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01.
arXiv (CS.AI) 2026-06-15

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

作者:

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.

02.
arXiv (quant-ph) 2026-06-17

Approximately Decoding the Colour Code

作者:

arXiv:2606.18035v1 Announce Type: new Abstract: Recently we showed that minimum weight decoding in the (6.6.6 planar) colour code is NP-hard. However, it remained an open question as to whether it was possible to approximate the minimum weight decoding arbitrarily closely in polynomial time. In this paper we prove that it is possible: for any $\varepsilon>0$ there is an polynomial time algorithm that, given a syndrome, can find an error-set generating that syndrome whose weight is at most $1+\varepsilon$ times the weight of the minimum weight decoding. As a consequence we see that, for any $\varepsilon>0$, there is a polynomial time algorithm that can correct all errors of weight up to $(1-\varepsilon)d/2$ in the distance $d$ colour code (so almost up to the theoretical $d/2$ limit). The polynomial we give is impractically large, but it does open the door for sensible polynomial time algorithms that approximate minimum weight decoding and, in particular, shows that approximate decoding is not NP-hard.

03.
medRxiv (Medicine) 2026-06-11

Decoding the Genetic Architecture of Autistic Traits in the Aging Population

Autism research has mostly focused on diagnostic frameworks in childhood. However, autistic traits including social skills, communication, attention switching, attention to detail, and imagination may also vary in many undiagnosed individuals beyond childhood, and the genetic architecture of autistic traits in undiagnosed aging adults remains poorly understood. Here, we performed an exome-wide association study of autistic traits in adults aged >=40 from the UK Biobank (n = 161,269) and independently validated key findings in the SPARK cohort (n = 142,357). We identified exome-wide significance at 17q21.31, represented by a lead variant associated with social skills (rs199533, beta = 0.081, P = 2.04e-11). In addition, we identified an independent signal for communication (rs12632110, beta = 0.042, P = 3.07e-12) and two independent signals for attention switching (rs690733, beta = 0.046, P = 4.26e-12; rs2164272, beta = -0.047, P = 1.73e-12). Gene-based analyses further implicated loss-of-function variation in ZSCAN2 (beta = 1.00, P = 2.44e-6), which was associated with communication differences. Enrichment analyses revealed preferential expression of implicated genes in the cerebral cortex, while phenotypic and neuroimaging analyses linked those variants to cortical brain structure and regional volume. Taken together, these findings delineate the genetic architecture of autistic traits in the aging population and link genetic variation to downstream molecular and neuroanatomical mechanisms.

04.
arXiv (CS.LG) 2026-06-18

A physical adaptive material motor unit neural network: a hygromorph composite material machine

arXiv:2606.18275v1 Announce Type: cross Abstract: Advances in novel materials science enable structures to function as intelligent machines by embedding memory and learning capabilities directly into materials. Our work introduces a physical adaptive material motor unit neural network,leveraging a new generation of controllable actuators composed of wood- and carbon black-based composites, sensitive to temperature and relative humidity. These material actuators are assembled into a motor unit-like structure inspired by muscle contraction trigger, forming an intelligent machine capable of dynamic shading control that can be used, for example, in buildings. The machine is governed by a neural network trained on over 350 experimental data points collected under diverse environmental conditions. By establishing a new data-aware backpropagation training, we show that the machine predicts shading responses and learns to predict appropriate behaviour incrementally as the database expands. We also demonstrate the ability of the machine to optimise configurations to achieve similar shading outputs under two distinct conditions.

05.
Nature (Science) 2026-06-11

Daily briefing: Deep-sea whale graveyard is a treasure trove of fossils

作者:

Researchers have uncovered more than 400 fossilized whale bones in an ocean-floor chasm. Plus, the working lives of scientists, in pictures, and how AI could slow the pace of research publication for the better. Researchers have uncovered more than 400 fossilized whale bones in an ocean-floor chasm. Plus, the working lives of scientists, in pictures, and how AI could slow the pace of research publication for the better.

