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01.
arXiv (CS.CV) 2026-06-17

A Quantitative Analysis of Multimodal Biomarkers in Alzheimer's Disease

Authors:
Antonio Scardace↗Daniele Rav\`i↗

Despite increasing adoption of multimodal approaches in Alzheimer's Disease (AD) research – aimed at integrating molecular, structural, clinical, and genetic biomarkers to enhance disease characterization – the relationships among these modalities remain poorly understood. A systematic analysis of their dynamic interaction is essential for improving disease modeling, identifying redundant assessments, and reducing patient burden and acquisition costs. In this paper, we present a quantitative analysis of multimodal AD biomarkers by integrating tau-PET, structural MRI, cognitive scores (MMSE and CDR), and APOE4 data from 789 subjects drawn from the ADNI dataset. In our analyses, we (A) quantify cross-modal mutual information and explained variance to assess redundancy and predictive dependencies; (B) examine associations between tau topologies and structural atrophy across brain regions to select informative ROIs; (C) perform a statistical decomposition of the tau-cognition association into atrophy-related and atrophy-independent components; (D) and identify a dominant neurodegenerative trajectory that aligns with cognitive decline. This study provides a systematic characterization of cross-modal relationships, improving the interpretability and selection of biomarkers in AD. Code is publicly available at: https://github.com/antonioscardace/Multimodal-AD.

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02.
arXiv (math.PR) 2026-06-24

On the stability of rarefaction for stochastic viscous conservation law

Authors:
Zhao Dong↗Feimin Haung↗Houqi Su↗

arXiv:2606.24167v1 Announce Type: new Abstract: We study the asymptotic stability of rarefaction waves for one-dimensional stochastic viscous conservation laws driven by nonlinear conservative noise. In a critical scaling where stochastic energy injection and viscous dissipation compete at comparable magnitudes, standard kinetic and viscosity frameworks encounter obstructions due to regularity gaps and non-integrable profiles. To address this, we introduce a stochastic area inequality controlling accumulated energy fluctuations, a local $L^1$ contraction principle via stochastic Kru\v{z}kov doubling-of-variables that yields pathwise uniqueness without global integrability, and a modified Galerkin scheme preserving the $H^2$ energy structure. Assuming local $H^2$ regularity, we prove almost sure algebraic convergence to the rarefaction wave. For sufficiently small initial perturbations, we establish global well-posedness and sharp decay estimates in expectation. The smallness condition identifies a regime where viscous dissipation dominates stochastic injection, reflecting a structural stability threshold rather than a technical artifact. Our approach extends the analytical framework for conservative SPDEs with rough fluxes.

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03.
bioRxiv (Bioinfo) 2026-06-19

StickForStats: automated statistical assumption validation for reproducible computational biology

Authors:
Bharti↗Chakraborty↗

Reproducible computational biology depends on statistical decisions that routine workflows often skip: verifying that a differential-expression test's assumptions hold across all genes, that a strategy-comparison ANOVA is robust to non-normality, or that a meta-analysis is not distorted by publication bias. Surveys consistently find that fewer than 20% of published biomedical studies report checking these assumptions, and existing statistical software leaves validation to the analyst as an optional step. We present StickForStats, an open-source web platform that reframes assumption validation as a default precondition for every analysis. Its Guardian system–a middleware pipeline of eight validators (normality, variance homogeneity, independence, outliers, sample size, modality, linearity, homoscedasticity)–checks assumptions before execution and, on critical violations, reroutes to an appropriate nonparametric alternative with a documented decision trail. At genome scale, applying Guardian to a 91-sample synovial-sarcoma RNA-seq study (GSE271517) cascaded 90.6% of 27,221 genes to a rank-based test and flipped the differential-expression verdict for 553 genes–479 rescued from an under-powered t-test and 74 outlier-driven false positives rejected–materially changing the gene list a biologist would act on. The same automatic validation generalizes across domains: a CRISPR editing-strategy comparison (ANOVA F = 1122, with Guardian recommending Kruskal-Wallis H = 36.6), an ordinal correlation (Pearson r = 0.476 corrected to Spearman {rho} = 0.479), and a sixteen-trial clinical meta-analysis revealing severe publication bias (Egger's t = -5.78, p < 0.001); a complementary module extends the same validators to published manuscripts, checking claims against CONSORT, STROBE, ICH-E9, and JARS-Quant reporting standards. By making assumption validation automatic and transparent, StickForStats targets a tractable, under-served contributor to irreproducibility. The platform is MIT-licensed, validated against SciPy and R, and freely available at https://github.com/visvikbharti/stickforstats_new.

