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

ReproRepo: Scaling Reproducibility Audits with GitHub Repository Issues

Reproducing research results from papers and released code is central to scientific progress. Existing works have introduced benchmarks to evaluate whether LLM agents can assist with reproducibility, but they are difficult to scale due to their reliance on substantial manual effort for data curation and evaluation. We introduce ReproRepo, a scalable framework for reproducibility evaluation that leverages human-raised GitHub issues as naturally occurring supervision on realistic reproduction blockers. We instantiate ReproRepo on 1,149 recent machine learning papers from major conferences and evaluate four frontier model-agent configurations. Our results show that LLM agents, even without executing code, can identify many real-world reproducibility problems from paper-repository pairs: the best agent in our study, namely Codex with GPT-5.5, surfaces at least one semantically related human-reported blocker for ~90% of papers in the study. Further analysis shows that agents are particularly effective for surfacing visible failures and identifying the right semantic region, but may still be insufficient in exact localization. ReproRepo can serve as a reusable, scalable framework for future evaluations of LLM agents on real-world reproducibility auditing. Our code is released at https://github.com/LithiumDA/ReproRepo.

02.
arXiv (CS.AI) 2026-06-11

Latent World Recovery for Multimodal Learning with Missing Modalities

arXiv:2606.12362v1 Announce Type: cross Abstract: We study multimodal learning under missing modalities, with particular motivation from bioscience applications in which heterogeneous modalities are often only partially available when decisions need to be made. We propose Latent World Recovery (LWR), a framework built on two key ideas: (i) modality-specific embeddings from different modalities are aligned in a shared latent space, and (ii) a unified representation is constructed by fusing only the embeddings of the modalities that are actually available at both training and inference time. Rather than imputing missing modalities or requiring a fixed modality set, LWR treats each modality as a partial perception of an underlying latent state and performs availability-aware representation learning directly from the observed modalities. This combination of neighbor-based latent alignment and availability-aware modality fusion enables robust multimodal prediction under partial observation, while avoiding error propagation from explicit reconstruction of missing modalities. We evaluate the proposed framework on real-world incomplete multi-omics benchmarks and demonstrate that it provides an effective approach to downstream tasks such as cancer phenotype classification and survival prediction.

03.
arXiv (CS.LG) 2026-06-17

Manifold GCN: Diffusion-based Convolutional Neural Network for Manifold-valued Graphs

arXiv:2401.14381v3 Announce Type: replace Abstract: We propose two graph neural network layers for graphs with features in a Riemannian manifold. First, based on a manifold-valued graph diffusion equation, we construct a diffusion layer that can be applied to an arbitrary number of nodes and graph connectivity patterns. Second, we model a tangent multilayer perceptron by transferring ideas from the vector neuron framework to our general setting. Both layers are equivariant under node permutations and the feature manifold's isometries. These properties have led to a beneficial inductive bias in many deep-learning tasks. Furthermore, they enable novel, more flexible feature designs. Numerical examples on synthetic data and an Alzheimer's classification application on triangle meshes of the right hippocampus demonstrate the usefulness of our new layers: While they apply to a much broader class of problems, they outperform task-specific state-of-the-art networks.

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

Using Explainability as a Training-Time Reliability Signal for Efficient ECG Classification

arXiv:2606.12252v1 Announce Type: cross Abstract: Training deep neural networks for clinical time-series analysis is computationally demanding, yet many healthcare settings lack the resources required for repeated model development and deployment. This challenge is particularly evident in electrocardiogram classification, where large datasets and long training schedules make efficiency practically important. Progressive Data Dropout reduces training cost by excluding samples from gradient updates once they are learned, but it relies on model confidence and may retain samples that are difficult due to noise or ambiguity rather than useful signal. In this work, we introduce ERTS, an explainability-based reliability training signal for efficient ECG classification. ERTS uses explanation quality during training to distinguish between informative and unreliable uncertainty. Building on progressive data selection, we compute Grad-CAM attention maps for candidate samples and derive a focus score that measures whether model predictions are supported by coherent and localised patterns. Samples with low focus are filtered out, while those with meaningful attention are prioritised for gradient updates. We evaluate ERTS across three ECG datasets and multiple backbone architectures, showing consistent improvements in macro-F1 alongside reduced effective training cost. These results suggest that explanation quality can serve as a practical signal for improving both efficiency and reliability in clinical time-series learning. Code will be released.

