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01.
arXiv (quant-ph) 2026-06-16

Real-space spectral functions of three-dimensional billion-size topological non-Hermitian matter with tensor networks

arXiv:2606.16424v1 Announce Type: cross Abstract: Non-Hermitian systems host a wide range of unconventional topological phenomena while large-scale simulations in finite three dimensional systems remain challenging because of the rapidly growing number of sites. In particular, higher-order topological corner modes are often studied only in small lattices, where strong finite-size effects can mask their intrinsic behavior. Here, we develop a tensor-network framework that combines quantics tensor cross interpolation with the kernel polynomial method, enabling compact representations of large non-Hermitian tight-binding Hamiltonians and direct calculations of real-space spectral functions for systems exceeding one billion lattice sites. Using this approach, we investigate three-dimensional non-Hermitian higher-order topological insulators with with structured real-space geometries. The unprecedented system size enables direct access to the macroscopic regime and allows corner-mode spectral responses to be resolved in genuinely three-dimensional systems.By tuning the loss strength, we identify distinct in-gap corner modes across weak- and strong-loss regimes.Our results establish tensor-network algorithms as a powerful strategy to perform real-space spectral calculations in exceptionally large non-Hermitian systems.

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

A Tool for the Synthesis of Adaptive Probabilistic Processors Based on the Ising Model

arXiv:2606.19533v1 Announce Type: cross Abstract: This work presents a tool for the synthesis and simulation of probabilistic architectures for solving combinatorial optimization problems by mapping them to the Ising model. The proposed approach automatically constructs the Ising Hamiltonian and determines the number of probabilistic elements (p-bits) based on problem characteristics such as size and topology. Furthermore, the tool introduces an adaptive strategy for selecting the most suitable update algorithm among Gibbs Sampling, Simulated Annealing (SA), Simulated Quantum Annealing (SQA), and cluster-based methods. Experimental results using benchmark problems demonstrate improved convergence behavior and flexibility compared to fixed approaches. The proposed framework enables systematic evaluation of probabilistic computing strategies and supports the development of future hardware implementations based on MTJs and p-bits.

03.
bioRxiv (Bioinfo) 2026-06-15

RepGene: Toward a Unified Gene Representation Space Robust to Missing Biological Views

Genes can be described through multiple heterogeneous biological views, including genomic sequence, transcript sequence, protein sequence, textual knowledge, and single-cell expression context, yet existing gene embeddings remain largely modality-specific and difficult to compare or reuse when many views are unavailable. We study a narrower but practically important question: whether pretrained embeddings from these distinct sources can be organized into a shared gene representation interface that remains usable under severe missing-modality conditions. To investigate this question, we introduce RepGene, a lightweight single-branch framework that combines modality adapters, a shared encoder, presence-aware fusion, and self-supervised cross-view objectives to map five biological views into one latent space. Our goal is not to claim a new multimodal learning principle or to establish superiority over all simpler fusion strategies, but to provide an initial technical instantiation for testing whether such a shared interface is feasible in a fixed-feature setting. Under a two-stage protocol in which RepGene is trained self-supervised on frozen upstream embeddings and evaluated by downstream linear probing, we find preliminary evidence that the learned representation is broadly competitive in the full-modality setting and remains informative when only partial modality subsets are observed at inference time. The strongest signal in our study is robustness under missing views: average performance changes are often limited when one modality is removed, and even single-view inference remains non-trivial in the evaluated benchmark regime.These results do not resolve unified biological representation learning, and they should be interpreted in light of incomplete simple-fusion baselines, limited architectural ablation, benchmark dependence, and possible upstream feature exposure. We therefore position RepGene as a feasibility study and a starting point for stronger comparisons, broader benchmarks, and leakage-aware validation.

