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01.
arXiv (CS.AI) 2026-06-16

Overcoming the Impedance Mismatch: A Theoretical Roadmap for Fusing Foundation Models and Knowledge Graphs

arXiv:2606.15656v1 Announce Type: new Abstract: Modern artificial intelligence remains fundamentally divided between the continuous, probabilistic spaces of Foundation Models and the discrete, deterministic structures of Knowledge Graphs. While Retrieval-Augmented Generation (RAG) attempts to connect them by serializing graph data into text, we argue this lexical bridging is merely a superficial patch. In this paper, we formalize the underlying structural and geometric friction as the Impedance Mismatch. By categorizing current neuro-symbolic integration strategies into a three-tiered hierarchy, we demonstrate that neither surface-level prompt injection nor continuous representation alignment can preserve the strict logical motifs required for reliable multi-hop reasoning. We define the specific mathematical limits, such as the Lexical Bottleneck and Topological Collapse, that show current architectures will eventually hallucinate or conflate semantic nodes. To achieve true semantic fusion, we propose a rigorous theoretical roadmap. We advocate for natively internalizing discrete symbolic structures through Structured Residual Streams, utilizing Vector Symbolic Architectures for latent sub-graph injection, and performing model updates via Orthogonal Subspace Editing. This actionable framework paves the way for models that seamlessly fuse the precision of symbolic logic with the expressivity of parametric memory.

02.
arXiv (CS.CV) 2026-06-16

FairGen: Preference-Aligned Diffusion for Demographically Equitable Medical Image Synthesis

Medical imaging is central to modern diagnostics, and artificial intelligence (AI) systems are increasingly used to support image-based analysis by improving efficiency, accuracy, and access to care. However, inequities in healthcare access and differential disease prevalence create severe demographic imbalances in clinical image data. Such imbalances are compounded by the fact that diseases can manifest with distinct features across demographic groups, rendering certain phenotypic presentations naturally rare. AI models trained on such imbalanced data risk perpetuating diagnostic bias and widening healthcare disparities. Here we introduce FairGen, a fairness-aware diffusion framework that synthesizes demographically balanced medical images while preserving pathology-relevant visual features. By embedding physician-aligned preferences into the generation process, FairGen improves subgroup coverage during synthesis and downstream classification. Applied to dermatology, radiology, and neuroimaging benchmark tasks, FairGen achieves fairness improvements of 95.9% for skin images, 80.0% for chest radiography, and 35.2% for brain MRI, while maintaining competitive diagnostic accuracy relative to models trained on original clinical data. Clinician-facing expert review and external validation on independent cohorts further support that these gains extend beyond standard fidelity metrics and are not confined to the original in-distribution datasets.

03.
medRxiv (Medicine) 2026-06-22

Rare loss-of-function variants in POLD1, PMS1 and FAN1 modify age at onset of motor symptoms in Huntington's disease

Huntington's disease is a rare neurodegenerative disease whose primary risk factors are inherited expansions of a CAG repeat tract in the HTT gene. Somatic expansion of these tracts leads to neuronal toxicity, neuronal death and clinical disease progression. To identify genetic factors with a major impact on disease onset and progression, we genome sequenced 18,825 individuals for the ENROLL-HD study. Our results show rare inactivating mutations in three genes, all involved in DNA damage repair, are major determinants of age of onset for motor symptoms (n=10,610) and other clinical manifestations. Heterozygote carriers of predicted loss-of-function (pLoF) variants in POLD1 and PMS1 developed motor symptoms an average 20 years (n=3; P=1x10-5) and 7 years (n=6; P=2x10-3) later than non-carriers, respectively. Conversely, heterozygote carriers of pLoF variants in FAN1 (n=30) developed symptoms 10 years earlier (P=2x10-10). Our findings highlight therapeutic strategies and help predict age of onset for at-risk individuals.