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04.
arXiv (CS.CL) 2026-06-16

Encode Errors: Representational Retrieval of In-Context Demonstrations for Multilingual Grammatical Error Correction

Authors:
Guangyue Peng↗Wei Li↗Wen Luo↗Houfeng Wang↗

Grammatical Error Correction (GEC) involves detecting and correcting the wrong usage of grammar. While large language models (LLMs) with in-context learning (ICL) capabilities have shown significant progress on various natural language processing (NLP) tasks, their few-shot performance on GEC remains suboptimal. This is mainly due to the challenge of retrieving suitable in-context demonstrations that capture error patterns instead of semantic similarity. In this paper, we demonstrate that LLMs can inherently capture information related to grammatical errors through their internal states. From these states, we extract the Grammatical Error Representation (GER), an informative and semantically neutral encoding of grammatical errors. Our novel GER-based retrieval method significantly boosts performance in ICL settings on multilingual GEC datasets, improving the precision of correction. For high-resource languages, our results on 8B-sized open-source models match those of closed-source models such as Deepseek2.5 and GPT-4o-mini. For low-resource languages, our $F_{0.5}$ scores surpass the baseline by up to a factor of 1.20. This method provides a more precise and resource-efficient solution for multilingual GEC, offering a promising direction for interpretable GEC research.

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05.
arXiv (CS.LG) 2026-06-19

Capturing Intransitive Dominance in Tennis Forecasting: A Graph Neural Network Approach

Authors:
Lawrence Clegg↗John Cartlidge↗

arXiv:2510.20454v2 Announce Type: replace Abstract: Intransitive player dominance, where player A beats B, B beats C, but C beats A, is common in competitive tennis. Yet, there are few known attempts to incorporate it within forecasting methods. We address this problem with a graph neural network approach that explicitly models these intransitive relationships through temporal directed graphs, with players as nodes and their historical match outcomes as directed edges. Our model (65.7% accuracy, 0.214 Brier score) forecasts competitively with established rating systems such as Weighted Elo. Although it does not improve on the baseline in unconditional accuracy, a forecast-encompassing test shows that it carries complementary information. A combined forecast significantly outperforms Weighted Elo, and there is some indication that the gain grows more strongly on the intransitive matchups our model targets. A graph-based representation of player interactions thus captures a forecasting signal that transitive rating systems discard, even between players who share no common opponents.

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06.
medRxiv (Medicine) 2026-06-22

The Unsteady Return of Command-Following: Recovery and Instability of Bedside Motor Command-Following After Acute Brain Injury

Authors:
Gorenshtein↗Adiniaev↗Omar↗Barash↗Klang↗Daniel↗

Background/Objective: Following a verbal command marks the bedside transition from unresponsiveness to overt recovery of consciousness after acute brain injury. Its timing across phenotypes, stability once present, and dependence on sedation are uncharacterized at scale. Methods: Retrospective cohort of adults with acute brain injury, first intensive care unit stay, MIMIC-IV. Command-following was the Glasgow Coma Scale motor response "Obeys Commands." Among patients not following commands at admission, cumulative incidence was estimated with death or hospice and discharge without recovery as competing events. Instability was quantified as transient first recovery and threshold crossings; examinations were tagged for concurrent sedation. Principal findings were externally validated in the multicenter eICU Collaborative Research Database. Results: Of 13,900 brain-injured patients with three or more motor examinations, 5,498 (39.6%) were not following commands at admission. The cumulative incidence of first command-following was 43.5% by 24 hours and 65.0% by 14 days, ranging at 14 days from 36.9% in anoxic injury to 77.2% in ischemic stroke (anoxic versus ischemic stroke at 72 hours, difference 0.41; adjusted P = .002). Among 3,573 patients who recovered, the first recovery was transient in 22.2%, and 62.4% crossed the threshold repeatedly. Non-following was strongly associated with sedation, consistent with an arousal-dependent examination. In eICU, the 14-day incidence was 64.8%, and transient first recovery was 22.7%, closely matching the primary cohort. Conclusions: After acute brain injury, overt bedside command-following returns early but unsteadily, with phenotype-dependent timing, threshold fluctuation, and strong dependence on sedation. A single charted observation is an unreliable index of the underlying state.

