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01.
arXiv (CS.CL) 2026-06-11

When More Documents Hurt RAG: Mitigating Vector Search Dilution with Domain-Scoped, Model-Agnostic Retrieval

Retrieval-augmented generation degrades when scaled to large, heterogeneous document collections, where dense similarity loses discriminative power, and top-k retrieval increasingly returns semantically similar but contextually incorrect chunks. We refer to this failure mode as vector search dilution. Even when using hybrid dense+sparse retrieval, we observed this firsthand in a deployed Wyoming Department of Transportation corpus, where scaling from 54 to 1,128 documents (88,907 chunks) reduced accuracy from 75% to below 40%. To address this dilution, we propose MASDR-RAG ( Multi-Agent Scoped Domain Retrieval for RAG) and evaluate it on 200 expert-validated queries across five LLM backbones, six corpora, and two index stacks. Our results indicate that domain scoping using organizational metadata is the key fix, significantly improving P@10 from 0.77 to 0.86 ($p < 0.05$). Furthermore, our investigation of multi-agent orchestration revealed that a high degree of configuration dependence results –creating what we call the precision-faithfulness paradox. Based on these varied outcomes, our practical recommendation is simple: scope first, then perform a single synthesis call, reserving full multi-agent orchestration for genuinely multi-domain corpora paired with native-tool-call backbones. Code and Data will be made public upon acceptance.

02.
arXiv (CS.AI) 2026-06-19

Frequency-Aware Flow Matching for Continuous and Consistent Robotic Action Generation

arXiv:2606.20135v1 Announce Type: cross Abstract: Flow matching has emerged as a standard paradigm for robotic manipulation owing to its strong expressive power for modelling complex, multimodal action distributions, alongside similar approaches like diffusion policy. However, existing methods rely on discretized action chunks, making them brittle to demonstrations collected at heterogeneous control frequencies and prone to temporally inconsistent actions that degrade control stability. In this paper, we propose Frequency-Aware Flow Matching (FAFM), which outputs continuous, temporally consistent actions. To handle heterogeneous frequency input, we transform discrete action sequences into the frequency domain with the discrete cosine transform (DCT), perform flow matching over the resulting coefficients, and reconstruct continuous actions via cosine basis expansion. To generate temporally consistent actions, we regularize the first-order temporal derivative to promote smooth actions. This corresponds to a Sobolev-type constraint that suppresses high-frequency errors and discourages abrupt action changes. Our FAFM is simple, introduces no additional network parameters and applies to standalone flow-matching policies and vision-language action models. Across synthetic toy benchmark, obstacle avoidance, LapGym, and LIBERO, FAFM improves success rates, multimodal expressivity, motion smoothness, convergence speed, robustness to mechanical bias and mixed-frequency input. These gains are consistent when deployed on a real-world Franka robot. Code available at https://anonymous.4open.science/r/FAFM.

03.
arXiv (CS.LG) 2026-06-19

The Token Is a Group Element: On Lie-Algebra Attention over Matrix Lie Groups

arXiv:2606.20547v1 Announce Type: new Abstract: We place the attention token on the group: a token is an element $g_i$ of a matrix Lie group $G$ – a bare transformation, with no feature payload and no external action $\rho(g)$ carrying it. To our knowledge this is the first attention construction whose tokens are bare matrix Lie group elements: their score is the closed-form algebra norm of the relative pose rather than a learned kernel, and it reaches the affine full-frame groups that every irrep- or surjective-exp-based method must exclude. We call it Lie-Algebra Attention. Once tokens are group elements, the rest follows with none of the usual representation-theoretic machinery. The relative geometry of a pair is canonical, $g_i^{-1} g_j$, so the pairwise invariant $w_{ij} = \log(g_i^{-1} g_j)$ is intrinsic rather than designed; equivariance under the diagonal $G$-action is tautological, and the cocycle condition holds automatically. The attention score is the negative squared algebra norm, $s_{ij} = -\|\log(g_i^{-1} g_j)\|_\lambda^2/\tau$: the canonical proximity kernel under a block-weighted Frobenius inner product, with no irreducible representations, spherical harmonics, Clebsch-Gordan products, or learned kernel. The construction applies to any matrix Lie group on a chosen logarithm chart containing the relative poses, including the non-compact non-abelian affine groups with scale and shear that no vector-token attention method reaches: neither the irrep tradition nor surjective-exp methods. Three sequence-completion experiments, on SE(2), SO(3), and Aff(2), bear this out: the closed-form score matches a learned MLP kernel on the same invariant and outperforms it on SE(2), using 50 to 80x fewer score parameters, while a vector-token baseline breaks invariance by five to twelve orders of magnitude.