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

M-CTX: Exact and Scalable Spatial Context Retrieval for Trajectory Analytics

arXiv:2606.15244v1 Announce Type: new Abstract: Modern trajectory predictors increasingly condition on external spatial context, such as map geometry, signed distance fields (SDFs), and nearby moving agents. While this context improves prediction quality, constructing it for every training anchor has become a hidden systems bottleneck. In a representative maritime AIS pipeline, spatial context construction requires roughly 17 CPU-days for a 5.48M-anchor corpus, dominating the cost of the downstream predictor. We present M-CTX, an exact and scalable spatial context-retrieval framework for trajectory analytics. M-CTX recasts context construction as an ingest-once, query-many spatial database workload and replaces three brute-force stages – OSM range retrieval, SDF computation, and moving-vessel neighbour lookup – with composable, index-backed operators. Its learned range-index backend, BR-LZ, provides recall-complete MBR-overlap range retrieval and reduces candidate amplification by 1.1x–2.7x relative to global-expansion one-curve baselines. Across four maritime regions, eight baseline systems, synthetic workloads with up to 40M spatial features, and 10^7-record AIS streams, M-CTX reproduces the reference context exactly. On the 5.48M-anchor corpus, it reduces context construction from about 17 CPU-days to 1.8 hours, a measured 226x end-to-end speed-up. An optional storage mode further compresses SDF context by 64x with only a 0.04 m ADE change. These results establish exact spatial context retrieval as a first-class database problem in modern trajectory analytics. Code and datasets are publicly available at https://github.com/mark000071/M-CTX-Traj.

07.
arXiv (CS.LG) 2026-06-16

Diffusion Flow Matching: Dimension-Improved KL Bounds and Wasserstein Guarantees

arXiv:2606.16610v1 Announce Type: cross Abstract: Diffusion Flow Matching (DFM) has recently emerged as a versatile framework for generative modeling, yet its theoretical convergence properties remain only partially understood. In this work, we provide refined and novel convergence guarantees for Brownian motion based DFMs, focusing on the discretization error. Our analysis is conducted under the Kullback-Leibler (KL) divergence and the 2-Wasserstein distance. Under finite-moment conditions and a mild score integrability assumption, we derive KL convergence bounds with improved dimensional dependence compared to prior work, achieving, up to our knowledge, state-of-the-art scaling under minimal conditions. We further extend the analysis to the 2-Wasserstein distance: under an additional first-order score integrability assumption and a weak log-concavity condition, we obtain convergence guarantees with dimensional dependence consistent with the KL case.

08.
arXiv (CS.AI) 2026-06-11

Synthetic Homes: A Multimodal Generative AI Pipeline for Residential Building Data Generation under Data Scarcity

arXiv:2509.09794v5 Announce Type: replace Abstract: Computational models have emerged as powerful tools for multi-scale energy modeling research at the building and urban scale, supporting data-driven analysis across building and urban energy systems. However, these models require large amounts of building parameter data that is often inaccessible, expensive to collect, or subject to privacy constraints. We introduce a modular, multimodal generative Artificial Intelligence (AI) framework that integrates image, tabular, and simulation-based components and produces synthetic residential building datasets from publicly available county records and images, and present an end-to-end pipeline instantiating this framework. To reduce typical Large Language Model (LLM) challenges, we evaluate our model's components using occlusion-based visual focus analysis. Our analysis demonstrates that our selected vision-language model achieves greater visual focus than a GPT-based alternative for building image processing. We also assess realism of our results against a national reference dataset, finding that our synthetic data overlaps more than 95% for three of the four selected variables. This work reduces dependence on costly or restricted data sources, lowering barriers to building-scale energy research and Machine Learning (ML)-driven urban energy modeling, and therefore enabling scalable downstream tasks such as energy modeling, retrofit analysis, and urban-scale simulation under data scarcity.