05.
Nature Medicine 2026-06-15

Adaptive deep brain stimulation for dynamic gait control in Parkinson’s disease: a randomized feasibility trial

A randomized crossover study of five patients with Parkinson’s disease (PD) demonstrates that gait-synchronized adaptive deep brain stimulation is feasible and safe, and reduces falls compared with continuous stimulation. Gait dysfunction in PD is a major source of disability and is often insufficiently treated by continuous deep brain stimulation (cDBS). Although adaptive DBS (aDBS) has shown efficacy for other motor symptoms using β-based, state-driven neural signals, gait is a dynamic, cyclical behavior that may require temporally precise modulation. Here we evaluated a behavior-contingent aDBS approach that synchronizes stimulation to gait phase. We reported a single-center, blinded, randomized, crossover study evaluating the feasibility of identifying patient-specific biomarkers to drive aDBS. The primary outcome was feasibility of successful identification of gait-phase biomarkers to implement aDBS. Five participants with PD undergoing pallidal DBS and subdural electrode paddle implantation were enrolled. We successfully identified personalized gait-phase biomarkers from cortical or pallidal field potentials in all five patients and embedded them into a bidirectional neurostimulator. During acute in-clinic testing, aDBS improved step variability and step symmetry versus cDBS. Three participants subsequently completed a double-blinded, multi-day crossover phase. In this setting, aDBS maintained general motor symptom control, reduced falls and yielded patient-specific gait improvements. No adverse events occurred and aDBS was well tolerated. These findings establish the feasibility of biomarker-driven, movement-synchronized neuromodulation and support the development of a larger randomized trial to determine clinical efficacy. ClinicalTrial.gov registration: NCT04675398 . A randomized crossover study shows that gait-phase-synchronized adaptive deep brain stimulation is feasible and safe, and reduces falls compared to continuous stimulation in Parkinson’s disease.

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

Power-law hypothesis and (un)fairness of PageRank on undirected multi-type PAMs

arXiv:2606.19583v1 Announce Type: new Abstract: The preferential attachment model (PAM) describes the sequential growth of a network based on the "rich-get-richer" principle. Several versions of it have become established for modeling, e.g., citation networks, capturing a power-law degree distribution. Directed versions of the preferential attachment model where the edges are directed from the new to the old vertices have been the subject of extensive research. They have been shown to exhibit remarkable properties such as heavier tails for the limiting graph-normalized PageRank than for the in-degrees. By contrast, for the undirected version, we recently showed that PageRank has similar tails as the degree. In the present paper, we discuss the PageRank asymptotics for a multi-type version of the undirected PAM (here vertices have different colors), complementing previous results of Antunes, Bhamidi, Banerjee and Pipiras on the asymptotics of PageRank on similar directed multi-type or colored PAMs. Our studies are motivated by the aim to go beyond the rigid rule of edge orientation in directed preferential attachment models. As the main result, for the case of a finite set of colors, we show that the power-law hypothesis for PageRank is fulfilled also for the colored undirected PAM, where, by contrast to the directed case, the power-law exponent is color-dependent for some choices of the initial color distribution and the attractiveness function. For the specific case of a two-type model, we discuss implications of our results on fairness in sampling underrepresented nodes from the network.

07.
arXiv (CS.CV) 2026-06-17

RAVA: Retrieval-Augmented Viewpoint Alignment for Subject-Driven Image Generation

Reference-driven image generation has made rapid progress on identity preservation, but reliable viewpoint control across different subjects remains poorly understood. The difficulty is not merely generating a new image of the target subject: the model must infer the implicit viewpoint of one subject and transfer it to another subject using only image-level evidence, without camera poses, depth, or ray-based conditions. In this setting, existing generators conditioned on multiple image references often rely on spurious semantic correlations, which lead to viewpoint drift, part-level structural mismatches, and missing or unsupported target-specific content. We formulate this challenge as cross-subject viewpoint alignment and propose RAVA, a retrieval-augmented framework that supplies explicit geometric evidence before generation. RAVA first learns a cross-instance viewpoint embedding that retrieves target-subject images aligned with the anchor viewpoint, then applies a LogDet-based subset selection strategy to retain a compact reference set that is both view-consistent and structurally complementary. The selected references are finally consumed by a fine-tuned multi-reference image generator. Experiments show that generic semantic embeddings are nearly random for this task, while the proposed retriever substantially improves viewpoint retrieval quality. On cross-subject generation, RAVA consistently outperforms zero-shot baselines and stronger retrieval alternatives under the same generation backbone. These results indicate that cross-subject viewpoint alignment benefits from retrieval-augmented geometric grounding rather than relying on end-to-end generation alone.