04.
medRxiv (Medicine) 2026-06-11

Plasma protein prioritisation in rheumatoid arthritis reveals druggable targets and shared biology with cardiovascular diseases

Abstract Background Rheumatoid arthritis (RA) is an autoimmune inflammatory disease with complex and incompletely understood molecular mechanisms. Understanding circulating proteins associated with RA may improve understanding of disease biology and clarify its pathological links with cardiometabolic comorbidities. Methods A proteome-wide two-sample Mendelian randomisation (MR) drug target analysis was conducted using plasma proteins measured in 54,219 participants from the UK Biobank Pharma Proteomics Project as exposures and RA and cardiometabolic diseases as the outcomes. Summary statistics for RA included 53,663 cases and 1,070,200 controls. Colocalisation analysis was performed to confirm shared single causal variants and prioritise RA proteins supported by both MR and colocalisation. The prioritised proteins were then evaluated in the Accelerating Medicines Partnership RA Phase II synovial single-cell dataset for cell-type expression patterns. Druggability was then assessed followed by analysis of genetic overlap between RA-associated proteins and cardiometabolic diseases. Results 37 plasma proteins had a causal effect on RA risk, supported by combined evidence from MR and conditional colocalisation. In synovial tissue, TPPP3, RARRES2, AKAP12, and GGT5 were predominantly expressed in stromal and endothelial cell clusters. Druggability assessment identified IFNGR2, IL6R, CD40, and FCGR2B as Tier 1 targets. However, several biologically relevant proteins, including RARRES2, AKAP12, TPPP3, and SNX2, had limited available druggability data. Genetic overlap analysis demonstrated shared protein signals between RA and cardiovascular diseases, including overlap of RARRES2 and TPPP3 with coronary artery disease (CAD) and FCGR2B with atrial fibrillation (AF). To approximate the therapeutic effect of target inhibition, the direction of effect estimates for proteins showing overlap between RA-CAD and RA-AF was reversed. Conclusion This study identified circulating proteins involved in RA pathogenesis and reveals shared mechanisms between RA and cardiovascular diseases. While some proteins showed clear translational potential targets, several prioritised proteins had limited available druggability information and could not be confidently classified. Addressing these gaps may help identify new targets relevant to RA management. Future work should also use phenome-wide MR studies to evaluate potential on-target adverse effects of protein inhibition across RA-CAD and RA-AF.

05.
arXiv (math.PR) 2026-06-16

Excursion Fluctuations and Spectral Universality in Gaussian Fields

arXiv:2606.15630v1 Announce Type: new Abstract: We study the large-scale spatial fluctuations of excursion volumes for a class of smooth stationary Gaussian fields. In the case of Berry's random wave model in dimension $d \geq 2$, we show that the spatial fluctuations for fixed $u>0$ converge to the fractional Gaussian field $(-\Delta)^{-1/4}W$ in the space of tempered distributions $\mathcal S'(\mathbb{R}^d)$, where $W$ is the $d$-dimensional Gaussian white noise. This explains the long-range correlations in the apparent filament structure of the Random Plane Wave model. For a class of smooth planar Gaussian fields whose spectral density has a power-law singularity at the origin, we prove convergence to fractional Gaussian fields with an index determined by the singularity exponent. More generally, the results illustrate that, for stationary random measures, large-scale spatial fluctuations are determined by the behaviour of the spectral measure density exponent near zero.

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

DN-Hypo-Pipeline: An AI-Driven Workflow for Hypothesis Generation via Large Language Models and Scientific Explanations

arXiv:2606.08532v2 Announce Type: replace Abstract: A scientific hypothesis is the first step in research and undergoes experimental validation, yet it also reflects a deep understanding of and reasoning about scientific phenomena. We introduce DN-Hypo-Pipeline, an AI-powered workflow based on large language models, designed to support structured scientific thinking and hypothesis generation by leveraging scientific explanations as prior knowledge. This pipeline assists researchers in deriving novel hypotheses from existing literature. Given the explanandum (i.e., the conclusion) of a research paper, it identifies underlying laws, theories, and principles, and reconstructs a new, yet-to-be-verified explanation for the observed phenomenon. We evaluated DN-Hypo-Pipeline in the field of data science modeling using three highly cited papers. Statistical inference, supported by both LLM-as-judge assessment and human expert evaluation, demonstrates that our pipeline is more effective than direct generation methods. Additionally, we validated the two highest-scoring generated hypotheses by developing corresponding novel algorithms, which outperformed the baseline models presented in the original papers. Beyond application in data science, DN-Hypo-Pipeline provides a theoretical framework that not only encompasses theory-guided data science modeling methods but also reveals a more fundamental structure of the modeling process. Moreover, this approach is essentially a generalization of theory-guided modeling, offering potential for extension to other domains and across a broader range of scientific disciplines.

