10.
arXiv (quant-ph) 2026-06-11

Classical representation of the dynamics of quantum spin chains

作者:

arXiv:2502.10502v3 Announce Type: replace-cross Abstract: Since the advent of quantum mechanics, classical probability interpretations have faced significant challenges. A notable issue arises with the emergence of negative probabilities when attempting to define the joint probability of non-commutative observables. In this work, we propose a resolution to this dilemma for quantum spin chains, by introducing an exact representation of their dynamics in terms of classical continuous-time Markov chains (CTMCs). These CTMCs effectively model the creation, annihilation, and propagation of pairs of classical particles and antiparticles. The quantum dynamics then emerges by averaging over various realizations of this classical process.

11.
arXiv (CS.LG) 2026-06-12

Differentiable Thermodynamic Phase-Equilibria for Machine Learning

arXiv:2603.11249v3 Announce Type: replace Abstract: Accurate prediction of phase equilibria remains a central challenge in chemical engineering. Physics-consistent machine learning methods that incorporate thermodynamic structure into neural networks have recently shown strong performance for activity-coefficient modeling. However, extending such approaches to equilibrium data arising from an extremum principle, such as liquid-liquid equilibria, remains difficult. Here we present DISCOMAX, a differentiable algorithm for phase-equilibrium calculation that guarantees thermodynamic consistency at both training and inference, only subject to a user-specified discretization. The method combines discrete enumeration of feasible phase states with masked softmax aggregation in the backward pass, with the propagation of the true equilibrium state in the forward pass, using a straight-through gradient estimator to enable physics-consistent end-to-end learning of neural \gls{gE}-models. We show that this approach bears analogy to statistical thermodynamics, and we evaluate it on binary liquid-liquid equilibrium data where it outperforms existing surrogate-based methods, while offering a general framework for learning from different kinds of equilibrium data.

12.
arXiv (CS.CL) 2026-06-18

UniECG: Understanding and Generating ECG in One Unified Model

Electrocardiogram (ECG) interpretation is a fundamental skill in medical education, yet students often need more than static examples to connect waveform evidence with diagnostic reasoning. This paper presents UniECG as a step toward interactive ECG education. UniECG supports two complementary learning interactions: given an ECG signal or image, it generates an evidence-based explanation; given a textual learning objective, it generates a corresponding ECG signal example for case-based learning. The model follows a two-stage design. First, it learns grounded ECG explanation from ECG signal–image–text data. Second, it introduces special ECG generation tokens and aligns their hidden representations with a pretrained text-conditioned ECG diffusion model, enabling controllable signal-level ECG generation. We evaluate UniECG through grounded ECG explanation and generation-oriented qualitative analysis, examining its potential to support explanation and case-based learning. UniECG is intended as an educational aid and a research step toward interactive AI-assisted ECG learning, rather than a clinically validated diagnostic system.

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

S3OD: Towards Generalizable Salient Object Detection with Synthetic Data

Salient object detection exemplifies data-bounded tasks where expensive pixel-precise annotations force separate model training for related subtasks like DIS and HR-SOD. We present a method that dramatically improves generalization through large-scale synthetic data generation and ambiguity-aware architecture. We introduce S3OD, a dataset of over 139,000 high-resolution images created through our multi-modal diffusion pipeline that extracts labels from diffusion and DINO-v3 features. The iterative generation framework prioritizes challenging categories based on model performance. We propose a streamlined multi-mask decoder that handles the inherent ambiguity in salient object detection by predicting multiple valid interpretations. Models trained only on synthetic data achieve 20-50% error reduction in cross-dataset generalization, while fine-tuned versions reach state-of-the-art performance across DIS and HR-SOD benchmarks.

14.
arXiv (quant-ph) 2026-06-19

Exploiting More Than Symmetry in Variational Quantum Machine Learning

arXiv:2606.20316v1 Announce Type: new Abstract: The success of variational quantum learning models crucially depends on choosing parametrizations that reflect the structure of the problem at hand. Symmetries provide one of the clearest such structures: whenever transformations of the input leave the desired outcome unchanged, this invariance should be built into the model rather than discovered during training. However, imposing a symmetry does not by itself determine a useful ansatz. Even within the symmetry-preserving space, one must decide where the trainable degrees of freedom should be placed. In this work, we study this remaining design freedom in equivariant variational quantum circuits. Building on symmetry-based parameter sharing, we disentangle two architectural choices: how much symmetry should be enforced, and which symmetry-respecting interactions should be trainable. Using Tic-Tac-Toe as a fully enumerable and structurally transparent test case, we find that suitable subgroups preserve most of the generalization benefit. By contrast, the dominant gains arise from gates acting directly on decisive task motifs. Thus, symmetry defines the admissible design space, while effective ansatze require an additional task-informed choice of trainable interactions.