04.
arXiv (math.PR) 2026-06-11

Stochastic Reaction Networks Within Interacting Compartments with Content-Dependent Fragmentation

arXiv:2511.10223v4 Announce Type: replace Abstract: Stochastic reaction networks with mass-action kinetics provide a useful framework for understanding processes – biochemical and otherwise – in homogeneous environments. However, cellular reactions are often compartmentalized, either at the cell level or within cells, and hence non-homogeneous. We investigate a model of compartmentalization in which the rate of fragmentation of a compartment depends on the abundance of some designated species inside that compartment. The particular model of study is part of a general framework for compartmentalized chemistry with dynamic compartments that was proposed in (Duso and Zechner, PNAS, 2020). This paper builds on (Anderson and Howells, Bull. Math. Biol., 2023) where the special case where the compartment dynamics do not depend on their contents was studied mathematically. In particular, we demonstrate that the explosivity characterization from (Anderson and Howells, Bull. Math. Biol., 2023) fails in this setting and provide new sufficient conditions for non-explosivity and positive recurrence, under the assumption that the underlying CRN admits a linear Lyapunov function. These results extend the theoretical foundation for modeling content-mediated compartment dynamics, with implications for systems such as cell division and intracellular transport.

05.
arXiv (CS.CL) 2026-06-15

Beyond Perplexity: UTF-8 Validity in Byte-aware Language Models

Byte-level tokenization enables language models to handle any Unicode input, but models can generate invalid UTF-8 sequences when encountering rare or unseen characters. We investigate the relationship between training scale and UTF-8 generation reliability with a 355M parameter model trained on 80B tokens from a balanced multilingual corpus of English, Japanese, Korean, and Chinese. We introduce multiple evaluation protocols that isolate UTF-8 structural validity from language modeling. UTF-8 validity convergence lags perplexity by a roughly a factor of two: perplexity stabilizes after 2.1B tokens, but UTF-8 validity requires 4.2B tokens. In context-free generation, rare characters achieve higher structural validity than common characters, suggesting over-specialization of frequent character representations. Through experiments, we observed that reliable UTF-8 generation is a distinct capability requiring evaluation beyond perplexity.

06.
medRxiv (Medicine) 2026-06-18

Rare Coding Variants Reveal Distinct Genetic Architectures Across Multidimensional Sleep Phenotypes

Sleep and circadian traits have been widely studied using common variants, but the contribution of rare coding variation remains unclear. We analyzed rare coding variants in 397,065 whole-exome sequenced UK Biobank participants across 36 sleep phenotypes from self-report, diagnoses, sleep medication use and accelerometry, and meta-analyzed results with 171,536 whole-genome sequenced All of Us participants of diverse ancestries, with replication in the Mass General Brigham Biobank (N = 31,275). We identified 260 genes associated with sleep phenotypes, including novel associations with sleep medication use in 29 genes and 24 out of 29 have not previously been reported with any sleep phenotypes. We observed modest but significant rare variant heritability and strong genetic correlations between sleep medication use, insomnia and fatigue. Temporal gene expression trajectory analyses indicate that genes associated with self-reported sleep traits show constant high prenatal expression, whereas genes linked to sleep medication phenotypes exhibit peak expression in the late prenatal period. These findings highlight distinct biological mechanisms captured by different measurement sources of sleep phenotypes and reveal rare-variant-informed targets for therapeutic discovery.