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

Quantum optimal control of the Dicke manifold in dipolar Rydberg atom arrays

arXiv:2606.02283v2 Announce Type: replace Abstract: The ability to engineer and control quantum states of many-body systems is a central challenge in quantum information science. For a register of $N$ qubits, the full Hilbert space dimension grows exponentially as $2^N$, rendering generic state preparation and control infeasible without exploiting structure or symmetry. A particularly important and physically motivated restriction is to the fully symmetric subspace, spanned by the Dicke states, which are simultaneous eigenstates of collective spin $J=N/2$. Ensembles of Rydberg atoms interacting via electric dipoles in two-dimensional tweezer arrays form a promising platform for achieving such control. However, the finite range of dipole-dipole interactions poses a challenge to generating and controlling the Dicke manifold because the Hamiltonian incurs leakage from the computational subspace. To counteract this leakage, we perform quantum optimal control algorithms on a truncated Hilbert space according to our newly developed method of ``irrep distillation'' (IRD), which captures the process by which the symmetric subspace couples to leakage error-spaces, using only linear-scaling Hilbert dimension. We implement gradient ascent pulse engineering (GrAPE) on control schemes with little or no local addressing, to generate resourceful states like Greenberger-Horne-Zeilinger, Dicke, and extremal quantum states. We benchmark each scheme of IRD-GrAPE for its quantum speed limit (QSL), as well as exactly testing pulse fidelities on small system sizes and predicting fidelities using higher-order IRD on larger systems.

09.
arXiv (CS.AI) 2026-06-18

AI Sandboxes: A Threat Model, Taxonomy, and Measurement Framework

arXiv:2606.18532v1 Announce Type: cross Abstract: AI systems are increasingly evaluated in bounded environments that combine isolation, simulation, instrumentation, supervision, and evidence capture. For physical AI, AIoT, and cyber-physical systems, this shift is not a matter of terminology: the system under test may sense, decide, actuate, communicate, and fail through physical processes, networked devices, and human operators. This article develops an assurance-oriented account of AI sandboxes as controlled environments for testing, evaluation, verification, and validation across digital AI, embodied autonomy, and cyber-physical deployments. We formalize the sandbox boundary and a weakest-link rule for composing per-dimension evidence into a bounded deployment claim; separate major sandbox archetypes; define a cyber-physical threat model that includes attacks on the assurance apparatus itself; and introduce a measurement framework spanning fidelity, controllability, observability, containment, reproducibility, and governance artifacts, instantiated on three worked case studies of real sandboxes. The resulting threat model, taxonomy, and measurement framework clarify what a sandbox can validly test, which risks it can contain, and what forms of evidence it can support for safety, security, and regulatory assurance.

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

Stochastic-Dimension Frozen Sampled Neural Network for High-Dimensional Gross-Pitaevskii Equations on Unbounded Domains

arXiv:2604.09361v4 Announce Type: replace Abstract: This paper introduces the Stochastic-Dimension Frozen Sampled Neural Network (SD-FSNN), a novel computational framework for solving high-dimensional Gross-Pitaevskii equation (GPE) on unbounded domain. The proposed method circumvents the curse-of-dimensionality that plagues traditional discretizations and the computational bottlenecks of gradient-based neural network solvers through a synergistic combination of techniques. First, a prescribed Gaussian envelope encodes the far-field decay of the wavefunction, enabling a space-time separation where the spatial approximation is handled by a frozen, single-hidden-layer neural network with data-driven sampled features. This yields a gradient-free formalism where spatial derivatives are analytically precomputed and time-dependence is evolved via reduced ODEs. Second, a stochastic-dimension sampler provides a conditionally unbiased estimate of the spatial operator by evaluating only a small subset of spatial dimensions at each time step, essentially reducing computational and memory costs. Discrete conservation laws are also enforced, ensuring long-term stability. Extensive numerical experiments on GPE in up to 1000 dimensions demonstrate that SD-FSNN achieves significantly higher accuracy and efficiency compared to state-of-the-art methods, including PINNs, randomized feature methods, and tensor-network approaches. The results confirm that SD-FSNN effectively mitigates the Kolmogorov $n$-width barrier for frozen-basis models on structured solution manifolds.