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

Sinkhorn-CPD: Robust point cloud registration via unbalanced entropic optimal transport

Coherent Point Drift (CPD) is widely used for rigid point cloud registration because of its soft correspondences and closed-form parameter updates. However, CPD's target-side marginal constraint forces every observation, including outliers, to receive exactly unit probability mass. This assumption degrades registration accuracy under heavy outliers and partial overlap. Optimal transport (OT) methods can handle missing mass through unbalanced formulations, but require hand-tuned annealing schedules. In this paper, we propose Sinkhorn-CPD, which replaces CPD's target-side marginal constraint with dual Kullback-Leibler penalties, allowing the algorithm to discard outliers on both sides. The resulting formulation is a fully unbalanced entropic optimal transport problem, which can be efficiently solved by generalized Sinkhorn iterations. Moreover, Sinkhorn-CPD preserves the closed-form Procrustes and variance updates of CPD. In our method, the variance sigma^2 plays the role of the entropic regularization parameter, which induces an automatic annealing schedule from diffuse to sharp correspondences without manual temperature tuning. Experiments on synthetic, cross-category, and scan-to-CAD benchmarks show that Sinkhorn-CPD achieves state-of-the-art accuracy, with strong robustness to outliers and partial overlap.

05.
arXiv (CS.CV) 2026-06-18

Do as I Do: Dexterous Manipulation Data from Everyday Human Videos

How can we scalably generate data for robotic manipulation, especially on human-like platforms such as dexterous multi-fingered hands? Learning from human videos has recently emerged as a likely answer to this question. However, difficulties in estimating hand-object interaction and crossing the human-to-robot embodiment gap have hindered the adoption of abundant monocular RGB-only human videos as the primary source of robot manipulation data. In this work, we present DO AS I DO, an algorithm to reconstruct and retarget monocular RGB human videos to multi-fingered dexterous robotic hands. DO AS I DO reconstructs hand-object interactions from various egocentric and exocentric in-the-wild video sources. The algorithm then retargets these hand-object interaction estimates into a sequence of actions executable in the real world, yielding robot-complete manipulation data from disparate human videos. Overall, DO AS I DO outperforms previous state of the art in estimating hand-object interactions and extracting dexterous manipulation trajectories from RGB videos, as we show in experiments on datasets with ground truths and on a dataset of video clips collected online. Our experiments enable us to propose an efficacy playbook for practitioners collecting human data for manipulation.

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

3D-PLOT-LLM: Part-Level Object Tokens for 3D Large Language Models

3D multimodal large language models (3D MLLMs) describe a 3D object as a whole but cannot address, name, or reason about its parts. Prior part-aware attempts add segmentation decoders, heavier 3D encoders, or bounding-box grammars at substantial parameter cost. We take a fundamentally different path: we reorganize the input token stream so that parts become directly addressable through the LLM's own vocabulary. Our model, 3D-PLOT-LLM, partitions the frozen point encoder's patches into K locally coherent regions and inserts, before each region's patch tokens, a learnable per-region marker and a reserved vocabulary token ; a Marker-Space Refinement (MSR) module then conditions each marker on its region's spatial statistics and adjacency neighbors. The model thus cites parts in its output and follows prompts that refer to parts by token, a capability absent from prior object-level 3D MLLMs. To probe this interface, we construct PartVerse-QA, a vocabulary-level part-QA benchmark adapted from PartVerse mesh annotations (77K training pairs and 588 held-out queries on disjoint object splits), on which 3D-PLOT-LLM reaches caption-to-slots Jaccard 0.459 and Exact-match 13.78%, with a slot-to-caption GPT-4o judge of 44.68. On the 3DCoMPaT-GrIn part-aware grounded description benchmark, 3D-PLOT-LLM outperforms PointLLM, Kestrel, PARIS3D, and SegPoint on every text-output metric, and ShapeLLM on 3 of 4, with up to +3.03 GPT-4o judge over PointLLM. On Objaverse whole-object captioning, adding PartVerse-QA at Stage 2 yields +0.65 SBERT and +1.85 GPT-4o over PointLLM, and tops PointLLM-PiSA on 4 of 5 traditional metrics (SBERT, SimCSE, BLEU-1, METEOR) despite targeting a different (part-grounded) objective. All with under 1M new trainable parameters on a frozen point encoder, an order of magnitude below prior part-aware 3D MLLMs, and no segmentation decoder or bounding-box head.