07.
bioRxiv (Bioinfo) 2026-06-16

Evidence for recombination in dengue virus genomes

Recombination is a key driver of RNA virus evolution, yet its extent and evolutionary implications in dengue virus (DENV) remain incompletely understood. We conducted a comprehensive, genome-wide recombination screen across 6,905 complete DENV genomes representing all four serotypes, 82 countries, and eight decades of sampling (1944-2023) retrieved from the Bacterial and Viral Bioinformatics Resource Center. Using seven complementary recombination detection methods implemented in RDP5, we identified 66 recombination events across 53 unique recombinant sequences, of which 29 are newly described. Events included intra-genotypic (n = 18), inter-genotypic (n = 32), and inter-serotypic (n = 16) exchanges spanning 14 genotypes and four continents, with no meaningful serotype-level enrichment (Cramer's V = 0.054). Recombination was concentrated in non-structural genes, most frequently NS3 (19 events), NS5 (17), and NS2 (12), while the capsid gene contained no recombination events, consistent with strong functional constraint. Single-nucleotide polymorphism analyses confirmed low divergence between recombinants and their inferred parents in both recombinant and non-recombinant regions. Phylogenomic analysis of 6,642 sequences revealed that recombinants cluster significantly closer to their major parents (p = 8.9 x 10-6 ) and that their removal does not significantly alter tree topology (p = 0.898), suggesting that the short length of recombinant regions limits phylogenetic conflict. We also introduce RECOSIM, an unsupervised machine-learning tool for recombination detection that achieved higher precision than RDP5 on both simulated (93.4% vs. 80.0%) and empirical (98.1% vs. 39.3%) datasets. Collectively, these results establish recombination as a widespread, pan-serotypic phenomenon in DENV with implications for genomic surveillance, vaccine evaluation, and evolutionary inference.

08.
arXiv (CS.AI) 2026-06-15

CADET: Physics-Grounded Causal Auditing and Training-Free Deconfounding of End-to-End Driving Planners

Authors:

arXiv:2606.14438v1 Announce Type: cross Abstract: End-to-end (E2E) autonomous-driving planners trained by imitation are prone to statistical shortcuts: they associate scene elements that merely co-occur with expert actions (a roadside object, a building facade) with driving decisions, rather than the variables that causally determine them. Such causal confusion silently compromises reliability in long-tail scenarios, and it is difficult to detect, because prevailing open-loop metrics (L2 displacement and collision rate) are dominated by ego status and do not indicate whether a planner depends on spurious cues. Existing remedies based on causal-intervention training require retraining large models and cannot audit a planner that is already deployed. We present CADET, a training-free framework that audits, benchmarks, and repairs spurious reliance in pretrained E2E planners without any parameter update.

09.
arXiv (CS.LG) 2026-06-24

Adversarial dynamical systems characterize when data-driven learning succeeds or fails

arXiv:2407.06312v2 Announce Type: replace-cross Abstract: Many systems resist analytical modeling, making data-driven inference of dynamics important. Yet data-driven methods can fail to converge or generalize, leaving open a central question: When can system behavior be learned reliably from data, and when is such learning impossible? We answer this question using adversarial dynamical systems to identify the boundary between accessible and inaccessible regimes. In Koopman operator learning, a leading framework for representing nonlinear dynamics through linear spectral objects, we design optimal data-driven spectral algorithms with convergence and certification guarantees under conditions arising broadly in physical systems. This yields a convergence theory for Koopman-operator approximations and resolves a longstanding open problem in Koopman spectral analysis. Conversely, by constructing adversarial systems, we prove matching impossibility results: without these conditions, no single-sequence limiting procedure can guarantee learning, regardless of data quality. These results sharply characterize when data-driven spectral learning can succeed and when it must fail. We validate the framework on oscillators, chaotic fluid flows and Arctic sea ice concentration forecasting. In the latter, we uncover hidden modes of Arctic sea ice decline, deliver long-range forecasts with geographic error bounds, and outperform state-of-the-art dynamical and deep learning models at substantially lower computational cost, enabling real-time deployment on standard CPUs.