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

When Does Mixing Help? Analyzing Query Embedding Interpolation in Multilingual Dense Retrieval

While mixed-language querying is ubiquitous in multilingual communities, the sensitivity of dense retrievers to such queries remains poorly understood. We present a ratio-controlled study on mMARCO that systematically evaluates retrieval performance by varying the mixing proportion of parallel query translations via embedding-level mixing – constructing mixed queries as an interpolation of monolingual embeddings. Experiments with BGE-M3 demonstrate that an optimal mixing ratio outperforms the best monolingual endpoint in 88/105 cases. We uncover a distinct asymmetry driven by English dominance: mixing is uniformly beneficial when retrieving from non-English document indices, whereas indices containing English are best served by pure English queries. Furthermore, English acts as the strongest mixing partner for every non-English document language. Finally, when controlling for English dominance, mixing gains correlate negatively with typological distance. We conclude that language-mix sensitivity is structured and predictable, and we validate the robustness of these patterns across model families and scales.

12.
Science (Express) 2026-05-21

Nodeless superconducting gap and electron-boson coupling in (La,Pr,Sm)3Ni2O7 films | Science

作者: 未知作者

The discovery of superconductivity in Ruddlesden-Popper (RP) bilayer nickelate films under ambient pressure provides an opportunity to directly investigate electronic energy scales of the superconducting state and the pairing mechanism. We report angle-resolved photoemission spectroscopy measurements of superconducting (La,Pr,Sm) 3 Ni 2 O 7 thin films by developing an ultra-high vacuum cryogenic sample quenching and transfer technique. A superconducting gap of ~18 meV with coherence peaks is observed along the Brillouin zone diagonal. The finite gap persists across the entire Brillouin zone, revealing the absence of gap nodes. A kink is observed in the energy-momentum dispersion at ~70 meV below Fermi level, indicating an electron-boson coupling. The simultaneous observation of a nodeless superconducting gap and electron-boson coupling provides insight into the pairing symmetry and gluing mechanism in RP bilayer nickelates.

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

CmdNeedle: Measuring the Incompleteness of Command Denylists for AI Agents

arXiv:2606.15549v1 Announce Type: cross Abstract: The adoption of AI agents is increasing rapidly. Terminal AI agents, i.e., AI agents that run in terminal environments, are a widely used type of AI agents. Terminal AI agents rely heavily on shell command execution to interact with the host systems. They adopt a three-list command-gating mechanism to mitigate security risks introduced by command execution, with denylists serving as the load-bearing component. However, modern operating systems often ship a large, ever-expanding set of shell commands with complex functionalities. Our observation is that even a built-in denylist of Claude Code, well-maintained by its developers, can overlook bypass commands that invalidate its effectiveness. Such negligence leads to fragile command denylists that cannot even block operations that practitioners expect them to block. This paper presents the first systematic characterization of command denylist fragility in terminal AI agents. The paper formalizes the command denylist fragility problem and proposes an LLM-driven pipeline, CmdNeedle, to detect such fragility. It prompts the LLM to propose possible bypasses and iteratively repairs them using feedback from a validator that executes them in a sandbox. In the evaluation, we applied CmdNeedle to 1,709 real-world command denylists (containing 13,332 denylist rules) collected from GitHub. The evaluation shows several key findings, including that 69.0–98.6% of the denylists are fragile, that this fragility occurs consistently across projects and agents, and the validity of several possible root causes for this fragility. Our pipeline and findings will hopefully facilitate future research and practice regarding the command denylists used by AI agents.