07.
arXiv (CS.CV) 2026-06-11

Wild3R: Feed-Forward 3D Gaussian Splatting from Unconstrained Sparse Photo Collection

Feed-forward 3D Gaussian Splatting (3DGS) removes the need for time-consuming per-scene optimization required by traditional 3DGS. However, existing feed-forward approaches struggle with real-world photo collections that include diverse lighting conditions and transient objects. In this paper, we present Wild3R, a feed-forward approach for unconstrained sparse photo collections. The main bottleneck is the lack of training data that provides multiple viewpoints, a variety of illuminations, and transient variations necessary for learning robust scene representations. To address this, we introduce the WildCity dataset, which comprises 200 scenes, 170 lighting conditions, and transient objects, resulting in 337,500 images in total. By leveraging the dataset, our model learns appearance consistency across viewpoints conditioned on reference views, while removing transient content. Extensive experiments demonstrate that our method outperforms existing feed-forward approaches and achieves results competitive with prior per-scene optimization-based methods.

08.
Nature Medicine 2026-06-08

Effects of SGLT2 inhibition on incident heart failure in carriers of cardiomyopathy-associated genetic variants

Although the beneficial effects of sodium–glucose cotransporter 2 (SGLT2) inhibition in heart failure (HF) have been well established, it is unknown whether SGLT2 inhibition confers benefit in carriers of rare variants in cardiomyopathy-associated genes. Here we evaluated whole-exome sequencing data from the randomized DECLARE-TIMI 58 trial, in which adults with type 2 diabetes and increased cardiovascular risk were randomized to dapagliflozin or placebo treatment. Pathogenic or likely pathogenic variants (P/LP) in high-confidence cardiomyopathy genes were identified, and treatment effects on hospitalization for HF (HHF) were compared between carriers of such variants and noncarriers. Among 12,685 patients for whom sequence data were obtained, 121 carried a cardiomyopathy variant (76 dilated cardiomyopathy, 25 hypertrophic cardiomyopathy and 25 arrhythmogenic cardiomyopathy). Over a median follow-up of 4.2 years, dapagliflozin lowered the risk of HHF more strongly in carriers (hazard ratio 0.18, 95% confidence interval 0.04–0.86) than in noncarriers (hazard ratio 0.70, 95% confidence interval 0.57–0.86; P interaction 0.03). Absolute risk reduction was 13.0% in carriers and 1.0% in noncarriers (P interaction 0.03). Most carriers (82%) had no prior HF, and in carriers without prior HF, treatment with dapagliflozin reduced the absolute risk of HHF by 12.8%, compared with a reduction of 0.6% in noncarriers (P interaction 0.01). The findings from this cohort of older and high-risk patients raise the possibility that SGLT2 inhibitor treatment should be started early to prevent HF in individuals who carry P/LP cardiomyopathy variants. These results need to be confirmed in a prospective, dedicated trial of preventive HF treatments in carriers of P/LP cardiomyopathy-associated variants. In a whole-exome sequencing analysis, the beneficial effects of the SGLT2 inhibitor dapagliflozin in reducing the risk of future heart failure hospitalization in individuals with type 2 diabetes were markedly greater in individuals who carried a cardiomyopathy-associated genetic variant compared with noncarriers, suggesting a personalized preventative therapy based on genetic information.

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

DAM-VLA: Decoupled Asynchronous Multimodal Vision Language Action model

Vision-language-action (VLA) models inherit a shared synchronous clock from vision-language pretraining, processing every input at one rate. This is misaligned with physical interaction, where a high-frequency modality changes at hundreds of hertz, vision evolves more slowly, and language stays constant across an episode. A synchronous VLA oversamples slow modalities, undersamples fast ones, and caps action generation at the lowest effective frequency. We hypothesize that decoupling temporal processing per modality, letting each update and retain information at its own sensor rate, yields stronger representations and more robust control. We present DAM-VLA, which maintains per-modality latent buffers refreshed at sensor rates and read continuously by the action head, integrating new high-frequency modalities through gated cross-attention that leaves the pretrained backbone intact. Across seven contact-rich real-world manipulation tasks, DAM-VLA more than doubles the average success rate of the strongest synchronous baseline (95.2\% vs.\ 40.95\%) while sustaining smooth, reactive 100\,Hz control. Project website: \href{https://intuitive-robots.github.io/DAM-VLA/}{intuitive-robots.github.io/DAM-VLA/}