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

LLM Features Can Hurt GNNs: Concatenation Interference on Homophilous Graph Benchmarks

Adding LLM-generated node features to graph neural networks (GNNs) is widely reported to improve accuracy on standard benchmarks. We document a contrasting observation: when LLM features are introduced through pure input concatenation (rather than joint training, distillation, or prompt-conditioning), they can systematically degrade accuracy on the same homophilous benchmarks where end-to-end LLM pipelines succeed. With an MLP backbone on the Planetoid public split and bag-of-words original features, concatenating SBERT-encoded GPT-4o-mini TAPE features reduces PubMed test accuracy by -17.0 +/- 0.3 pp and Cora by -4.3 +/- 0.6 pp (CiteSeer -0.6 +/- 0.8 pp, within seed noise). The drop attenuates as we relax each condition (GCN / GCNII / GAT backbones, random splits, smaller encoders) and reverses on medium-homophily WikiCS (+4.4 pp) and ogbn-arxiv (+11.7 pp). To predict when concatenation helps versus hurts, we report a simple measure of LLM-alone discriminability, Delta_sig. Across 9 datasets Delta_sig correlates with the concatenation cost more strongly than homophily at point estimate (r^2 = 0.38 vs. 0.06; N=9, bootstrap CIs overlap). The bootstrap-best change-point is tau = 13.8 pp, and the rule "Delta_sig

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

Integrated Sensing and Communications for Real-time Avatar Control in XR over 5G

arXiv:2606.23771v1 Announce Type: cross Abstract: Extended Reality (XR) presents a challenging use case for 5G and 6G networks, requiring high data-rates and lowlatency communication to deliver a truly immersive experience. Moreover, in order to seamlessly translate physical actions to the virtual world, accurate gesture recognition and pose estimation are required. Current XR interaction solutions based on handheld controllers and cameras cannot easily capture full-body poses, inhibit the free use of hands, and require good visibility and a clear line of sight. In this work, we propose a multimodal sensing architecture for XR that combines 5G MillimeterWave (mmWave) Integrated sensing and communication (ISAC) and surface electromyography (sEMG) signals. 5G mmWave ISAC cannot only be used to deliver content wirelessly to the Head-mounted display (HMD), but also the same communication signals can be used to derive coarse body-level gestures and poses of the user, to support real-time avatar control. For fine-grained finger-level gestures, our architecture leverages lightweight sEMG sensors that capture forearm muscle activity. To illustrate the need of both modalities, we present evaluations of both sensing technologies. At the body level (5G), our architecture relies on power-per-beam-pair (PPBP), which can be computed from standard beam management or beam sweeping procedures of the 5G NR standard. PPBP-based sensing achieves 82.2$\pm$5.9% average accuracy when evaluated on users not seen during training. For fine-grained finger-level interactions, we show that surface electromyography (sEMG) carries strong discriminative information achieving consistent promising performance across different movement settings. Thus, combining the two modalities enables multi-scale gesture recognition, at the body level via existing 5G signals and finger level via lightweight sEMG sensors, forming a complete XR framework.

12.
arXiv (math.PR) 2026-06-11

Construction of ergodic IDLA forests in $\mathbb{Z}^d$

arXiv:2506.10476v2 Announce Type: replace Abstract: We prove the existence of infinite-volume IDLA forests in $\mathbb{Z}^d$ , with $d \geq 2$, based on a multi-source IDLA protocol. Unlike IDLA aggregates, the laws of the IDLA forests studied here depend on the trajectories of particles, and then do not satisfy the famous Abelian property. Their existence is due to a stabilization result (Theorem 1.1, our main result) that we establish using percolation tools. Although the sources are infinitely many, we also prove that each of them play the same role in the building procedure, which results in an ergodicity property for the IDLA forests (Theorem 1.2).

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

Decomposing one-class support vector machine into an ensemble of one-data support vector machines

arXiv:2606.16002v1 Announce Type: new Abstract: One-class classification (OCC) is a classification problem in which the training data contains only one class. The one-class support vector machine (OCSVM) is one of the most competitive OCC algorithms. However, OCSVM has scalability issues with large-scale datasets. This paper proposes the acceleration strategy of OCSVM. The idea is to decompose the dataset into samples and train OCSVM models for single data points. Subsequently, ensemble learning is applied to combine all models to compute the OCSVM model for the dataset. In addition, further acceleration is achieved through a data-reduction strategy with an OCSVM model trained on the average of the training samples. The experiment compared the proposal and traditional OCSVM using the Python package. The proposed strategy is faster than traditional OCSVM, while achieving similar classification results. Moreover, the proposed strategy can create one-to-one correspondence between samples and models. Source code is uploaded at https://github.com/ToshiHayashi/ODSVM