09.
arXiv (CS.LG) 2026-06-15

Towards Efficient Large Language Reasoning Models via Extreme-Ratio Chain-of-Thought Compression

arXiv:2602.08324v5 Announce Type: replace Abstract: Chain-of-Thought (CoT) reasoning successfully enhances the reasoning capabilities of Large Language Models (LLMs), yet it incurs substantial computational overhead for inference. Existing CoT compression methods often suffer from a critical loss of logical fidelity at high compression ratios, resulting in significant performance degradation. To achieve high-fidelity, fast reasoning, we propose a novel EXTreme-RAtio Chain-of-Thought Compression framework, termed Extra-CoT, which aggressively reduces the token budget while preserving answer accuracy. To generate reliable, high-fidelity supervision, we first train a dedicated semantically-preserved compressor on mathematical CoT data with fine-grained annotations. An LLM is then fine-tuned on these compressed pairs via a mixed-ratio supervised fine-tuning (SFT), teaching it to follow a spectrum of compression budgets and providing a stable initialization for reinforcement learning (RL). We further propose Constrained and Hierarchical Ratio Policy Optimization (CHRPO) to explicitly incentivize question-solving ability under lower budgets by a hierarchical reward. Experiments on three mathematical reasoning benchmarks show the superiority of Extra-CoT. For example, on MATH-500 using Qwen3-1.7B, Extra-CoT achieves over 73\% token reduction with an accuracy improvement of 0.6\%, significantly outperforming state-of-the-art (SOTA) methods. Our source codes have been released at https://github.com/Mwie1024/Extra-CoT.

10.
medRxiv (Medicine) 2026-06-11

PCRAgent: A Multi-Agent Framework for Transforming Noisy clinical conversations into Structured Pre-Consultation Medical Records and Reusable Clinical Data Resources

In primary care and outpatient settings, clinically important patient information is often embedded in fragmented, ambiguous, repetitive, and noisy communication between physicians and patients. This limits physicians ability to obtain a clear preconsultation overview of symptoms, history of present illness, and visit intent, while also preventing real world clinical dialogues from being reused in hospital information systems and medical artificial intelligence applications. To address this challenge, we developed PCRAgent, a centrally coordinated multi agent framework for preconsultation clinical information organization. Guided by physician inquiry logic, PCRAgent identifies, extracts, corrects, and standardizes patient-reported information from noisy consultations. Its coordinated modules including error detection, semantic editing, output control, contextual memory, and intent recognition enable robust parallel handling of spelling errors, repetitions, grammatical inconsistencies, medical ambiguities, and non-medical interference. A traceable edit list records intermediate corrections and context, allowing iterative refinement without redundant modifications. PCRAgent generates two complementary outputs. One is a PreConsultation Clinical Report for rapid physician review. The other is a Structured Clinical Conversation Dataset for hospital data construction and downstream AI applications. In evaluations using 220000 strongly perturbed consultations, PCRAgent maintained high robustness, achieving a clinical information accuracy of 4.99 out of 5 and key element completeness of 5 out of 5, outperforming GPT4o. Expert review of Chinese and English dialogues confirmed high clinical accuracy of 4.85 out of 5 and high safety of 4.79 out of 5. Multicenter validation in real-world outpatient workflows further demonstrated practical utility. These findings indicate that PCRAgent can efficiently transform noisy and unstructured consultations into physician ready reports and AI ready structured data, improving outpatient efficiency, reducing cognitive burden, ensuring information completeness, supporting precise decision-making, and enabling high-quality reuse of clinical data.

11.
arXiv (CS.AI) 2026-06-15

From Sorting Algorithms to Scalable Kernels: Bayesian Optimization in High-Dimensional Permutation Spaces

arXiv:2507.13263v4 Announce Type: replace-cross Abstract: Bayesian Optimization (BO) is a powerful tool for black-box optimization, but its application to high-dimensional permutation spaces is severely limited by the challenge of defining scalable representations. The current state-of-the-art BO approach for permutation spaces relies on an exhaustive $\Omega(n^2)$ pairwise comparison, inducing a dense representation that is impractical for large-scale permutations. To break this barrier, we introduce a novel framework for generating efficient permutation representations via kernel functions derived from sorting algorithms. Within this framework, the Mallows kernel can be viewed as a special instance derived from enumeration sort. Further, we introduce the Merge Kernel , which leverages the divide-and-conquer structure of merge sort to produce a compact, $\Theta(n\log n)$ to achieve the lowest possible complexity with no information loss and effectively capture permutation structure. Our central thesis is that the Merge Kernel performs competitively with the Mallows kernel in low-dimensional settings, but significantly outperforms it in both optimization performance and computational efficiency as the dimension $n$ grows. Extensive evaluations on various permutation optimization benchmarks confirm our hypothesis, demonstrating that the Merge Kernel provides a scalable and more effective solution for Bayesian optimization in high-dimensional permutation spaces, thereby unlocking the potential for tackling previously intractable problems such as large-scale feature ordering and combinatorial neural architecture search.