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

A Comprehensive Survey of Medical Image Segmentation: Challenges, Benchmarks, and Beyond

Authors:
Pengyu Zhu↗Xiaojing Zhang↗Kunbo Zhang↗Chunyan Zhang↗Zhenyu Wang↗

Medical image segmentation plays a critical role in clinical diagnostics, treatment planning, disease monitoring, and neurological disorder identification. This article presents a comprehensive review of its systematic development, covering widely used public datasets, representative methods built on the U-Net, Transformer, and SAM architectures, and key evaluation metrics with their differences, followed by an analysis of major challenges from multiple perspectives. Unlike surveys that focus on a single model family or a specific clinical application, this review organizes U-Net-, Transformer-, and SAM-based methods within a unified analytical framework, with a particular focus on their effectiveness in improving segmentation accuracy and efficiency. This work aims to guide future research and support clinical translation of medical image segmentation, with all related resources publicly available in our GitHub repository: https://github.com/andrew-pengyu/Awsome_MedSeg/tree/main.

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09.
arXiv (CS.AI) 2026-06-25

AI Snitches Get Glitches: Towards Evading Agentic Surveillance

Authors:
Hyejun Jeong↗Dzung Pham↗Amir Houmansadr↗Eugene Bagdasarian↗

arXiv:2606.25836v1 Announce Type: new Abstract: To better assist users with completing challenging tasks, AI agents mediate communications, access data, and interact with different APIs. Many employers (and even nation-states) already provide their users with this technology. However, widespread adoption of AI agents creates a new risk to abuse access to user data for another goal: surveilling users. These users might not even have the ability or permission to control the actions and data accesses of the surveilling agents. We introduce and formalize the problem of agentic surveillance: the ability of an AI agent to analyze available information, craft a report, and send it out using available tools. To evaluate surveillance capabilities across different models, we create SurveilBench, a dataset of various reporting scenarios focusing on three domains: corporate, education, and police. We find that some models exhibit emergent (i.e., unprompted) tendencies to help surveillance, but they also report the attempts to surveil users to the government. Finally, we repurpose prompt injections for evading surveillance and develop three evasion techniques that hide from, deceive, or induce over-escalation in surveillance agents. We conclude that agentic surveillance can already be easily implemented and, therefore, call for a comprehensive technical, ethical, and legislative framework to protect users.

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10.
bioRxiv (Bioinfo) 2026-06-21

DeepCDS: Ab initio coding sequence prediction in prokaryotic short reads

Authors:
Nielsen↗L. S↗Winther↗

Accurate coding sequence prediction in short prokaryotic metagenomic reads remains challenging due to sequence fragmentation, unknown sequence origins, and sequencing errors. Here we introduce DeepCDS, a deep learning-based ab initio coding sequence predictor trained on short prokaryotic sequences with and without simulated Illumina-like sequencing errors. DeepCDS integrates ESM-2 protein language model embeddings with nucleotide-level information to predict complete and fragmented coding sequence regions. Benchmarking on 215 phylogenetically diverse prokaryotic organisms demonstrates that DeepCDS consistently outperforms current state-of-the-art methods in coding sequence detection, start and stop codon localization, and robustness to different sequencing error profiles, while remaining operational at shorter sequence lengths than existing tools support. These findings demonstrate that protein language models capture distinct signals relevant for nucleotide-level coding sequence detection, especially at very short lengths. Ultimately, DeepCDS may help uncover the functional potential of the vast microbial diversity that remains genomically uncharacterized.

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11.
Nature Medicine 2026-06-24

Automated reanalysis of genomic data for rare disease diagnostics at scale

Authors:
Matthew J. Welland↗

Reanalysis of genomic data in rare disease is highly effective in increasing diagnostic yields but remains limited by manual approaches. Automation and optimization for high specificity will be necessary to ensure scalability, adoption and sustainability of iterative reanalysis. We developed Talos, an open-source tool that automates variant prioritization by integrating dynamically updated gene−disease and variant-level evidence with inheritance-aware filtering and validated its performance using data from 1,089 individuals with rare disease. Trio-based analysis identified 90% of known diagnoses, returning 1.3 variants per case on average. Variant burden reduced to one variant per 200 cases on iterative monthly reanalysis. Application to an unselected cohort of 4,735 undiagnosed individuals identified 241 diagnoses (5.1% yield): 78 (32%) due to new gene−disease relationships, 54 (22%) due to new variant-level evidence and 109 (45%) due to improved analysis strategies. Our automated, iterative reanalysis model demonstrates the feasibility of delivering frequent, systematic reanalysis at scale. Talos, a new tool for the automated analysis of genomic data, demonstrates the feasibility and diagnostic utility of systematic reanalyses of data in rare diseases.