14.
bioRxiv (Bioinfo) 2026-06-20

RNAStabFormer: Region-Aware Multi-Task Hybrid Learning for RNA Stability Prediction from Pulse-Chase Transcriptomics

Authors:

RNA stability is a central layer of post-transcriptional gene regulation, yet large-scale stability labels derived from pulse-chase transcriptomics depend strongly on quantification region, time-window definition, and replicate quality control. We present RNAStabFormer, a controlled learning framework for predicting human RNA stability proxies from transcript sequence. Its core model, RAMHT, combines region-specific nucleotide Transformer encoders for CDS, and sequence, a CDS codon stream, engineered sequence-grammar features, gated fusion, and four task-specific regression heads. We construct four strict consensus labels from ENCODE BrU-seq/BruChase-seq data by crossing gene-sense and exon-sense quantification with late-chase 6 h/2 h and total-chase 6 h/0 h retention ratios, and evaluate all models on fixed repeated-random and chromosome-holdout splits. Across chromosome holdouts, XGBoost remains the strongest standalone model, with median Pearson correlations of 0.504, 0.544, 0.546, and 0.778 on the four labels. RAMHT is competitive with raw-sequence deep models but does not universally exceed engineered-feature baselines. A strict nested RAMHT–XGBoost blend nevertheless improves gene total-chase prediction by 0.017 mean Pearson and exon late-chase prediction by 0.004 mean Pearson over XGBoost. Region and mechanism analyses show that CDS, local k-mer composition, and codon-sensitive signals dominate predictive information. RNAStabFormer therefore provides both a multi-task neural model and a leakage-controlled evaluation protocol for RNA stability prediction from pulse-chase data.

15.
arXiv (math.PR) 2026-06-16

Collapsibility in Multiparametric Models of Random Simplicial Complexes

Authors:

arXiv:2606.15276v1 Announce Type: cross Abstract: We study collapsibility in the multiparametric models of random simplicial complexes, namely the lower and upper models. In the upper model, we improve upon a result of Farber and Nowik, and assert that the homology is a.a.s concentrated in a single dimension by proving that the complex collapses to that \di. In the lower model, we prove that the complex a.a.s collapses to the \di\ with maximal non-trivial cohomology. We then compare this threshold to the ones derived previously for the special cases of the clique complex (by Kahle) and the Linial-Meshulam model.

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

Dressed Floquet scars from protected zero modes in a Rydberg chain

arXiv:2606.15605v1 Announce Type: cross Abstract: In this Letter, we present an approximate analytic construction of two zero quasienergy quantum many-body scars in a periodically driven model of Rydberg atoms on a ring, which persist over a range of driving amplitudes and frequencies for finite sizes. An index theorem protects an exponentially large number (in system size) of exact zero energy modes of the Floquet Hamiltonian in this setting. Unlike most of these zero modes which continuously change with drive parameters, these two quantum many-body scars retain the memory of particular states. They can be expressed as {\it dressed versions} of two contrasting states, the Rydberg vacuum and a unitarily rotated variant of a volume-law scar [Ivanov and Motrunich, Phys. Rev. Lett. {\bf 134}, 050403 (2025)], respectively. We provide an analytic understanding of their existence using a Floquet perturbation theory and show their resilience beyond the perturbative regime using exact diagonalization in finite systems. Our study provides insight into the structure of protected zero modes in interacting Floquet settings.

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

HiPath: Hierarchical Vision-Language Alignment for Structured Pathology Report Prediction

arXiv:2603.19957v2 Announce Type: replace-cross Abstract: Pathology reports are structured, multi-granular documents encoding diagnostic conclusions, histological grades, and ancillary test results across one or more anatomical sites; yet existing pathology vision-language models (VLMs) reduce this output to a flat label or free-form text. We present HiPath, a lightweight VLM framework built on frozen UNI2 and Qwen3 backbones that treats structured report prediction as its primary training objective. Three trainable modules totalling 15M parameters address complementary aspects of the problem: a Hierarchical Patch Aggregator (HiPA) for multi-image visual encoding, Hierarchical Contrastive Learning (HiCL) for cross-modal alignment via optimal transport, and Slot-based Masked Diagnosis Prediction (Slot-MDP) for structured diagnosis generation. Trained on 749K real-world Chinese pathology cases from three hospitals, HiPath achieves 68.9% strict and 74.7% clinically acceptable accuracy with a 97.3% safety rate, outperforming all baselines under the same frozen backbone. Cross-hospital evaluation confirms generalisation with only a 3.4pp drop in strict accuracy while maintaining 97.1% safety.