14.
arXiv (CS.LG) 2026-06-17

AoiZora: Topology-Aware Auto-Parallel Optimization for Inference of Diffusion Transformers

arXiv:2606.17566v1 Announce Type: cross Abstract: Video diffusion has quickly grown into a key generative serving workload, yet producing each clip demands many denoising iterations over large spatio-temporal latents, which puts low-latency inference out of reach on a single device. A denoising step is therefore typically distributed across multiple accelerators, and TPU sub-slices have become an attractive and practical fabric for doing so. Current auto-parallel systems, however, search almost exclusively over logical device meshes and disregard how a chosen sharding is actually laid out on the physical TPU interconnect – an oversight that leaves large, topology-dependent performance on the table. We address this gap with AoiZora, a compiler-mediated topology planner built for low-latency video diffusion inference on TPU sub-slices. Its guiding principle is to reconnect logical sharding with physical placement by drawing on different points in the compilation flow: AoiZora first eliminates weak sharding candidates from inexpensive pre-compilation IRs, then compiles only the ones that survive and orders their physical placements using compiled HLO together with a topology-aware communication model. The winning plan is realized along the ordinary compiler path, leaving model code, compiler lowering, collective kernels, and network routing entirely intact. On TPU v5e sub-slices, AoiZora reduces Wan 2.1 one-step denoising latency by as much as 1.42x relative to existing solutions.

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

Dealing with locality in QAOA

arXiv:2606.14447v1 Announce Type: new Abstract: Shallow-depth QAOA on sparse, high-diameter MaxCut instances faces a locality bottleneck: at depth \(p\), local observables can depend only on a bounded neighborhood of the circuit interaction graph. We propose a transport-augmented QAOA that keeps the MaxCut cost Hamiltonian unchanged but enriches the mixer with optimized, unweighted shortcut couplings (scheduled \(XX+YY\)) to collapse the effective interaction-graph diameter. Using exact finite-depth support recursions, we relate optimal shortcut placement to bounded-diameter graph augmentation, and show in benchmarks that (unlike ma-QAOA) performance becomes effectively size-invariant once the diameter is reduced. For bipartite families (base diameter 4), reducing the interaction path to \(d=1\) raises the ensemble-averaged approximation ratio from 0.7378 (ma-QAOA) to 0.9767 at \(p=1\) (\(\sigma=0.0251\), nine system sizes); on random trees (base diameter 10), at \(p=2\) it improves from 0.9226 to 0.9997 (\(\sigma=0.0001\)).

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

Closing the Auto-Research Loop: An AI Co-Scientist for Production Search Ranking

arXiv:2603.22376v2 Announce Type: replace-cross Abstract: We present an AI Co-Scientist framework that closes the research loop for the production search-ranking system of a large online travel platform – pairing LLM agents with direct cloud-compute access so that idea generation, code implementation, GPU experimentation, and result analysis iterate end-to-end with a human scientist in the loop. The framework uses a hybrid agent architecture: single-LLM agents handle routine work, while multi-LLM consensus (GPT-5.2, Gemini Pro 3, Claude Opus 4.5) is invoked for higher-stakes decisions. On the production ranking task, a human-designed transformer baseline (V2) yielded $+0.118\%$ over a pre-transformer baseline (V1); the AI Co-Scientist's automated loop on top of V2 contributed an additional $+0.083\%$, for a combined $+0.201\%$ offline gain delivered in roughly one extra week of wall-clock time (single-run numbers; statistical limits discussed in the paper). The most useful AI proposals – unified long-sequence layouts, slot-type embeddings, and multi-phase learning-rate schedules – are standard practice in NLP and Vision but were absent from our production stack, suggesting that LLM agents can serve as cross-disciplinary connectors for ranking teams. We also report deployment context, negative results, and lessons learned.

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

DRIVESPATIAL: A Benchmark for Spatiotemporal Intelligence in VLMs for Autonomous Driving