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

Task-Adaptive Parameter-Efficient Fine-Tuning for Weather Foundation Models

arXiv:2509.22020v2 Announce Type: replace Abstract: While recent advances in machine learning have equipped Weather Foundation Models (WFMs) with substantial generalization capabilities across diverse downstream tasks, the escalating computational requirements associated with their expanding scale increasingly hinder practical deployment. Current Parameter-Efficient Fine-Tuning (PEFT) methods, designed for vision or language tasks, fail to address the unique challenges of weather downstream tasks, such as variable heterogeneity, resolution diversity, and spatiotemporal coverage variations, leading to suboptimal performance when applied to WFMs. To bridge this gap, we introduce WeatherPEFT, a novel PEFT framework for WFMs incorporating two synergistic innovations. First, during the forward pass, Task-Adaptive Dynamic Prompting (TADP) dynamically injects the embedding weights within the encoder to the input tokens of the pre-trained backbone via internal and external pattern extraction, enabling context-aware feature recalibration for specific downstream tasks. Furthermore, during backpropagation, Stochastic Fisher-Guided Adaptive Selection (SFAS) not only leverages Fisher information to identify and update the most task-critical parameters, thereby preserving invariant pre-trained knowledge, but also introduces randomness to stabilize the selection. We demonstrate the effectiveness and efficiency of WeatherPEFT on three downstream tasks, where existing PEFT methods show significant gaps versus Full-Tuning, and WeatherPEFT achieves performance parity with Full-Tuning using fewer trainable parameters. The code of this work is available at https://github.com/ShileiCao/WeatherPEFT.

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

Entropic order parameters and topological holography

arXiv:2512.24225v2 Announce Type: replace-cross Abstract: We show that the symmetry topological field theory (SymTFT) construction, also known as the topological holography, provides a natural and intuitive framework for the entropic order parameter characterising phases with (partially) broken symmetries. Various examples of group and non-invertible symmetries are studied. In particular, the origin of the distinguishability of the vacua resulting from spontaneously broken non-invertible symmetries is made manifest with an information-theoretic perspective, where certain operators in the SymTFT are excluded from observation.

17.
PLOS Medicine 2026-05-29

Availability, appeal, and addictiveness by design: Tobacco and nicotine industry deliberate targeting of youth

by Raglan Maddox, Becky Freeman, Charlotta Pisinger, Emily Banks Contemporary tobacco and nicotine products, particularly e-cigarettes, are deliberately designed, marketed, and distributed to maximize youth appeal, uptake, dependence, and use. Youth uptake is a predictable outcome of systems designed to maximize product availability, appeal, and addictiveness. In recognition of the World No Tobacco Day 2026 theme, "unmasking the appeal", this Perspective by Raglan Maddox and colleagues discusses how tobacco and nicotine products, particularly e-cigarettes, are deliberately designed and marketed to maximize youth appeal, and highlight the need for policies to ensure greater industry accountability and to tackle concerning uptake trends.

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

SuperThoughts: Reasoning Tokens in Superposition

Long Chain-of-Thought (CoT) reasoning improves LLM problem-solving but is computationally expensive due to sequential token generation. While recent works explore reasoning in continuous latent spaces to bypass discrete token generation, they often struggle with training stability and fail to scale to complex, long-horizon tasks due to lack of supervision signal. We propose SuperThoughts, which compresses pairs of consecutive CoT tokens into single latent representations and decodes two tokens per step via a lightweight Multi-Token Prediction (MTP) module. This preserves discrete token supervision at training time while doubling throughput at inference time. We finetune Qwen2.5-Math-1.5B-Instruct, Qwen2.5-Math-7B-Instruct, Qwen2.5-Math-14B-Instruct, and evaluate on MATH500, AMC, OlympiadBench, and GPQA-Diamond. With a confidence-based adaptive mechanism that falls back to standard decoding when uncertain, SuperThoughts achieves $\sim$20–30\% CoT length reduction while maintaining accuracy with minimal degradation (1-2 points accuracy drop on most tasks).