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

Ill-Posed by Design: Probing Evidence Use in VLMs

Counterfactual analysis is widely used to study evidence use in vision-language models, but its diagnostic value is limited on well-posed tasks: when several cues independently support the same answer, removing one may not change the prediction. We propose monocular metric object-size estimation as an ill-posed diagnostic setting for evidence selection: because physical size cannot be determined from a single uncalibrated image, models must rely on imperfect cues category priors, target appearance, local context, apparent image size, and scene geometry. We assemble Metric VQA ($10{,}813$ dimension queries from Objectron and $331$ tape-measured in-the-wild scenes) and evaluate $12$ open-weight VLMs ($3$–$397$\,B parameters) with counterfactual analysis decomposing six visual and language evidence channels. Even the largest VLMs tested (Qwen3-VL-235B, Qwen3.5-397B, InternVL3.5-241B) trail a text-only frontier LLM on the in-the-wild split. The diagnostic analysis shows: target identity is the most load-bearing cue, target pixels and local context help only some models, apparent size shifts predictions without a directional readout, and global scene geometry is largely unused. We analyze LoRA fine-tuning as an actionable intervention specific to metric estimation: while the task is learnable, the models do not learn to leverage scene geometry.

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

Rethinking One-Step Image Editing through ChordEdit: Reproduction, Simplification, and New Insights

One-step image editing is important for making text-guided editing fast, practical, and easy to deploy, but its underlying mechanism is still not fully understood. We revisit ChordEdit through reproduction, ablation, and simplification. Our analysis shows that a) the chord window $\delta$ largely acts as an effective timestep shift from $t$ to $t - \delta$; b) chord transport acts on high-noise images and mainly performs low-frequency semantic editing; and c) proximal alignment acts on low-noise images and complements it by adding high-frequency target details. In this view, ChordEdit naturally decomposes editing into a coarse low-frequency transport stage and a fine high-frequency alignment stage. These findings suggest a path toward prompt-conditioned dynamic timestep selection for adaptive image editing. All code and results can be found at \href{https://github.com/Harvard-AI-and-Robotics-Lab/ChordEdit-Reproduction}{link}.

20.
arXiv (math.PR) 2026-06-11

Heat kernel estimates for Markov processes with blowing-up jump kernels

arXiv:2512.24807v2 Announce Type: replace Abstract: In this paper, we establish sharp two-sided heat kernel estimates for a large class of purely discontinuous symmetric Markov processes on closed subsets $F$ of $\mathbb{R}^d$, whose jump kernels blow up on a Borel subset $\Sigma$ of $F$. We assume that $F\setminus \Sigma$ is a $\kappa$-fat set and is dense in $F$. To the best of our knowledge, this is the first work establishing sharp heat kernel estimates for jump processes whose jump kernels blow up on part of the state space. The jump kernels under consideration take the form $J(x,y)=|x-y|^{-d-\alpha}{\mathcal B}(x,y)$, where $\alpha\in (0,2)$ and the function ${\mathcal B}(x,y)$ blows up at a subset $\Sigma$ of $F$. A fundamental obstacle is that the tails of the jump measures are not uniformly bounded, and hence standard techniques in heat kernel analysis do not provide a priori off-diagonal estimates. To overcome this difficulty, we develop a new approach based on weighted integral estimates for the heat kernel that are sensitive to both the blow-up behavior of the jump kernel and the geometry of $F\setminus \Sigma$. Examples of processes falling within our general framework include traces of isotropic $\alpha$-stable processes in $C^{1,\rm Dini}$ sets, processes in Lipschitz sets arising in connection with the nonlocal Neumann problem, and a large class of resurrected self-similar processes in the closed upper half-space.