07.
bioRxiv (Bioinfo) 2026-06-23

FateLimit quantifies the prediction horizon of cell fate

Single-cell technologies have enabled increasingly detailed reconstruction of developmental trajectories, yet a fundamental question remains unresolved: when does future cellular identity become predictable from cells current molecular state? Existing approaches infer lineage relationships, transition probabilities or future transcriptional dynamics, but do not directly quantify the emergence of fate predictability during cellular state transitions. Here we present FateLimit, an information-theoretic framework for measuring the temporal dynamics of cell-fate predictability from single-cell omics data. FateLimit combines probabilistic fate assignment, fate entropy and mutual information to quantify how information about future cellular outcomes is encoded in present molecular states. We introduce two quantitative descriptors: the Fate Information Half-Life (FIHL), which measures the characteristic timescale of fate-information dynamics, and the Prediction Horizon (PH), defined as the earliest developmental stage at which observed fate predictability exceeds the 95th percentile of a permutation-derived null distribution. We applied FateLimit across developmental, lineage-tracing and reprogramming systems, including pancreatic endocrinogenesis, CellTag reprogramming, human hematopoiesis and zebrafish embryogenesis. Across all datasets, FateLimit identified significant fate information and reproducible prediction horizons that were robust to cell-state representation, lineage structure and biological context. Comparative analysis revealed that prediction horizons differ substantially among cellular lineages, indicating that distinct developmental programs acquire predictive information at different rates. FateLimit establishes a general framework for quantifying the predictability of future cellular identity from present molecular states. By transforming developmental trajectories into predictability landscapes, FateLimit enables systematic comparison of commitment dynamics across biological systems and establishes prediction horizons as a quantitative measure of cell-fate determination.

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

Instrumental and Proximal Causal Inference with Gaussian Processes

arXiv:2603.02159v2 Announce Type: replace-cross Abstract: Instrumental variable (IV) and proximal causal learning (Proxy) methods are central frameworks for causal inference in the presence of unobserved confounding. Despite substantial methodological advances, existing approaches rarely provide reliable epistemic uncertainty (EU) quantification. We address this gap through a Deconditional Gaussian Process (DGP) framework for uncertainty-aware causal learning. Our formulation recovers popular kernel estimators as the posterior mean, ensuring predictive precision, while the posterior variance yields principled and well-calibrated EU. Moreover, the probabilistic structure enables systematic model selection via marginal log-likelihood optimization. Empirical results demonstrate strong predictive performance alongside informative EU quantification, evaluated via empirical coverage frequencies and decision-aware accuracy rejection curves. Together, our approach provides a unified, practical solution for causal inference under unobserved confounding with reliable uncertainty.

09.
medRxiv (Medicine) 2026-06-17

Investigating shared genetic overlap of immune-mediated inflammatory diseases and cardiometabolic diseases