10.
arXiv (CS.AI) 2026-06-17

IsabeLLM: Automated Theorem Proving Applied to Formally Verifying Consensus

arXiv:2606.18098v1 Announce Type: new Abstract: Advances in Artificial Intelligence (AI) have led AI for Theorem Proving to become a promising means of formally verifying computer systems. Whilst formal verification is traditionally reserved for safety-critical systems due to the required amount of expertise and effort, AI can help to automate a large amount of this workload and make it far more accessible. Blockchain-based systems are becoming increasingly popular and are frequently targeted by malicious actors, often resulting in huge financial losses, highlighting the need to better verify these systems and mitigate vulnerabilities. Arguably the most important component of these systems is the consensus protocol, which allows nodes to agree on decisions in a potentially adversarial environment. In this paper, we improve upon IsabeLLM, the automated theorem proving tool in Isabelle. Namely, we implement a Retrieval-Augmented Generation framework, Error tracing and counterexample generation for improved context supplied to the Large Language Model. Compatibility with the latest version of Isabelle and Sledgehammer is also implemented for improved efficiency. We compare the performance of the two versions of IsabeLLM in their ability to complete the verification of Bitcoin's Proof of Work consensus.

11.
arXiv (CS.CL) 2026-06-24

Meet UD_Czech-PDTC: A Large and Genre-Rich Treebank in Universal Dependencies

Czech has been part of Universal Dependencies since its first release in 2015. It has also been one of the best represented languages, with the Prague Dependency Treebank being order of magnitude larger than most other UD treebanks. More recently, three other datasets from the Prague family were added and the annotations thoroughly revisited, forming the "Prague Dependency Treebank-Consolidated" (PDT-C). In comparison to the original PDT, PDT-C is more than twice as large, but it is also much more diverse in terms of genres and domains. In this paper, we describe the conversion of the new resource to Universal Dependencies. While the two annotation schemes are relatively similar at the first sight, there are numerous small differences in topology of the dependency structures and in granularity of the POS and relation type inventories. We demonstrate a selection of such differences on examples, discuss the diverging motivations, as well as ways to overcome the differences during conversion. We argue that while PDT is less "universal" and more tightly bound to one language, its multi-layer annotation is rich and provides all information needed for basic UD trees, and much more.

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

Recurrent neural networks approximate continuous functions

arXiv:2606.20325v1 Announce Type: new Abstract: Classical approximation theorems ask for a new neural network whenever the target accuracy is improved. This paper studies the opposite possibility: can the network be chosen once and for all, and can accuracy be bought only by letting it run longer? We prove that this is possible for every continuous function on [-1,1]. More precisely, each such function is uniformly approximated by the time evolution of a single ReLU recurrent neural network with fixed weights and fixed hidden dimension. The mechanism behind the construction is a new intermediate model, the Turing machine with neural units (TMNU). This model retains the algorithmic freedom needed to implement polynomial approximation schemes, while remaining rigid enough to be simulated by RNNs with explicit bounds on hidden dimension and weight magnitude. The resulting convergence rates reflect the underlying polynomial approximation rates. We complement the construction with minimax lower bounds showing that runtime is not merely a proof artifact, but an unavoidable resource in this fixed-network approximation paradigm.