21.
PLOS Computational Biology 2026-06-01

BeetleAtlas 2: An enhanced <i>Tribolium castaneum</i> web resource for tissue and developmental transcriptomics allowing refinement of gene predictions

by David P. Leader, Muhammad T. Naseem, Janina L. Rinke, Kenneth Veland Halberg BeetleAtlas is an online resource for tissue- and stage-specific transcriptomics in the red flour beetle, Tribolium castaneum. On updating from the original Tcas5.2 genome assembly to the more recent improved icTriCast1.1 genome assembly it became evident that there were major discrepancies between the gene models of the two genome annotations in use: the OGS3 and the NCBI gene sets. As neither was clearly superior we implemented a new design in BeetleAtlas 2 (beetleatlas.org) comprising two parallel ‘modes’ — one incorporating results using the NCBI gene models and a second incorporating those using the OGS3 gene models. This allows direct comparison where equivalent gene models exist: 50–57% of cases. To aid resolution of discrepancies between the two gene model sets and verification of results, gene models are linked to a custom visualization of RNA-seq read coverage of the genome in the UCSC Genome Browser. This displays reads from 22 tissues and life stages superimposed on the icTriCast1.1 genome assembly. Reference tracks show the NCBI gene models, the OGS3 gene models after translation of their coordinates from the Tcas5.2 assembly, and 1050 discontinued NCBI gene models from the previous assembly after a similar transfer of coordinates. We document various situations in which distinct patterns of expression of the tissues can be used to confirm and extend correlations between the two gene sets, resolve discrepancies between them, make corrections and identify putative genes or exons absent from the current gene sets. BeetleAtlas 2 allows those involved in Tribolium research to avoid the pitfalls inherent in incorrect gene models when planning experiments on specific genes and interpreting the results. It also demonstrates how BeetleAtlas 2 might play an important role in establishing a revised gene set for Tribolium castaneum in the future.

22.
arXiv (quant-ph) 2026-06-19

Nearest-neighbour gates are all you need: High-rate quantum low-density parity-check codes on a planar grid

arXiv:2606.19482v1 Announce Type: new Abstract: High-performance quantum low-density parity-check codes promise substantial reductions in the overhead of fault-tolerant quantum computation, but most constructions require long-range connectivity or qubit shuttling, both of which are difficult to realise in superconducting architectures. Here we introduce a family of quantum low-density parity-check codes that, for the first time, combines planar open-boundary layouts, finite-size advantages over surface codes, and syndrome extraction using only nearest-neighbour gates on a square grid of qubits. The key idea is to generate check-data connectivity dynamically: nearest-neighbour iSWAP walks both define the stabiliser supports and implement their measurement, avoiding the need for a long-range hardware graph. The resulting circuits achieve optimal constant-depth stabiliser measurement, independent of code size, and naturally remove leakage from the system by exchanging the role of check and data qubits at each syndrome extraction round. We find finite-size instances such as a [[323,14,15]] code, whose code-efficiency ratio is nearly an order of magnitude larger than that of rotated surface-code patches. At around 30 circuit qubits per logical qubit, the best directional tile-code layouts reduce the per-logical per-round logical error rate by up to a factor of 1000 relative to rotated surface-code memories. These results show that the advantages of quantum low-density parity-check codes can survive compilation into strictly planar nearest-neighbour circuits, bringing low-overhead fault-tolerant memories closer to near-term hardware.

23.
arXiv (CS.CL) 2026-06-18

From Sparse Features to Trustworthy Proxies: Certifying SAE-Based Interpretability

Sparse autoencoders (SAEs) are increasingly used to extract interpretable features from language models (LMs), yet a central question remains: when can an SAE-based explanation be treated as a faithful view of an underlying frozen LM We study this through a post-hoc generalization framework that certifies the LM via a sparse proxy, obtained by replacing a native hidden activation with its pretrained SAE reconstruction. Our framework derives an upper bound on the base model's expected risk using four measurable quantities: proxy risk, SAE reconstruction gap, concept-pool mismatch, and sparse complexity. We interpret this certificate as an operational criterion for explanatory faithfulness. In particular, a non-vacuous bound indicates that the extracted sparse features retain meaningful predictive information, while small reconstruction and mismatch errors indicate that the proxy remains behaviorally close to the original model. Empirically, we show that the bound becomes non-vacuous on GPT-2 Small, Gemma-2B, and Llama-3-8B at practical sample sizes. A detailed layerwise analysis of Llama-3-8B reveals a strong depth dependence, with later layers becoming much easier to certify, associated with both stronger local fidelity and weaker downstream error amplification. Finally, through feature-shuffling ablations, we show that the decomposition distinguishes genuine semantic alignment from mere statistical sparsity, providing a useful diagnostic for when SAE-based explanations become less reliable.