Abstract Background: Immune-mediated inflammatory diseases (IMIDs) are associated with increased risk of cardiometabolic diseases. Investigating genetic overlap among these conditions can provide insights into their clinical management. Methods: Genetic correlation was assessed using linkage disequilibrium score regression (LDSC). Then, a meta-analysis was conducted using Association Analysis Based on SubSETs (ASSET) to pinpoint independent single nucleotide polymorphisms (SNPs) shared across the diseases. Each independent SNP was then used to define a genomic window (+/-500KB) for colocalisation analysis and Local Analysis of [co]Variant Association (LAVA) to offer multiple layers of regional pleiotropic evidence. Over-representation analysis was then run to identify enriched biological pathways, which then were used for drug target analysis. Results: The LDSC analysis showed a significant global genetic correlation for rheumatoid arthritis (RA) and cardiometabolic diseases including hypertension, coronary artery disease (CAD), heart failure (HF), stroke, atrial fibrillation (AF), and type two diabetes mellitus (T2DM) ranging from rg = 0.09 to 0.24. ASSET meta-analysis identified 164 independent SNPs shared across RA and the cardiometabolic diseases with P < 5 x 10- in the overall one-sided meta-analysis P-value, FDR < 0.05 in both individual GWASs, and TRUE phenotype matrix. Colocalisation analysis revealed multiple loci with strong evidence (Posterior probabilities [&ge;] 80) of single causal SNPs between the trait pairs. LAVA analysis was then used as an additional layer of confirmation for the findings generated by ASSET and colocalisation and thus several loci were highlighted. Over-representation analysis showed significant enriched immune-related pathways across RA-hypertension, RA-CAD, RA-AF, and RA-T2DM trait pairs. Drug target analysis highlighted several drugs which could be further tested for their effectiveness in RA and its common comorbidities. Conclusion: The findings revealed a shared genetic architecture and key immune-related biological pathways underlying RA and its associated cardiometabolic comorbidities. The identified genes and drugs provide opportunities for further therapeutic assessment which could improve clinical management strategies.

10.
arXiv (CS.AI) 2026-06-25

On-Policy Self-Distillation with Sampled Demonstrations Reduces Output Diversity

arXiv:2606.26091v1 Announce Type: cross Abstract: On-policy self-distillation achieves strong pass@1 accuracy by using a single model as both teacher and student, with the teacher conditioned on a correct demonstration to provide dense token-level feedback. We show that this could come at a hidden cost: rollout diversity decreases and pass@k curves flatten (i.e., generating more rollouts fails to improve accuracy). We trace this to compounding biases in the design of self-distillation with sampled demonstrations. The teacher scores each student rollout while conditioned on a sampled correct rollout, channeling its feedback through the model's own biases. We theoretically analyze the optimal self-distillation policy and show that it tilts the base distribution by a pointwise conditional mutual information score between the student's rollout and the correct rollout used as context. Unlike the ideal optimal on-policy reinforcement learning (RL), which preserves probability ratios among equally correct rollouts, self-distillation can amplify existing probability gaps, concentrating mass on already-dominant modes. On a controlled graph path-finding task and science question-answering benchmarks, self-distilled models match or exceed RL on average performance but exhibit substantially lower functional and semantic diversity, failing on out-of-distribution settings that require diverse strategies.

11.
arXiv (CS.AI) 2026-06-16

CONCORD: Asynchronous Sparse Aggregation for Device-Cloud RAG under Document Isolation

arXiv:2606.15179v1 Announce Type: new Abstract: Retrieval-augmented generation (RAG) has emerged as a pivotal technique for improving language models by incorporating external knowledge at inference time. As device-cloud collaborative inference makes it feasible to deploy small language models on edge devices, a new setting arises in which private documents remain on the device and public knowledge resides in the cloud. Privacy and policy constraints often forbid raw document exchange, creating a document-isolated dual-end RAG setting. However, existing methods rely on frequent remote synchronization and dense evidence transfer, limiting throughput under realistic latency and bandwidth conditions. To address this issue, we propose CONCORD, an asynchronous sparse aggregation framework for dual-end RAG under document isolation. CONCORD treats the cloud as an asynchronously arriving evidence source rather than a continuously synchronized co-generator. Specifically, we introduce waiting debt control to decide whether each decoding step should continue waiting for remote participation based on the observed return of waiting. We also design a certificate-guided minimal supplementation mechanism that requests only the remote evidence needed to determine the current greedy decision. Steps that consult the cloud preserve the same greedy token as dense dual-end aggregation, while the remaining steps commit locally without remote evidence. Experiments on Natural Questions and WikiText-2 show that CONCORD improves end-to-end throughput over baselines by $1.66\times$ and $2.15\times$, respectively, while reducing per-token communication by over two orders of magnitude and maintaining comparable answer quality and perplexity.