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

Active Reference Acquisition in Few-Shot Font Generation

Few-shot font generation aims to synthesize the remaining glyphs of a font given one or a few reference glyphs while preserving stylistic consistency, thereby supporting font designers in efficiently completing a typeface. Existing methods primarily focus on improving generation quality given a fixed reference set. However, when the current reference glyphs are insufficient to represent the target style, few-shot font generation may fail to produce satisfactory results. In practical scenarios, additional reference glyphs can often be obtained from the designer when necessary. Accordingly, we propose a new framework, Active Reference Acquisition in Few-Shot Font Generation, in which the model sequentially decides which character to acquire next as an additional reference. Furthermore, we propose a reference part-coverage-based acquisition function to efficiently query the designer. Motivated by the observation that font styles are well characterized by local structural parts, we represent each glyph using a histogram of local features and select query characters that maximize the expected part coverage of the reference set. By prioritizing characters that contain parts not yet covered by the current references, the proposed method progressively expands the diversity of visual parts in the reference set. As a result, generation quality is improved with fewer queries. Experiments on the Google Fonts dataset demonstrate that the proposed method achieves higher generation quality than random querying and reference-agnostic baselines. The code is available at https://github.com/matsuo-shinnosuke/ActiveRef-FontGen.

14.
arXiv (CS.AI) 2026-06-15

Adversarial Concept Search: Predicting Compositional Errors From Feature Geometry

arXiv:2606.13934v1 Announce Type: new Abstract: Humans cannot always intuit what scenarios are most challenging to LLMs. Hoping to capture challenging edge cases, developers either design problems to be difficult for humans or curate extensive benchmarks. What if we could instead anticipate which scenarios a model will fail on? In this paper, we use an LLM's representational geometry to predict which concept combinations it will fail on. We attribute this compositional failure to interference between salient features. In tasks that require systematic composition - toy programmatic settings, multihop reasoning, multilingual factual recall - we find that when a pair of concepts is encoded near-orthogonally, the model reliably composes them. When their linear encodings are close, producing interference, the model fails to compose them. Our method reliably anticipates failure modes across different compositional tasks, without evaluating specific inputs. These results lay the groundwork to use representational geometry to identify high-risk examples, construct targeted stress tests, and provide a scalable foundation for active learning in real-world deployment.

15.
arXiv (quant-ph) 2026-06-17

Variational Quantum Eigensolver-Based Quantum Bootstrap Embedding for Molecules

作者:

arXiv:2606.17095v1 Announce Type: cross Abstract: Simulating strongly correlated molecular systems on near-term quantum hardware remains challenging due to modern hardware's limited quantum volume and moderate-fidelity qubits. One potential way to circumvent this challenge is through bootstrap embedding (BE). Bootstrap embedding breaks molecules into smaller fragments that are then embedded into the "bath" of other fragments in an iterative way. Bootstrap embedding is appealing for quantum simulation because fragmenting the system reduces the qubit requirements for any given fragment. In this work, we develop a quantum bootstrap embedding (QBE) workflow that uses variational quantum eigensolver (VQE) fragment solvers and study the algorithmic choices that determine the overall VQE-QBE algorithm's success. To improve efficiency, we introduce FastAdaptVQE, a sparse matrix-accelerated form of the adaptive variational quantum eigensolver (ADAPT-VQE) that replaces symbolic commutator evaluation with direct statevector linear algebra, and MatrixFreeAdaptVQE, a matrix-free extension that removes the sparse-matrix memory bottleneck that appears when treating larger fragments. We also modify the ADAPT-VQE operator selection step by replacing the purely greedy choice with a look-ahead strategy. Benchmarks on $H_4$ and $F_2$ reach chemical accuracy, within 1 kcal/mol of bootstrap embedding results using a full configuration interaction (FCI) solver. These results show that combining QBE with VQE can accurately calculate energies of molecular systems. This research lays the foundation for extending energy calculations to larger molecular systems and quantum materials on near-term quantum hardware.

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

Beyond the GUI Paradigm: Do Mobile Agents Need the Phone Screen?