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

Space Is Intelligence: Neural Semigroup Superposition for Riemannian Metric Generation

作者:

arXiv:2606.18828v1 Announce Type: cross Abstract: Traditional approaches place intelligence in the agent, whether as a learned policy or a search procedure. We instead place intelligence in the space itself: a scene induces a Riemannian metric on the configuration manifold, and action reduces to following the geodesics of that metric rather than invoking a separate planner or collision checker. A single Encoder-Router network realizes this idea through three complementary parameter groups – frame parameters that orient the generators, modulation parameters that govern their spatial propagation, and basic coefficients that determine their strength. These groups combine through a shared semigroup-superposition mechanism to produce a single Riemannian metric field, yielding a compact architecture whose geometry scales naturally with scene complexity. Trained on a single two-obstacle scene, the model demonstrates robust zero-shot generalization across unseen obstacle configurations, with orders-of-magnitude separation between collision-free and obstacle-penetrating path costs.

20.
arXiv (CS.CL) 2026-06-17

Perceptual compensation for tonal context in self-supervised speech models

This study examines the extent to which the wav2vec2.0 architecture exhibits evidence of compensation for phonological context. We conducted a pseudo-replication of a perceptional compensation experiment on Mandarin Chinese tones, and compared the embedding similarities and probing classifier outputs between a purely self-supervised pre-trained model and a model fine-tuned for Mandarin ASR. No evidence of compensation was found in the embedding similarities of the purely pre-trained model. Probing classifiers showed some evidence of compensation in addition to the expected layer-wise improvements in categorization, but failed to replicate human performance on isolated test syllables. Our findings contrast with previous reports of sensitivity to phonological structure emerging through pre-training alone, and suggest that supervised objectives may be necessary to encourage the abstraction of at least some types of phonological regularities.

21.
arXiv (quant-ph) 2026-06-15

Quantitative and Optimal Device-Independent Lower Bounds on Detection Efficiency

arXiv:2511.19302v2 Announce Type: replace Abstract: This paper examines a quantitative and optimal lower bound on the detector efficiency in a (2,2,2) Bell experiment within a fully device-independent framework, whereby the detectors used in the experiment are uncharacterized. We provide a tight lower bound on the minimum efficiency required to observe a desired Bell-CHSH violation using the Navascués-Pironio-Acín (NPA) hierarchy, confirming tightness up to four decimal places with numerical optimization over explicit quantum realizations. We then introduce the effect of dark counts and demonstrate how to quantify the minimum required efficiency to observe a desired CHSH violation with an increasing dark count error. Finally, to obtain an analytical closed-form expression of the minimum efficiency, we consider the set of no-signaling behaviors that satisfy the Tsirelson bound, which are easier to characterize than the quantum set. Using such behaviors, we find a simple closed-form expression for a lower bound on the minimum efficiency which is monotonically increasing with the CHSH violation, though the analytically obtained lower bounds are meaningfully below the numerically tight lower bound.

22.
arXiv (CS.LG) 2026-06-18

Protein-Based Fish Species Identification: Dataset, Models, and Insights from Native Bangladeshi Fish

arXiv:2606.18302v1 Announce Type: cross Abstract: Correct identification of fish species is highly significant for food security, economic development, and climate resilience in Bangladesh. Protein sequences directly reflect functional and evolutionary constraints which are important for species authentication and biodiversity monitoring. Yet there exists no benchmark for native Bangladeshi fish species identification from protein sequence. In this study, we addressed this gap by introducing the first curated dataset for nine native Bangladeshi fish species of 2845 high quality protein sequences. We also established the first protein sequence classification baseline for this domain through a systematic benchmarking of seven architectural paradigms. Moreover, we propose a realistic deployable novel hybrid architecture of MotifCNN and Transformer with Terminal-Aware Positional-Encoding (MotifCNN-Transformer+TA-PE). Our novel architecture achieves 79.80% accuracy with macro-F1 of 0.80. The highest 83.04% accuracy is achieved by finetuned protein language model ProtBERT that has 420M parameters and requires dual 16GB GPUs for inference. According to McNemar's test, ProtBERT's 3.24% accuracy gain over our MotifCNN-Transformer+TA-PE is statistically insignificant (p = 0.1120). Our novel architecture beats it among six of the nine classes in per class identification. Also our MotifCNN-Transformer+TA-PE is approximately 5x faster, 42x smaller, and supports 16x larger batch size than ProtBERT and has GPU free inference, making it more practical for deployment in resources constrained areas such as rural Bangladesh. Beyond this, our foundational work shows effects of phylogenetic relationships on sequence similarity and establishes pathways for fisheries management, food authentication and biodiversity conservation in South Asia's protein dependent economy.