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

SHIFT: Semantic Harmonization via Index-side Feature Transformation for Multilingual Information Retrieval

Authors:
Youngjoon Jang↗Seongtae Hong↗Hyeonseok Moon↗Heuiseok Lim↗

arXiv:2606.18801v1 Announce Type: cross Abstract: With the rapid expansion of massive multilingual corpora, Multilingual Information Retrieval (MLIR) has emerged as a critical technology for global information access. MLIR enables users to retrieve semantically relevant documents from multilingual text collections using a single-language query. However, recent multilingual dense retrieval models often exhibit a strong preference for documents in the same language as the query. This leads to severe language bias, where top-ranked results are dominated by documents of specific languages, even when documents in other languages contain more semantically relevant information. To address this issue, we propose SHIFT, a training-free method applicable in the indexing stage. Specifically, SHIFT utilizes parallel translation pairs to estimate a relative language vector for each target language with respect to a source language. Subsequently, SHIFT corrects the language-specific offset by subtracting this relative language vector from document embeddings during indexing. Our comprehensive evaluation across four MLIR benchmarks and diverse dense retrieval models confirms that SHIFT can effectively mitigate language bias and enhance MLIR performance.

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13.
arXiv (CS.CL) 2026-06-11

Agreement in Representation Space for Open-Ended Self-Consistency

Authors:
Paula Ontalvilla↗Gorka Azkune↗Aitor Ormazabal↗

Self-consistency improves LLM reasoning by sampling multiple outputs and selecting the most consistent answer, but existing formulations largely rely on exact matching and therefore remain limited to tasks with categorical outputs. In this work, we study self-consistency in open-ended generation tasks such as code synthesis and text summarization. We hypothesize that consistency can be understood as a geometric property of the generation space, where semantically compatible generations concentrate in similar regions of representation space. To study this hypothesis, we introduce Embedding-Based Agreement (EBA), a simple training-free operationalization that estimates agreement by clustering sampled generations in embedding space. Through experiments on mathematical reasoning, code generation, and summarization, we show that agreement in representation space provides a robust and scalable signal of self-consistency for open-ended tasks. In particular, EBA consistently outperforms random selection and exhibits more stable scaling behavior than recent selection approaches based on LLM evaluation or uncertainty estimation. We further show that these agreement signals remain stable across model families and embedding spaces, even with native hidden representations. Finally, our analysis shows that the geometric location occupied by sampled generations is strongly correlated with generation quality: generations concentrated near central regions of representation space tend to correspond to more reliable outputs, whereas peripheral generations are substantially less accurate. Overall, our findings support viewing self-consistency as a property of the geometric organization of sampled generations rather than exact symbolic overlap.

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14.
arXiv (quant-ph) 2026-06-12

Metabolic quantum limit to the information capacity of magnetoencephalography

Authors:
E. Gkoudinakis↗S. Li↗I. K. Kominis↗

arXiv:2511.06401v3 Announce Type: replace-cross Abstract: Magnetoencephalography measures the magnetic fields generated by neural currents using quantum sensors such as superconducting quantum interference devices and atomic magnetometers. Here we combine the energy resolution limit of magnetic sensing with the metabolic power available to neural currents to derive a technology-independent bound on the information capacity of MEG. The bound factorizes into geometry, metabolism, and Planck's constant, and gives an estimated maximum information rate of 2.2~Mbit/s for representative human-brain parameters. Further, we show that the externally measurable magnetic field has a finite angular bandwidth, with high multipole components being geometrically attenuated and falling below the quantum-limited noise floor. This yields an information-limited spatial scale of order $1~cm$ and renders the accessible measurement space effectively finite-dimensional. The energy resolution limit therefore defines an information-theoretic Nyquist scale for magnetoencephalography, beyond which denser spatial sampling provides redundant measurements rather than additional recoverable information. Since the energy resolution limit also makes the noise variance grow linearly with measurement bandwidth, temporal and spatial bandwidths compete, producing a fundamental spatio-temporal trade-off. These results show how quantum-limited measurements constrain the observable complexity and information content of noninvasive brain imaging, providing a quantitative link between fundamental physics and neuroscience.