Recent advances in mobile agents are dominated by the GUI paradigm, in which agents perceive UI information and emit screen interactions. However, mobile platforms also expose a command-line interface (CLI) that provides direct access to device services and data. We argue CLI deserves first-class consideration alongside GUI. We evaluate three coding agents (Claude Code, Terminus-2, mini-swe-agent) across four model APIs on AndroidWorld and MobileWorld without any mobile-specific post-training, comparing against three reproducible GUI baselines (GUI-Owl-1.5-32B, MAI-UI, Qwen3-VL-32B). Claude Code (Opus 4.7) reaches 71.8\% and 51.9\%, outperforming every reproducible GUI baseline (69.3/68.1/57.8\% on AndroidWorld; 43.2/26.3/13.3\% on MobileWorld), while every other CLI configuration remains competitive. To establish the paradigm's ceiling, we provide oracle CLI solutions that reach 88.8\% on AndroidWorld (103/116 tasks CLI-solvable) and 86.3\% on MobileWorld (101/117 tasks CLI-solvable), indicating substantial room for future improvement. To cover everyday user intents beyond the GUI scope, we introduce the CLI-Advantage Task Suite, comprising 45 templates across five categories: bulk operations, multi-condition filtering, aggregation, cross-app workflows, and hidden device state. Every CLI agent outperforms every GUI baseline in all five categories, with substantially fewer steps per task (10.7 vs.\ 18.6). To support future research on mobile CLI agents, we will open-source agent implementations, oracle solutions, the CLI-Advantage suite, and evaluation infrastructure.

17.
arXiv (quant-ph) 2026-06-11

Planted-Solution Pauli Hamiltonians as a Quantum Benchmarking Primitive

arXiv:2606.11455v1 Announce Type: new Abstract: We introduce a construction of Pauli Hamiltonians with exactly known ground-state energies, intended as reference instances for ground-state energy estimation algorithms. The construction embeds a planted block-product state as the simultaneous ground state of a sum of frustration-free local clauses on overlapping supports, exposes the resulting model only as a polynomial-size linear combination of Pauli operators, and admits optional Clifford conjugation that preserves the spectrum. The framework subsumes classical planted constraint-satisfaction problems as a diagonal special case, providing a direct embedding channel through which classical hardness properties can be inherited. Open-source software, certification keys, and example instances are made publicly available.

18.
arXiv (quant-ph) 2026-06-12

Non-invertible symmetries out of equilibrium: Eigenstate order and Floquet physics

arXiv:2508.14213v2 Announce Type: replace-cross Abstract: Through the study of the Rep($D_8$) non-invertible symmetry, we show how non-invertible symmetries manifest in dynamics. Results are presented for dynamics generated by Hamiltonians as well as Floquet unitaries. For both examples, the role of the non-invertible symmetry is studied through the appearance of non-invertible symmetry protected edge modes. In addition, the role of the non-invertible symmetry for the Hamiltonian is studied through eigenstate order. In particular, by considering the effect of symmetry preserving disorder, the non-invertible symmetry is shown to give rise to degeneracies in the spectra of the Hamiltonian that can only be completely lifted at orders of perturbation that scale with system size. The eigenstates of disordered Hamiltonians, whose ground state correspond to non-trivial symmetry protected topological (SPT) states, are shown to have either trivial or non-trivial SPT order that are detected as non-zero expectation value of string order-parameters. In contrast, non-trivial SPT order is absent in the eigenstates of trivial SPT Hamiltonians with disorder. The interface between two different SPT phases host edge modes whose dynamics is studied numerically and analytically. The edge mode is shown to oscillate at frequencies related to different effective chain lengths that are weighted by the temperature, becoming an exact zero mode in the limit of zero temperature. A Floquet model with the non-invertible symmetry is constructed whose edge mode is shown to exhibit period-doubled dynamics at low effective-temperatures. The zero and period-doubled edge modes differ from those in conventional SPTs by being symmetric under the invertible symmetry, while being charged under the non-invertible symmetry.