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

CausalT5k: Diagnosing Refusal and Failure Modes in Trustworthy Causal Reasoning Across Causal Rungs

arXiv:2602.08939v2 Announce Type: replace Abstract: Large language models increasingly produce fluent causal explanations, yet they often fail in ways aggregate accuracy cannot diagnose: confusing association with intervention, abandoning correct judgments under pressure, over-refusing valid claims, or answering when evidence is underdetermined. We introduce CTK, a diagnostic benchmark of 5,147 cases and growing, across 10 domains and all three levels of Pearl's Ladder of Causation. Unlike benchmarks that only score correctness, CTK reveals why a model failed by annotating causal rung, trap type, pressure sensitivity, refusal quality, and Utility-Safety tradeoffs. Its Sheep/Wolf taxonomy separates valid causal designs from inferential traps; paired neutral/pressure variants measure sycophantic drift through Bad Flip Rate; and Wise Refusal fields test whether a model identifies the missing information needed before endorsing a claim. CTK exposes failure modes hidden by aggregate accuracy: the Skepticism Trap, Rung Collapse under scaling, pressure-induced drift, Detection-Correction gaps, and counterfactual error modes. Rather than prescribing a correction method, it provides the diagnostic substrate for studying causal-reasoning failure profiles.

13.
arXiv (quant-ph) 2026-06-16

Efficient Magic State Factory Via Transversal Non-Clifford Gate

arXiv:2606.16199v1 Announce Type: new Abstract: Magic-state preparation is a central component of fault-tolerant quantum computing. Recent theoretical and experimental successes in code-switch-based magic-state preparation have underscored the promise of these methods for quantum error correction. Similarly, magic-state cultivation has likewise been demonstrated in both numerical and experimental settings. However, a thorough comparison between magic-state cultivation and code-switch-based magic-state factories is still missing. In this work, we carry out end-to-end simulations of magic-state preparation using code switching and compare its resource requirements and performance against magic-state cultivation. As part of this analysis, we develop a lattice-surgery protocol for transfer between the doubled color code and the rotated surface code. We extend the complete code-switching protocol to the $d=5$ doubled color code and perform the corresponding end-to-end simulations. Finally, we propose two fault-tolerant magic-state preparation protocols that combine phase-kickback checks with a transversal non-Clifford gate.

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

Ensembling Sparse Autoencoders

arXiv:2505.16077v2 Announce Type: replace Abstract: Sparse autoencoders (SAEs) are used to decompose neural network activations into human-interpretable features. Typically, features learned by a single SAE are used for downstream applications. However, it has recently been shown that a single SAE captures only a limited subset of features that can be extracted from the activation space. Motivated by this limitation, we introduce and formalize SAE ensembles. Furthermore, we propose to ensemble multiple SAEs through naive bagging and boosting. In naive bagging, SAEs trained with different weight initializations are ensembled, whereas in boosting SAEs sequentially trained to minimize the residual error are ensembled. Theoretically, naive bagging and boosting are justified as approaches to reduce reconstruction error. Empirically, we evaluate our ensemble approaches with three settings of language models and SAE architectures. Our empirical results demonstrate that, compared to an expanded SAE that matches the number of features in the ensemble, ensembling SAEs improves the reconstruction of language model activations along with SAE stability. Additionally, on downstream tasks such as concept detection and spurious correlation removal, SAE ensembles achieve better performance, showing improved practical utility.