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

AI Economist Agent: An Agentic Framework for Model-Grounded Economic Analysis with RAG, Knowledge Graphs, and Large Language Models

Authors:
Masahiro Kato↗

arXiv:2606.20041v1 Announce Type: cross Abstract: We propose a model-grounded RAG-based AI economist with an agentic framework for economic scenario analysis using large language models (LLMs) and knowledge graphs. While LLMs can generate fluent economic narratives, economists are often required to make economic claims grounded by economic theory and real-world data. Based on this motivation, this study proposes an RAG-based AI economist, which utilizes knowledge graphs including economic data and theory and LLM-based agents to plan the analysis, retrieve relevant evidence, select appropriate models, and generate reports. In our framework, we do not produce quantitative claims directly with the language model alone; instead, we generate narratives grounded in explicit model-based computations and linked to the retrieved evidence via AI agents. We refer to our framework as an AI economist agent. We evaluate the AI economist agent in two applications: economist report generation for U.S. inflation persistence and Federal Reserve policy, and bank stress-test narrative generation for U.S. commercial real estate refinancing stress. The results illustrate how grounding the generated reports improves their economic coherence and traceability.

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16.
arXiv (CS.CV) 2026-06-25

FlowID : Enhancing Forensic Identification with Latent Flow-Matching Models

Authors:
Jules Ripoll↗David Bertoin↗Alasdair Newson↗Charles Dossal↗Jose Pablo Baraybar↗

Every day, many people die under violent circumstances, whether from crimes, war, migration, or climate disasters. Medico-legal and law enforcement institutions document many portraits of the deceased for evidence, but cannot immediately carry out identification on them. While traditional image editing tools can process these photos for public release, the workflow is lengthy and produces suboptimal results. In this work, we leverage advances in image generation models, which can now produce photorealistic human portraits, to introduce FlowID, an identity-preserving facial reconstruction method. Our approach combines single-image fine-tuning, which adapts the generative model to out-of-distribution injured faces, with attention-based masking that localizes edits to damaged regions while preserving identity-critical features. Together, these components enable the removal of artifacts from violent death while retaining sufficient identity information to support identification. To evaluate our method, we introduce InjuredFaces, a novel benchmark for identity-preserving facial reconstruction under severe facial damage. Beyond serving as an evaluation tool for this work, InjuredFaces provides a standardized resource for the community to study and compare methods addressing facial reconstruction in extreme conditions. Experimental results show that FlowID outperforms state-of-the-art open-source methods while maintaining low memory requirements, making it suitable for local deployment without compromising data privacy.

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17.
arXiv (CS.CL) 2026-06-25

Emergent Capabilities Arise Randomly from Learning Sparse Attention Patterns

Authors:
Vatsal Baherwani↗Zixi Chen↗Shikai Qiu↗Andrew Gordon Wilson↗Pavel Izmailov↗

Neural scaling laws for transformer language models predict smooth improvements in pretraining loss with increasing parameters, but downstream capabilities such as in-context learning are known to emerge abruptly past a certain model scale. In this paper, we show that emergent capabilities arise stochastically throughout training, with larger models acquiring them earlier on average. We demonstrate that the emergence of capabilities such as pattern completion and indirect object identification corresponds to the abrupt learning of task-relevant attention patterns. To isolate this phenomenon, we train transformer models on synthetic linear map and cellular automata datasets, and we show that the difficulty of learning attention patterns depends on context length and pattern sparsity. Moreover, scaling the number of attention heads improves learning efficiency on our synthetic tasks, while increasing the head dimension yields diminishing returns past a minimum capacity. We additionally investigate architectures with alternative attention mechanisms, showing that MLP-Mixer outperforms a transformer on linear map tasks with complex attention patterns. Our findings provide a mechanistic insight into emergence, showing that downstream capabilities arise abruptly due to the intrinsic difficulty of learning sparse attention patterns in transformer models.