12.
arXiv (CS.AI) 2026-06-17

Gaussian DP for Reporting Differential Privacy Guarantees in Machine Learning

arXiv:2503.10945v3 Announce Type: replace-cross Abstract: Current practices for reporting differential privacy (DP) guarantees for machine learning (ML) algorithms such as DP-SGD provide an incomplete and potentially misleading picture. For instance, if only a single $(\varepsilon, \delta)$ is known about a mechanism, standard analyses show that there could exist highly accurate inference attacks against training data records, when, upon a more careful analysis, such accurate attacks do not exist for most practical mechanisms. In this position paper, we argue that using _non-asymptotic_ Gaussian Differential Privacy (GDP) as the primary means of communicating DP guarantees in ML avoids these potential downsides. Using two recent developments in the DP literature: (i) open-source numerical accountants capable of computing the privacy profile and $f$-DP curves of DP-SGD to arbitrary accuracy, and (ii) a decision-theoretic metric over DP representations, we show how to provide non-asymptotic bounds on GDP using numerical accountants, and show that GDP can capture the entire privacy profile of DP-SGD and related algorithms with virtually no error, as quantified by the metric. To support our claims, we investigate the privacy profiles of state-of-the-art DP large-scale image classification, and the TopDown algorithm for the U.S. Decennial Census, observing that GDP fits their profiles remarkably well in all cases. We conclude with a discussion on the strengths and weaknesses of this approach, and discuss which other privacy mechanisms could benefit from GDP.

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

On The Effectiveness-Fluency Trade-Off In LLM Conditioning: A Systematic Study

Controlling the output of Large Language Models (LLMs) is a central challenge for their reliable deployment, yet a clear understanding of the involved trade-offs remains elusive. Current approaches to conditioning are often evaluated with a narrow focus on their effectiveness at injecting or removing a target concept, neglecting generation quality. We systematically investigate a range of conditioning methods in both injection and removal scenarios. We find that efficient steering methods frequently achieve conditioning at a steep cost to fluency. Furthermore, we identify a critical yet previously overlooked interaction with the training paradigm: activation steering methods are far less effective on instruction-tuned models than on their base counterparts. Simple prompting and full-fledged supervised fine-tuning, on the other hand, are viable options for concept injection, but are not as good at concept removal. Finally, cheaply computed textual metrics highly correlate to costly LLM-as-judge scores, and provide insights on the behavior of conditioning methods.

14.
arXiv (CS.AI) 2026-06-18

IPSL-AID: Generative Diffusion Models for Climate Downscaling from Global to Regional Scales

arXiv:2604.03275v2 Announce Type: replace-cross Abstract: Effective adaptation and mitigation strategies for climate change require high-resolution projections to inform strategic decision-making. Conventional global climate models, which typically operate at resolutions of 150 to 200 kilometers, lack the capacity to represent essential regional processes. IPSL-AID is a global to regional downscaling tool based on a denoising diffusion probabilistic model designed to address this limitation. Trained on ERA5 reanalysis data, it generates 0.25 degree resolution fields for temperature, wind, and precipitation using coarse inputs and their spatiotemporal context. It also models probability distributions of fine-scale features to produce plausible scenarios for uncertainty quantification. The model accurately reconstructs statistical distributions, including extreme events, power spectra, and spatial structures. This work highlights the potential of generative diffusion models for efficient climate downscaling with uncertainty

15.
arXiv (CS.CV) 2026-06-12

An Extensible and Lightweight Unified Architecture for Demosaicing Pixel-bin Image Sensors

Pixel-bin image sensors are becoming the default choice for smartphone cameras due to their resolution vs light-gathering trade-off. However, their larger inter-color separation compared to the Bayer color filter array (CFA) makes them challenging to demosaic. Furthermore, existing deep learning-based demosaicing methods are CFA-specific, requiring multiple individual models that take up precious onboard resources and demand larger development and maintenance efforts. In this work, we propose a modular unified architecture for demosaicing various pixel-bin sensors that provides higher image quality while being extensible and lightweight. Additionally, to enable plug-and-play operation, we introduce a learning-free CFA-identification module to detect the CFA type of raw data accurately.