Spatiotemporal intelligence in autonomous driving (AD) requires an agent to integrate multi-view observations into a coherent scene representation, maintain object continuity across viewpoints and time, and reason about spatial relations, interactions, and future dynamics. However, existing AD vision-language benchmarks largely focus on single-view, static, ego-centric, or single-source question answering, leaving it unclear whether current Vision-Language Models (VLMs) can truly construct and reason over dynamic driving scenes. We introduce DriveSpatial, a benchmark of 15.6K human-verified QA pairs across 20 tasks from five large-scale AD datasets. DriveSpatial evaluates four abilities: Cognitive Scene Construction, Multi-view Relational Understanding, Temporal Reasoning, and Generalization. Unlike prior benchmarks, DriveSpatial is generated from a dynamic multi-relational scene graph that encodes object states, spatial relations, interactions, camera visibility, and temporal correspondences, enabling QA pairs that enforce genuine cross-view and spatiotemporal reasoning. Evaluating 15 representative VLMs reveals a substantial human-model gap: the strongest model trails humans by 28.4 points, with Cognitive Scene Construction emerging as the key bottleneck. Further diagnostics show that language-only prompting is insufficient, while explicit BEV grounding consistently improves performance. These results suggest that current VLMs lack the scene-construction ability needed for reliable spatiotemporal driving intelligence. DriveSpatial and its construction pipeline will be released to support future research.

18.
arXiv (CS.AI) 2026-06-16

QoS-Aware Token Scheduling and Private Data Valuation for Multi-Modal Agentic Networks

arXiv:2606.15573v1 Announce Type: new Abstract: In agentic systems, human-generated data records anchor the value of AI services. Yet cloud compute pipelines centralize processing on remote servers. Data centralization reduces personal data sovereignty and may potentially degrade the quality of service (QoS). Meanwhile, user contributions are diverse in quantity and quality: decentralized records can be biased, noisy, and heterogeneously distributed. To address the data challenge, we study fair token allocation and private data valuation for decentralized and resource-constrained agentic systems. Our approach embeds multi-modal representations in a shared semantic space and releases differentially private (DP) prototypes to preserve utility while reducing semantic leakage. With the DP guarantee, we design a fair token allocation scheme that rewards effective contributions and remains robust to data heterogeneity and AI resource scarcity. Extensive simulations demonstrate improved contribution-based fairness and QoS compared to standard benchmarks. The improved resistance to image reconstruction attacks indicates enhanced privacy for multi-modal personal data.

19.
arXiv (quant-ph) 2026-06-12

New bounds on private simultaneous quantum message passing

arXiv:2606.12557v1 Announce Type: new Abstract: In the private simultaneous message (PSM) setting, $k$ players obtain inputs $x_i\in\{0,1\}^n$ and then each send messages to a referee, who should learn $f(x_1,...,x_k)$ but no other information about $(x_1,...,x_k)$. The PSM setting was introduced as a minimal model for secure multiparty computation and has connections to Boolean function complexity. In the quantum setting, PSM has been related to non-local quantum computation (NLQC). The communication and correlation cost of implementing PSM remains poorly understood. Here, we give new upper and lower bounds on the (quantum) PSM model. For lower bounds, we show: 1) Nečiporuk's measure lower bounds the entanglement required for $k$-player quantum PSM with perfect correctness. This leads to quadratic lower bounds for explicit functions. 2) The rank of the communication matrix of $f(x_1,x_2)$ lower bounds 2-player quantum PSM with perfect privacy but imperfect correctness. This implies a previously unknown lower bound on classical PSM with imperfect correctness. When allowing quantum communication and shared entanglement, these are the first lower bounds on quantum PSM that make use of the privacy condition. For upper bounds, we show: 1) Letting $s$ be the size of a quantum circuit computing $f$, $d_f$ be the circuit depth, $k$ the number of players, $n$ the number of bits received by each player, and $\epsilon$ a correctness parameter, we obtain $\mathsf{PSM}_k^*(f) \leq (kn +s) \cdot \log^{O(d_f)}(s/\epsilon)$. 2) The square of the Fourier 1 norm of $f$, $\Vert \hat{f}\Vert_1^2$, upper bounds the classical PSM complexity, $\mathsf{PSM}(f)\leq O(\Vert \hat{f} \Vert^2_1)$. In proving the first upper bound, we generalize existing $T$-depth based techniques for NLQC from $2$ to $k\geq 2$ parties, and consider cases where the Clifford layers are restricted to having small light cones.