23.
arXiv (CS.CV) 2026-06-15

Efficient Online 3D Multi-Camera Multi-Object Tracking and Pose Estimation

This paper proposes a fast and online method for jointly performing 3D multi-object tracking and pose estimation using multiple monocular cameras. Our algorithm requires only 2D bounding box and pose detections, eliminating the need for costly 3D training data or computationally expensive deep learning models. Our solution is an efficient implementation of a Bayes-optimal multi-object tracking filter, enhancing computational efficiency while maintaining accuracy. We demonstrate that our algorithm is significantly faster than state-of-the-art methods without compromising accuracy, using only publicly available pre-trained 2D detection models. We also illustrate the robust performance of our algorithm in scenarios where multiple cameras are intermittently disconnected or reconnected during operation.

24.
bioRxiv (Bioinfo) 2026-06-14

Somatic variant detection in normal tissues from single-cell sequencing data

A crucial advantage of single-cell sequencing (SCS) is its ability to identify somatic variants in individual cells, enabling phylogenetic analysis of cellular populations within bulk tissues. While identifying somatic variants in tumor tissues via SCS has become a common practice, doing so in normal tissues remains challenging due to the rarity of somatic variants in normal cells. To evaluate the feasibility of somatic variant calling from widely available single-nucleus RNA-seq (snRNA-seq) and single-nucleus ATAC-seq (snATAC-seq) data, we profiled a Cell-line mix of six HapMap samples prepared by the SMaHT consortium using 10x Genomics 5' snRNA-seq (12k cells with 36k mean reads per cell) and snATAC-seq (11k cells with 14k median high-quality fragments per cell) for variant calling. PacBio long-read whole genome sequencing (WGS) data (109x) generated from individual cell lines were used as ground truth. Two computational tools, Monopogen and SComatic, were used for somatic variant calling from the SCS data. Monopogen achieved single nucleotide variant (SNV) detection accuracies of 93.30% in the snRNA-seq and 99.64% in the snATAC-seq data, both of which outperformed SComatic (74.35% and 94.29%, respectively). Monopogen also consistently detected somatic SNVs at cellular fractions as low as 0.5% (2.54% in snRNA and 0.81% in snATAC) in individual samples. Notably, snATAC-seq exhibited higher genomic coverage breadth and larger number of variants detected than snRNA-seq. While the SCS data have lower overall genome coverage than that of the bulk WGS, the single-cell level variant resolution allows Monopogen to assign variants to their cells of origin with over 80% accuracy in both RNA and ATAC modalities, thereby facilitating studies of clonal evolution and cell-type-specific mutagenesis. Other benchmarking methods were also evaluated (DeepVariant, Cellsnp-lite and Mutect2) for comparison. In conclusion, our study demonstrated the feasibility of performing reliable single-cell somatic mutation calling in a cell-line mixture and discussed the strengths and limitations of current computational methods when applied to normal tissues.

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

Triangular Consistency as a Universal Constraint for Learning Optical Flow

arXiv:2606.19938v1 Announce Type: cross Abstract: We propose triangular consistency as a first-principled constraint for optical flow, which is agnostic to network architecture, supervision type, and dataset, and applies to both image-pair and multi-frame settings. This simple but powerful constraint is to compose two flows to induce a third flow and enforce consistency among the three. The composed flows may arise from (i) image pairs, yielding cycle consistency; (ii) multiple video frames, producing longer-range motion through temporal chaining; or (iii) image pairs combined with controlled synthetic transformations, which becomes data augmentation. This triangular consistency introduces negligible computational overhead and requires no additional annotations. Since it is derived directly from the geometry of optical flow, it does not rely on model-specific assumptions and serves as a ``universal'' plug-and-play component for optical flow training. Experiments show consistent improvement across supervised, unsupervised, and transfer learning settings.