16.
medRxiv (Medicine) 2026-06-15

Dysplasia-Stratified Management of Barrett's Esophagus: An Incidence-Based U.S. Cost-Effectiveness Analysis

作者:

Background and Aims Barrett's esophagus (BE) is the principal precursor of esophageal adenocarcinoma (EAC), whose incidence has risen sharply in Western countries since the 1960s. Effective, dysplasia stratified surveillance strategies are needed to prevent progression. This study evaluated the cost effectiveness of dysplasia stratified surveillance intervals and endoscopic eradication therapy (EET) across the BE spectrum. Methods We developed an incidence-based Markov state transition model of BE progression calibrated to U.S. epidemiologic data from a healthcare sector perspective over a lifetime horizon. Four hypothetical cohorts of 50-year-old individuals with short segment BE (SSBE), nondysplastic BE (NDBE), low grade dysplasia (LGD), or high-grade dysplasia (HGD) were evaluated. Strategies included no surveillance; surveillance at 1-, 2-, 3-, 4-, 5-, or 10-year intervals; standard or AI assisted endoscopy; non endoscopic screening (sponge, breath, miRNA tests); and EET for LGD and HGD. Outcomes included costs, quality adjusted life years (QALYs), incremental cost effectiveness ratios (ICERs), net monetary benefits (NMBs), EAC cases, and EAC-related deaths. Sensitivity analyses used a willingness to pay threshold of US$100,000 per QALY. Results No surveillance was the most cost-effective strategy for SSBE and NDBE. For LGD, upfront EET was more cost effective than all surveillance strategies, with results sensitive to EAC incidence and recurrence. For HGD, EET was cost saving and yielded the greatest QALYs, with findings robust in 99.9% of simulations. EET prevented 12,614 and 44,295 EAC related deaths per 100,000 individuals with LGD and HGD, respectively. Conclusion Dysplasia-stratified management is essential for optimizing surveillance and treatment strategies in BE. Any degree of dysplasia should receive EET followed by targeted post-treatment monitoring, establishing EET as the central therapeutic pathway for dysplastic BE.

17.
arXiv (CS.AI) 2026-06-18

The Long Delay to Arithmetic Generalization: When Learned Representations Outrun Behavior

arXiv:2604.13082v2 Announce Type: replace-cross Abstract: Grokking in transformers trained on algorithmic tasks is characterized by a long delay between training-set fit and abrupt generalization, but the source of that delay remains poorly understood. In encoder-decoder arithmetic models, we argue that this delay reflects limited access to already learned structure rather than failure to acquire that structure in the first place. We study one-step Collatz prediction and find that the encoder organizes parity and residue structure within the first few thousand training steps, while output accuracy remains near chance for tens of thousands more. Causal interventions support the decoder bottleneck hypothesis. Transplanting a trained encoder into a fresh model accelerates grokking by 2.75 times, while transplanting a trained decoder actively hurts. Freezing a converged encoder and retraining only the decoder eliminates the plateau entirely and yields 97.6% accuracy, compared to 86.1% for joint training. What makes the decoder's job harder or easier depends on numeral representation. Across 15 bases, those whose factorization aligns with the Collatz map's arithmetic (e.g., base 24) reach 99.8% accuracy, while binary fails completely because its representations collapse and never recover. The choice of base acts as an inductive bias that controls how much local digit structure the decoder can exploit, producing large differences in learnability from the same underlying task.