20.
arXiv (CS.CV) 2026-06-12

Multi-Label Test-Time Adaptation with Bayesian Conditional Priors

Multi-label recognition with frozen Vision-Language Models (VLMs) is brittle under distribution shift: standard zero-shot inference scores labels independently, ignoring co-occurrence structure and producing incoherent label sets where dominant concepts suppress weaker but compatible labels. We introduce Bayesian Conditional Priors (BCP) Estimation, a gradient-free test-time adaptation method that injects label dependency without tuning the backbone. BCP views zero-shot logits as a proxy for marginal posteriors under a fixed image-text likelihood and attributes shift-induced errors mainly to a mismatched label prior. For each test image, it selects a high-confidence anchor label and applies an anchor-conditioned Bayesian refinement. This update is closed-form in logit space and admits a pointwise mutual information (PMI) interpretation, explicitly promoting compatible labels and suppressing incompatible ones. BCP operates without target annotations by estimating anchor-conditioned priors online from the unlabeled test stream via lightweight second-order co-occurrence statistics, adding negligible overhead beyond a single forward pass. Across standard multi-label benchmarks and multiple CLIP backbones, BCP consistently outperforms strong TTA baselines, e.g., improving RN50 average mAP from 57.31 to 69.22 and ViT-B/16 from 62.61 to 71.79.

21.
medRxiv (Medicine) 2026-06-15

Long-read sequencing enables high-accuracy mitochondrial heteroplasmy detection in Parkinson's disease

Background: Low-frequency heteroplasmic mitochondrial DNA (mtDNA) variants are associated with aging and neurological diseases, including Parkinson's disease (PD). Targeted deep mtDNA sequencing using PacBio HiFi long reads has the potential to resolve heteroplasmy across the full mitochondrial genome with high accuracy. Methods: To validate Vega PacBio sequencing for detecting mtDNA heteroplasmy, we analyzed four predefined mixtures of two mtDNA haplotypes. We generated a single long-range PCR amplicon covering the entire mitochondrial genome. These amplicons were mixed at predefined ratios (minor mixture haplotype component: 5%, 2%, 1%, and 0.1%). Variant calling was performed using Mutserve2, and accuracy was assessed by calculating the F1 score from comparisons between expected and detected variants. Full-length mtDNA PacBio sequencing was applied to investigate heteroplasmy across fibroblast passages derived from five LRRK2 p.Gly2019Ser variant carriers (n=3 affected with PD and n=2 unaffected carriers). Changes in mtDNA heteroplasmy level and variant load were assessed longitudinally using a linear mixed model. Results: The single-amplicon approach enabled full-length haplotype resolution without amplification bias associated with overlapping PCR strategies. The F1 score of the predefined mixtures was 1.0 for heteroplasmy levels between 5% and 1% and remained high (0.91) at 0.1%. We detected n=10/62 variants discordant with the Illumina reference at the 0.1% mixture, but sensitivity remained very high at 1.00 in that mixture. Detected minor variants closely matched expected heteroplasmy levels, with average variant levels of 0.057 (5%), 0.022 (2%), 0.011 (1%), and 0.001 (0.1%). Across twelve fibroblast passages, we observed fewer mtDNA heteroplasmic variants ({beta}=-3.2, p=0.026). Increased heteroplasmic variant load over time was also associated with older age ({beta}=1.50, p=0.001) and PD affection status ({beta}=5.0, p=1.0 x 10-4) in LRRK2 variant carriers. Notably, we observed distinct patterns of heteroplasmic variants that either increased or decreased in heteroplasmy level across passages. Conclusion: PacBio HiFi sequencing, combined with a single-amplicon strategy, enables accurate full-length mtDNA heteroplasmy detection and longitudinal analysis, providing a valuable tool for studying mitochondrial variation and dynamics in disease.

22.
arXiv (quant-ph) 2026-06-12

Quantum Stochastic Inflation

arXiv:2606.12636v1 Announce Type: cross Abstract: We formulate stochastic inflation in an open quantum system framework. The field coarse-grained in a patch of fixed physical size, and the total momentum of that patch, form a canonical pair and act on a one-mode Fock space which we identify as the "bulk". At each time step, new comoving modes join the coarse-grained patch and the bulk has to be redefined. This redefinition produces an entangled mode that is traced over, yielding a non-unitary evolution equation for the bulk's density matrix. For a free test field in de Sitter, one obtains GKLS dynamics, generated by an effective Hamiltonian and a single non-Hermitian Lindblad operator, hence diffusion and Hubble friction originate from the same quantum channel. The Wigner-Weyl transform of the GKLS equation leads to a Fokker-Planck equation for the Wigner function, which matches the one that applies to the classical phase-space distribution of stochastic inflation. We also provide several schemes under which one can unravel the GKLS dynamics into stochastic Schrodinger equations when continuous measurements of the decoupled mode are performed, making contact with Langevin formulations of stochastic inflation. In the light-field regime, an additional overdamped reduction can be performed by integrating out the momentum variable in the Wigner distribution, leading to Starobinsky's slow-roll Fokker-Planck equation. In that regime, the purity of the patch is strongly suppressed. In contrast, for heavy fields, field diffusion is suppressed and the coarse-grained patch remains close to a pure underdamped oscillator, which prevents a classical stochastic treatment.