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

Dynamic Free-Rider Detection in Federated Learning via Simulated Attack Patterns

Authors:
Motoki Nakamura↗

arXiv:2604.04611v2 Announce Type: replace Abstract: Federated learning (FL) enables multiple clients to collaboratively train a global model by aggregating local updates without sharing private data. However, FL often faces the challenge of free-riders, clients who submit fake model parameters without performing actual training to obtain the global model without contributing. Chen et al. proposed a free-rider detection method based on the weight evolving frequency (WEF) of model parameters. This detection approach is a leading candidate for practical free-rider detection methods, as it requires neither a proxy dataset nor pre-training. Nevertheless, it struggles to detect ``dynamic'' free-riders who behave honestly in early rounds and later switch to free-riding, particularly under global-model-mimicking attacks such as the delta weight attack and our newly proposed adaptive WEF-camouflage attack. In this paper, we propose a novel detection method S2-WEF that simulates the WEF patterns of potential global-model-based attacks on the server side using previously broadcasted global models, and identifies clients whose submitted WEF patterns resemble the simulated ones. To handle a variety of free-rider attack strategies, S2-WEF further combines this simulation-based similarity score with a deviation score computed from mutual comparisons among submitted WEFs, and separates benign and free-rider clients by two-dimensional clustering and per-score classification. This method enables dynamic detection of clients that transition into free-riders during training without proxy datasets or pre-training. We conduct extensive experiments across three datasets and five attack types, demonstrating that S2-WEF achieves higher robustness than existing approaches.

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19.
medRxiv (Medicine) 2026-06-15

Multidimensional nutritional assessment in Crohns disease: cross-sectional comparison of active disease and remission

Authors:
Sarker↗Ghosh↗C. K↗Chowdhury↗

Malnutrition is common in Crohns disease (CD), and its assessment requires multiple tools. Comprehensive evaluation of nutritional status in a population with CD, predominantly characterized by metabolic phenotype, was inadequately reported. This study evaluated the nutritional status of CD patients using anthropometric, clinical, and biochemical measures and compared patients with active disease with those in remission. This cross-sectional study included 127 adults with CD: 63 with active disease and 64 in remission. Disease activity was classified using the Crohns Disease Activity Index, the Simple Endoscopic Score for Crohns Disease, and magnetic resonance enterography. Nutritional assessment included body mass index (BMI), mid-upper arm circumference, calf circumference, triceps skinfold thickness, mid-arm muscle circumference, Mini Nutritional Assessment-Short Form (MNA-SF), and biochemical markers including hemoglobin, serum iron, folate, vitamin B12, albumin, and zinc. Malnutrition was defined using the Global Leadership Initiative on Malnutrition criteria. Overall, 47.2% of participants were malnourished. Malnutrition was significantly more frequent in active disease than in remission (81.0% vs. 14.1%, P

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20.
arXiv (CS.AI) 2026-06-25

Surrogate models for Rock-Fluid Interaction: A Grid-Size-Invariant Approach

Authors:
Nathalie C. Pinheiro↗Donghu Guo↗Hannah P. Menke↗Aniket C. Joshi↗Claire E. Heaney↗Ahmed H. ElSheikh↗Christopher C. Pain↗

arXiv:2602.22188v2 Announce Type: replace-cross Abstract: Modelling rock-fluid interaction requires solving a set of partial differential equations (PDEs) to predict the flow behaviour and the reactions of the fluid with the rock on the interfaces. Conventional high-fidelity numerical models require a high resolution to obtain reliable results, resulting in huge computational expense. This restricts the applicability of these models for multi-query problems, such as uncertainty quantification and optimisation, which require running numerous scenarios. As a cheaper alternative to high-fidelity models, this work develops eight surrogate models for predicting the fluid flow in porous media. Four of these are reduced-order models (ROM) based on one neural network for compression and another for prediction. The other four are single neural networks with the property of grid-size invariance; a term which we use to refer to image-to-image models that are capable of inferring on computational domains that are larger than those used during training. In addition to the novel grid-size-invariant framework for surrogate models, we compare the predictive performance of UNet and UNet++ architectures, and demonstrate that UNet++ outperforms UNet for surrogate models. Furthermore, we show that the grid-size-invariant approach is a reliable way to reduce memory consumption during training, resulting in good correlation between predicted and ground-truth values and outperforming the ROMs analysed. The application analysed is particularly challenging because fluid-induced rock dissolution results in a non-static solid field and, consequently, it cannot be used to help in adjustments of the future prediction.