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

KEPLA: A Knowledge-Enhanced Deep Learning Framework for Accurate Protein-Ligand Binding Affinity Prediction

arXiv:2506.13196v5 Announce Type: replace Abstract: Accurate prediction of protein-ligand binding affinity is critical for drug discovery. While recent deep learning approaches have demonstrated promising results, they often rely solely on structural features of proteins and ligands, overlooking their valuable biochemical knowledge associated with binding affinity. To address this limitation, we propose KEPLA, a novel deep learning framework that explicitly integrates prior knowledge from Gene Ontology and ligand properties to enhance prediction performance. KEPLA takes protein sequences and ligand molecular graphs as input and optimizes two complementary objectives: (1) aligning global representations with knowledge graph relations to capture domain-specific biochemical insights, and (2) leveraging cross attention between local representations to construct fine-grained joint embeddings for prediction. Experiments on two benchmark datasets across both in-domain and cross-domain scenarios demonstrate that KEPLA consistently outperforms state-of-the-art baselines. Furthermore, interpretability analyses based on knowledge graph relations and cross attention maps provide valuable insights into the underlying predictive mechanisms.

20.
medRxiv (Medicine) 2026-06-12

An integrative multi-omics framework identifies epigenetic dysregulation of HAND2 as a potential primary driver of impaired enteric neural crest cell differentiation in Hirschsprung Disease

Hirschsprung disease (HSCR) is a congenital neurodevelopmental disorder characterized by segmental aganglionosis due to impaired developmental processes of enteric neural crest cells (NCCs). Despite being the leading genetic cause of functional intestinal obstruction in early childhood, HSCR represents a paradigmatic challenge in precision medicine: its multifactorial etiology, complex gene-environment interactions and limited resolution of single-modality analyses have long hindered mechanistic understanding and therapeutic translation. Here, we applied an integrative multi-omics approach combining genetic, phenotypic, epigenomic and transcriptomic analyses of matched ganglionic and aganglionic formalin-fixed paraffin-embedded (FFPE) patient tissues, complemented by patient-specific in vitro models. Beyond established genetic contributors, our integrative approach reveals novel regulatory pathways predominantly affecting enteric NCC differentiation, with convergent evidence pointing to epigenetic dysregulation as a primary disease mechanism. Notably, we identified over 1,300 differentially methylated positions between ganglionic and aganglionic FFPE samples, with HAND2 emerging as a key candidate due to multiple hypermethylated sites and consistently reduced expression levels in aganglionic tissues and in vitro models, suggesting a potential role in HSCR pathophysiology. We propose that our multi-omics approach offers a powerful and comprehensive framework for dissecting disease mechanisms. Beyond advancing biological understanding, this strategy holds promise for paving the way for molecularly informed patient stratification and supporting the development of personalized treatment and postoperative management strategies.

21.
arXiv (CS.CL) 2026-06-11

When Probing Accuracy Saturates, Fragility Resolves: A Complementary Metric for LLM Pre-Training Analysis

Standard linear probing declares a property "encoded" when a classifier on hidden states achieves high accuracy. The protocol works well on a snapshot but breaks across pre-training: probe accuracy saturates within the first few thousand steps, leaving most of training invisible to the instrument. We introduce fragility, a complementary per-layer metric defined as the activation-noise level at which probe accuracy collapses. Fragility is sensitive to both the margin of separability and the redundancy of representation, both of which keep evolving long after accuracy plateaus. Applied to open-checkpoint language models, fragility recovers structure that accuracy alone cannot see. Moralized representations emerge along a lexical $\to$ compositional gradient: lexical moral detection first, compositional moral encoding later. Because probe accuracy on its own tracks how lexically separable a dataset is, we establish the compositional encoding directly, by showing it transfers across construction types that share no contrast tokens. A layer-depth robustness gradient develops monotonically across training while accuracy stays flat. And matched fine-tuning corpora that produce identical probing accuracy leave distinct fragility fingerprints, showing that data curation reshapes probe robustness without changing probe accuracy. In every comparison we test, where probing accuracy returns a flat answer, fragility returns a structured one.