24.
arXiv (quant-ph) 2026-06-19

Quantum Algebraic Diversity: Single-Copy Density Matrix Estimation via Group-Structured Measurements

arXiv:2604.03725v3 Announce Type: replace Abstract: We extend the algebraic diversity (AD) framework from classical signal processing to quantum measurement theory. The Quantum Algebraic Diversity (QAD) Theorem establishes that a group-structured positive operator-valued measure (POVM) applied to a single copy of a quantum state produces a full-rank, group-averaged density matrix estimator whose eigenbasis and eigenvalue ordering track those of the true density matrix, with a bias toward the symmetrized state, analogous to the classical recovery of covariance eigenstructure from a single observation. We establish a Classical-Quantum Duality Map connecting classical covariance estimation to quantum state tomography, and an Optimality Inheritance Theorem showing that classical group optimality transfers to quantum settings via the Born map within the group-averaged family. SIC-POVMs are identified as AD with the Heisenberg-Weyl group and mutually unbiased bases as AD with the Clifford group, revealing the hierarchy $\mathrm{HW}(d) \subseteq \mathcal{C}(d) \subseteq S_d$ that mirrors the classical $\mathbb{Z}_M \subseteq G_{\min} \subseteq S_M$. The double-commutator eigenvalue theorem gives polynomial-time adaptive POVM selection. A worked qubit example shows the group-averaged estimator from a single computational-basis measurement, averaged over a matched $\mathbb{Z}_2$ group, reaching fidelity 0.99 where standard single-basis tomography gives a rank-1 estimate of fidelity 0.80. Monte Carlo simulations for $d = 2$ to $13$ confirm fidelity above 0.90 from a single outcome while standard fidelity degrades as $\sim 1/d$. The growing ratio reflects collapse of the rank-1 standard estimator, not fewer copies per parameter: the biased single-copy estimator reduces the number of distinct measurement settings, not the per-parameter sampling cost, and a genuine copy reduction holds only under exact symmetry.

25.
arXiv (math.PR) 2026-06-11

Feynman–Kac formula for the heat equation with a one-center point interaction in $d=3$

arXiv:2606.11677v1 Announce Type: new Abstract: We study Schrödinger operators with a one-center point interaction, formally defined by \begin{align*} -\Delta_\alpha=-\Delta+\alpha\,\delta_0(\cdot), \end{align*} for $\alpha\in\mathbb{R}$, and the associated heat equation \begin{align} \partial_t u=\tfrac{1}{2}\Delta_{\alpha} u,\quad u(0,x)=u_0(x)\in C_c^{\infty}(\mathbb{R}^3\setminus\{0\}).\label{eq:HEapp} \end{align} Here $\Delta$ denotes the Laplacian (self-adjoint on $L^2(\mathbb{R}^3)$) and $\delta_x$ the Dirac measure at $x$. The operator $-\Delta_\alpha$ can be realized either as a self-adjoint extension of $-\Delta|_{C_0^{\infty}(\mathbb{R}^3\setminus\{0\})}$ in $L^2(\mathbb{R}^3)$, or as the norm-resolvent limit of $-\Delta+\lambda_\varepsilon V(\cdot/\varepsilon)$ for suitable $\lambda_\varepsilon$ and $V:\mathbb{R}^3\to\mathbb{R}$. In this paper we construct, for each $t>0$ and $x\in\mathbb{R}^3\setminus\{0\}$, a probability law on path space and a normalizing function $G_t^\alpha(x)$ giving the following probabilistic representation of the solution to the associated equation: \begin{align*} u(t,x)=G_t^\alpha(x)\,\mathbb{E}\bigl[u_0\bigl(W^{t,x}(t)\bigr)\bigr], \end{align*} where $\{W^{t,x}(s):0\le s\le t\}$ is a continuous process depending on $(t,x,\alpha)$. The result provides a Feynman–Kac type formula for the heat equation with a one-point interaction in three dimensions.