18.
arXiv (CS.AI) 2026-06-11

TreeSeeker: Tree-Structured Trial, Error, and Return in Deep Search

arXiv:2606.11662v1 Announce Type: new Abstract: Deep search requires agents to answer complex questions through multi-step web search, browsing, evidence comparison, and synthesis. A central challenge is deciding how to search when several directions look plausible but only some will later lead to reliable evidence. If an agent greedily follows the current best-looking direction, it may keep extending a weak continuation. If it explores without discipline, it may waste budget on disconnected trials. We propose TreeSeeker, an inference-time framework for controlled trial-and-error in deep search. TreeSeeker organizes search as branch-and-return search over tree-structured states, where each branch is a tentative direction for a sub-goal. At each round, TreeSearch reads all sub-goal trees, identifies active goals, and uses textual UCB signals of value, uncertainty, and risk to select among exploiting a promising branch, exploring an uncertain alternative, or pruning an unproductive continuation and returning to an earlier branch point. TreeMem supports this control loop by keeping evidence, uncertainty, conflicts, progress, and failure cues attached to the branches that produced them, so trial outcomes can guide later decisions. Experiments on XBench-DeepSearch, BrowseComp, and BrowseComp-ZH show that TreeSeeker consistently outperforms strong open-source baselines, suggesting that explicit branch-and-return control complements stronger reasoning and tool execution.

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

Type Checking Project Haystack Grids using JSON Schema and Pydantic

arXiv:2606.24891v1 Announce Type: cross Abstract: Ontologies enable scalable energy services in buildings by supporting interoperability and automation. Project Haystack is a building ontology that is widely adopted due to its flexible, tag-based semantic model, openness, and extensibility, but suffers from ambiguous tag usage and limited automated validation. Although Project Haystack is formally open, its reliance on custom file formats and domain-specific languages that originate from the Haxall ecosystem creates a de facto barrier to integration. In this paper, we address these limitations by introducing a Python-based toolchain for Haystack. We present (i) a parser for Haystack definition files (Trio file format), and (ii) a code generator that derives Pydantic models and JSON Schema definitions from these parsed specifications. The resulting models enable static type checking and enable structural validation of Haystack grids within Python, as well as schema-based validation of JSON representations outside the Python ecosystem. All tools, generated models, and schemas are released publicly under an open-source license, with the goal of strengthening the Haystack ecosystem and opening a practical pathway beyond its current technical boundaries.

20.
arXiv (math.PR) 2026-06-18

The FBSDE approach to sine-Gordon up to $6\pi$

arXiv:2401.13648v3 Announce Type: replace-cross Abstract: We develop a stochastic analysis of the sine-Gordon Euclidean quantum field $(\cos (\beta \varphi))_2$ on the full space up to the second threshold, i.e. for $\beta^2 < 6 \pi$. The basis of our method is a forward-backward stochastic differential equation (FBSDE) for a decomposition $(X_t)_{t \geqslant 0}$ of the interacting Euclidean field $X_{\infty}$ along a scale parameter $t \geqslant 0$. This FBSDE describes the optimiser of the stochastic control representation of the Euclidean QFT introduced by Barashkov and one of the authors. We show that the FBSDE provides a description of the interacting field without cut-offs and that it can be used effectively to study the sine-Gordon measure to obtain results about large deviations, integrability, decay of correlations for local observables, singularity with respect to the free field, Osterwalder-Schrader axioms and other properties.

21.
arXiv (CS.CL) 2026-06-24

AfriqueLLM: How Data Mixing and Model Architecture Impact Continued Pre-training for African Languages

Large language models (LLMs) are increasingly multilingual, yet open models continue to underperform relative to proprietary systems, with the gap most pronounced for African languages. Continued pre-training (CPT) offers a practical route to language adaptation, but improvements on demanding capabilities such as mathematical reasoning often remain limited. This limitation is driven in part by the uneven domain coverage and missing task-relevant knowledge that characterize many low-resource language corpora. We present \texttt{AfriqueLLM}, a suite of open LLMs adapted to 20 African languages through CPT on 26B tokens. We perform a comprehensive empirical study across five base models spanning sizes and architectures, including Llama 3.1, Gemma 3, and Qwen 3, and systematically analyze how CPT data composition shapes downstream performance. In particular, we vary mixtures that include math, code, and synthetic translated data, and evaluate the resulting models on a range of multilingual benchmarks. Our results identify data composition as the primary driver of CPT gains. Adding math, code, and synthetic translated data yields consistent improvements, including on reasoning-oriented evaluations. Within a fixed architecture, larger models typically improve performance, but architectural choices dominate scale when comparing across model families. Moreover, strong multilingual performance in the base model does not reliably predict post-CPT outcomes; robust architectures coupled with task-aligned data provide a more dependable recipe. Finally, our best models improve long-context performance, including document-level translation. Models and code have been released on [Huggingface](https://huggingface.co/collections/McGill-NLP/afriquellm) and [Github](https://github.com/McGill-NLP/AfriqueLLM).