22.
arXiv (quant-ph) 2026-06-16

Reconstruction of detector error model for quantum error correction

arXiv:2606.16288v1 Announce Type: new Abstract: Fault-tolerant quantum computing fundamentally relies on the accurate characterization of circuit-level noise to optimize decoding algorithms. However, extracting complex multi-body error correlations remains challenging. Contemporary greedy inference algorithms can suffer from statistical distortion, discarding true physical mechanisms while introducing many unphysical false positives. Here, we introduce the Correlation-Analysis-based Hypergraph Reconstruction (CAHR) algorithm, a globally consistent framework to invert experimental syndrome statistics directly into discrete physical hypergraphs. By coupling exact algebraic correlation equations with a top-down concurrent-pruning strategy, CAHR recovers the fault topology without false positives for both $d=5$ rotated surface codes and dense 8-body 2D color codes in our benchmark settings. Furthermore, we show that exact continuous parameter extraction in dense codes is limited by a variance cascade, where absolute statistical variance accumulates linearly from high- to low-degree mechanisms. This motivates a two-stage inference paradigm: utilizing CAHR to extract the fault topology, followed by continuous probability optimization. This provides a practical approach for characterizing and decoding highly correlated noise in realistic quantum hardware.

23.
arXiv (CS.AI) 2026-06-16

Learning in the Recurrent State: Gradient Descent with Linear Recurrent Networks

arXiv:2410.11687v3 Announce Type: replace-cross Abstract: Linear recurrent networks (LRNNs) offer linear-time sequence modeling, but standard recurrent updates do not directly expose the supervised products needed for in-context gradient descent. We propose a sufficient constructive inductive bias for LRNNs: equip a diagonal recurrent state with multiplicative readout and a short sliding-window cross-product self-attention update. The resulting architecture, Gradient-based Recurrent In-context Learner (GRIL), can implement minibatch gradient descent on a task-specific linear predictor during a single forward pass. The same design extends to multi-step updates and cross-entropy classification, with a limited MLP-based extension to non-linear regression. Empirically, trained GRILs recover the behavior and parameters predicted by the construction on synthetic ICL tasks, and the same architectural bias yields useful performance on Long Range Arena and language modelling. These results present windowed cross-product self-attention as a practical, testable inductive bias for LRNNs that learn in context through gradient-descent-like updates.

24.
arXiv (quant-ph) 2026-06-24

Quantum turbulence in the many-body regime

arXiv:2606.23822v1 Announce Type: cross Abstract: We discuss phenomenology associated with turbulent hydrodynamics in quantum fluids from a condensed-matter perspective. We begin with weakly-interacting superfluids, often modeled by a mean-field theory governed by the Gross-Pitaevskii equation. Considering the effect of quantum fluctuations beyond the mean-field approximation, we propose a study of many-body quantum effects in turbulent hydrodynamics, especially near zero temperature. We motivate examples of quantum many-body systems where such effects may be uncovered. These include bosons confined in a periodic potential in low spatial dimensions (one and two), and the associated quantum critical point of the superfluid-insulator transition, realized in present-day ultracold-atom and quantum computing platforms. We conclude by listing a set of (open) questions that may be answered using modern quantum many-body techniques. This article is part of the theme issue 'Frontiers of turbulence and statistical physics'.

25.
bioRxiv (Bioinfo) 2026-06-22

From hotspot dependence to distributed robustness in resistance-aware lead optimization

Drug resistance remains a recurrent failure mode in targeted anticancer and antiviral therapy, and resistance evidence often enters only after compound selection. ResistAgent is an evidence-constrained framework that converts mutational liabilities into design-time objectives through site- and combo-aware resistance mapping, deterministic mechanism diagnosis and robust counter-design. In EGFR-Erlotinib and HIV-RT-Rilpivirine, the framework separated residue-level liabilities from observed HIV combination liabilities and linked prioritized mutations to anchor loss, pocket rearrangement, electrostatic shifts and contact redistribution. Same-budget paired searches showed that robust objectives changed lower-tail mutant-panel behavior and interaction-dependence profiles while prioritizing robustness over average-affinity behavior. Under predefined liability panels, selected robust-best trajectories shifted support away from mutable hotspot contacts toward more distributed interaction networks. Supplementary physical summaries and ranking-first benchmarks support the scope of this resistance-aware design strategy while preserving clear boundaries for prospective validation.