23.
bioRxiv (Bioinfo) 2026-06-16

RetroMol: Parsing a shared encoding from natural products and their biosynthetic gene clusters

Natural products such as polyketides and nonribosomal peptides (NRPs) are important sources of bioactive compounds, including many antibiotics. Many of them are assembled by modular enzyme complexes and further modified and diversified by tailoring reactions encoded by biosynthetic gene clusters (BGCs). Although natural products and their coding BGCs describe different data modalities of the same biochemical process, a unified language to jointly describe their biochemistry is lacking. Here we introduce a sequence-based representation of the core biosynthesis of modular natural products, which we call primary sequences, that bridges chemical structures and BGCs. We also present RetroMol, an algorithm that parses either natural product structures or their encoding BGCs into their primary sequences of natural product building blocks. RetroMol allows for similarity scoring between natural products and BGCs, enabling the retrieval of compounds, BGCs, and a combination of the two, based on their biosynthetic similarity. This can, for instance, be used to retrieve biosynthetically similar but structurally dissimilar compounds, or link natural products to candidate coding BGCs in large experimental datasets. We demonstrate the latter by rediscovering the nocardichelin B BGC as a proof of principle. We also exemplify the utility of biosynthetic similarity by showing various pairs of biosynthetically similar compounds with low structural similarity. Together, these results establish primary sequences as a shared biosynthetic encoding for natural product comparison and BGC prioritization.

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

A Diffusion Approximation for Temporal-Difference Learning with Linear Features under Markovian Noise

arXiv:2606.18183v1 Announce Type: cross Abstract: Temporal difference (TD) learning with linear function approximation is a core method for policy evaluation. Its classical continuous-time description is an ordinary differential equation (ODE), which captures the asymptotic mean dynamics but neglects stochastic fluctuations determining the error floor. We introduce a stochastic differential equation (SDE) approximation for linear TD(0) under Markovian noise. The resulting model distinguishes the contraction dynamics governed by the projected Bellman operator from the influence of Markovian sampling. As a consequence, the model explains the constant-stepsize error floor through the interaction between Markovian long-run covariance and the contraction geometry of the projected Bellman operator.

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

SpatioTemporal Causal Network Diagnostics for Geographic Tipping Point Early Warning

arXiv:2606.17553v1 Announce Type: new Abstract: Geographic tipping points in ecosystems, climate subsystems, or ice sheets pose severe challenges for localized early warning. Classical spatial indicators such as Moran's I summarize global spatial structure, but they struggle with three issues: spatial dilution, Euclidean assumptions, and correlated noise. This paper introduces SpatioTemporal Causal Network Diagnostics (ST-CND), a framework that addresses these three issues by representing the geographic field as a time-evolving directed causal network. The core workflow is as follows: (1) infer which spatial nodes help predict other nodes via transfer entropy, replacing fixed Euclidean neighborhoods with data-driven information-flow topology; (2) estimate local recovery rates within each candidate subnetwork via dynamic mode decomposition; and (3) identify the most vulnerable subnetwork by combining three signals, namely high internal fluctuation, high internal synchronization, and low external coupling, thereby suppressing false alarms from spatially correlated noise. Validated on synthetic bifurcations and two observational sea-surface temperature benchmarks, namely Indo-Pacific SST and North Atlantic AMOC, ST-CND delivers localized and interpretable warnings. On the AMOC task, it achieves an AUROC of 0.783 and a critical-subnetwork IoU of 0.378, outperforming recurrence-network and lambda-AR1 baselines. The framework provides an interpretable and scalable pipeline for spatial early warning in Earth system science.