22.
arXiv (math.PR) 2026-06-11

Additive Noise, Shift Recovery, and Signed Signals in the Cumulative Distribution Transform

arXiv:2606.11432v1 Announce Type: cross Abstract: The cumulative distribution transform (CDT) is a quantile-based transport representation that exactly linearizes one-dimensional translations of positive densities. We study how this structure behaves under additive perturbations and how it can be exploited for shift recovery. Under a local nondegeneracy condition, we derive a first-order expansion showing that additive noise in physical space induces a nonlocal perturbation in CDT space through the primitive of the noise, weighted by the reciprocal density. This yields an explicit description of transform-domain sensitivity and shows, in particular, that perturbations are amplified in low-density regions. When the physical-space perturbation is modeled as a centered Gaussian random field, the induced first-order CDT perturbation is again Gaussian, with an explicit covariance kernel. We then use this structure to study recovery in CDT coordinates. In the known-template setting, the transport shift is obtained by projection onto the constant mode, giving an explicit estimator together with exactness in the noiseless case and a stability bound under perturbations. In the unknown-template setting, multiple observations permit joint recovery of the shifts and a common template up to the natural constant-mode gauge, leading to a simple de-shift–and–average procedure. We also consider a signed-signal analogue based on the signed cumulative distribution transform (SCDT), where shifts are estimated numerically by feature matching and unknown templates are recovered by alternating alignment and averaging. Numerical experiments validate the perturbation analysis and illustrate effective recovery for both density-valued and signed signals.

23.
arXiv (CS.AI) 2026-06-24

Reentrant value fields as delayed coupled reaction-diffusion systems on finite graphs

arXiv:2605.03940v4 Announce Type: cross Abstract: We describe a dynamical system in which a symbolic field is coupled to a geometric field via a bipartite Hilbert-Schmidt kernel. The system is fully described by a retarded functional differential equation (RFDE) on the history space, subject to Lipschitz and small gain conditions. We show that the RFDE is well-posed under constant input and that it admits a compact global attractor. The principal subsystem $(H_L, X_R, P)$, which is comprised of the two primary fields as well as an executive field, is shown to be globally stable independent of delay, provided that the interfield coupling satisfies $C_{\mathcal{K}}^2

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

Finite Resources False Discovery Rate Control in Structured Hypothesis Spaces

arXiv:2606.15393v1 Announce Type: cross Abstract: Scientific discovery relies on large-scale hypothesis testing. However, the capacity to identify true discoveries while controlling false discovery faces major challenges: obtaining relevant reference data (the null distribution) is resource-intensive, leaving finite-data uncertainty, and the procedure should account for the inherent structure in the hypothesis space, when such structure exists. Here, we present a framework for controlling the false discovery rate both when each hypothesis is evidenced only by a finite count of null draws, leaving its p-value uncertain, and when the hypothesis space carries arbitrary structure, requiring only that the structure be represented through a suitable reproducing kernel. We present two decision rules that are both robust to structural mis-specification, yet offer a distinct trade-off between exact FDR control and statistical power. The first rule guarantees exact FDR control; the second maximizes power by adapting mirror-statistic control into count space, utilizing an analytical framework to assess FDR control when exact mirror symmetry is relaxed. Furthermore, the tractability gained by the RKHS framework allows us to directly investigate finite-data uncertainties, which we leverage to suggest a policy for the efficient allocation of null distribution samples.