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23.
medRxiv (Medicine) 2026-06-18

AlphaGenome identifies a deep intronic variant in a family with PLA2G6-associated neurodegeneration: Closing the diagnostic gap in rare genetic diseases

Authors:
Eger↗S. J↗Lopez↗Gomez Navarro↗L. F↗Pena-Tauber↗Cochran↗J. N↗Hiatt↗S. M↗Gelvez↗Garcia-Garcia↗…

A molecular diagnosis remains out of reach for a substantial subset of patients with clinically recognizable Mendelian disorders, even after comprehensive next-generation sequencing. Causal variants in non-coding regions are difficult to detect and interpret using standard pipelines. Deep intronic variants that disrupt splicing are a known but underexplored source of pathogenic alleles, and systematic tools to evaluate them at scale have only recently emerged. We aimed to resolve an incomplete genetic diagnosis in two siblings with early-onset parkinsonism, prominent neuropsychiatric features, and autonomic dysfunction consistent with PLA2G6-associated neurodegeneration (PLAN), an autosomal recessive condition. Prior clinical exome sequencing, genome sequencing, Multiplex Ligation-dependent Probe Amplification (MLPA), and long-read sequencing had identified only a single heterozygous PLA2G6 missense variant, c.2132C>G (p.Pro711Arg). We used AlphaGenome to score 91 non-coding variants shared among the affected siblings and their father within 1 megabase of the PLA2G6 locus. The deep-learning model identified an intronic variant (c.2034+355G>A) that was predicted to create a cryptic splice acceptor site that could result in inclusion of a 160-bp cryptic exon. Tissue-specific predictions indicated the aberrant splicing would be detectable in blood, confirmed by junction-spanning RNA-seq reads from an unrelated carrier. This analysis completed a compound heterozygous PLAN diagnosis nearly two decades after symptom onset and demonstrates the utility of sequence-to-function models. Systematic integration of tools like AlphaGenome into rare disease workflows offers a practical, low-barrier route to closing the diagnostic gap for patients with compelling Mendelian phenotypes and incomplete genetic diagnoses.

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

Multiple Descents in Deep Learning as a Sequence of Order-Chaos Transitions in LSTM Networks

Authors:
Wenbo Wei↗Fan Xu↗Nicholas Chong Jia Le↗Choy Heng Lai↗Ling Feng↗

arXiv:2505.20030v2 Announce Type: replace-cross Abstract: We observe a novel `multiple-descent' phenomenon during the learning process of a recurrent neural network called long-short-term memory (LSTM) networks during its training on real-world task, in which the performance goes through long cycles of up and down trends multiple times after the model is overtrained. By carrying out asymptotic stability analysis of the models, we found that the cycles in performance – indicated by loss function in test data – are closely associated with the phase transition process between order and chaos of the model, and the local optimal training step are consistently at the critical transition point between the two phases. More importantly, the most optimal point of the model usually occurs at the first transition from order to chaos, where the `width' of the `edge of chaos' is often the widest, allowing the best exploration of weight configurations for learning.

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

Stitching and dimensionality effects on large artificially generated volume datasets

Authors:
Lucas von Chamier↗Jan Philipp Albrecht↗Dagmar Kainm\"uller↗

Generating large images via deep learning requires patching input data to accommodate hardware memory limitations, then assembling output patches, a process that can introduce stitching artifacts when neighboring patches do not align at borders. While these artifacts are known to affect segmentation tasks, their impact on generative models for style-transfer remains poorly understood. We investigated three stitching approaches and two patch dimensionalities (2D vs 3D) using cycleGAN models trained on cryo-electron microscopy datasets. We evaluated both perceptual quality and performance on downstream mitochondria segmentation. Our key findings reveal that: (1) FID scores fail to detect subtle stitching artifacts that significantly impact downstream segmentation performance, (2) 3D models with artifact-free stitching marginally outperform 2D models on downstream tasks, though the improvement barely justifies the computational cost, and (3) 2D models train more stably due to larger batch sizes. Additionally, we demonstrate that ensembling predictions from three orthogonal directions can improve low-quality volumes but provides no benefit for high-quality outputs. These results demonstrate that maximizing generative model performance on large scientific datasets requires careful consideration and mitigation of stitching artifacts, and that perceptual metrics alone are insufficient for evaluating domain adaptation quality in biomedical imaging.

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