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

Sentinel: Decoding Context Utilization via Attention Probing for Efficient LLM Context Compression

Retrieval-augmented generation (RAG) often suffers from long and noisy retrieved contexts. Existing context compression methods typically rely on heuristic relevance estimation or supervised compression models rather than on how LLMs utilize retrieved context during inference. We propose Sentinel, a lightweight sentence-level compression framework that decodes inference-time contextual utilization behaviors from head-wise attention patterns of frozen LLMs. To ground supervision in retrieval-dependent answering behavior, Sentinel trains a lightweight probe using QA examples where the model succeeds only when retrieved context is available. Sentinel performs compression using only a single non-autoregressive forward pass without dedicated compression training or autoregressive scoring. Empirically, we find that effective contextual utilization signals remain accessible even in compact proxy models. On LongBench, Sentinel with a 0.5B proxy model achieves up to 5$\times$ compression while attaining question-answering performance competitive with compression methods built on 7B-scale models. Despite being trained only on English QA data, Sentinel also generalizes effectively to Chinese and out-of-domain settings.

16.
arXiv (CS.CV) 2026-06-12

VLADriveBench: Evaluating CoT-Action Relationship in VLA for Autonomous Driving

Vision-language-action (VLA) models generate chain-of-thought (CoT) reasoning alongside driving trajectories, but existing benchmarks evaluate only trajectory quality and do not assess whether the CoT is relevant, consistent, or causally connected to the driving action. We introduce VLADriveBench, a framework that combines observational metrics (mentioning, hallucination, contradiction, action alignment) with a CoT intervention protocol to provide complementary views of the CoT-action relationship. Applying VLADriveBench to three models across two architectures, we find that the two analyses can diverge sharply: ORION scores highest on observational alignment yet its CoT is epiphenomenal, while Alpamayo v1.5 scores lower yet its CoT is strongly causal, with visual salience gating the extent of CoT influence.

17.
medRxiv (Medicine) 2026-06-15

ICD-10 Code Ambiguity Obscures Treatment-Eligible Adults with Spinal Muscular Atrophy: A Single-Center Chart Review and Patient Outreach Study

Background. Three disease-modifying therapies (DMTs) for spinal muscular atrophy (SMA) have been approved since 2016, yet many adults remain untreated. Identifying them depends on ICD-10 codes that capture SMA but do not reliably distinguish it from other related conditions. We examined, in one U.S. health system, both patients' engagement with therapy and the accuracy of the codes used to find them. Methods. We conducted a retrospective chart review of adults in an academic health system identified by SMA-associated ICD-10 codes, with manual adjudication of diagnosis and DMT status. Confirmed SMA-positive, DMT-naive patients were invited to a structured telephone interview on treatment awareness and barriers. Results. Of 60 charts, 22 (36.7%; 95% CI 25.6-49.3%) were appropriately coded for SMA or a related disorder; only 16 (26.7%) had molecularly confirmed SMA. The other 38 (63.3%) were miscoded, spanning spinal and bulbar muscular atrophy, asymptomatic carriers, prenatal screening, and conditions unrelated to SMA. Ten of the 16 confirmed patients (62.5%) were DMT-naive; one was interviewed, one declined, and eight could not be reached. The non-response is itself a finding: the patients least visible to administrative data are the hardest to reach. Conclusions. ICD-10 ambiguity is a barrier to treatment access in adult SMA, as is loss to follow-up. We make two recommendations: continuous documentation-coding alignment that uses natural language processing to verify the genetic precondition, and type-specific SMA codes (subcodes for Types 0-4) anchored on molecular SMN1 confirmation. Together these would support cohort identification, outreach, and evidence generation without adding to clinician burden.

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

Bridging the Morphology Gap: Adapting VLA Models to Dexterous Manipulation via Intent-Conditioned Fine-Tuning

arXiv:2606.12109v1 Announce Type: cross Abstract: Vision-Language-Action (VLA) models have demonstrated remarkable zero-shot generalization in robotic manipulation, yet the vast majority of pre-trained pipelines remain strictly confined to low-DoF parallel grippers. Adapting these rich semantic priors to high-DoF dexterous hands introduces a severe morphology gap, direct end-to-end joint fine-tuning inherently causes catastrophic forgetting of spatial reasoning and acute action manifold collapse due to data scarcity. In this paper, we present InDex, a novel, data-efficient adaptation framework rooted in cross-morphology semantic inheritance. Rather than discarding the pre-trained 1-DoF parallel grasp output, we repurpose it as a continuous, macroscopic virtual grasp intent proxy to sequentialize the control topology. We implement a two-stage decoupled learning architecture: the first stage parameter-efficiently aligns the VLA backbone to predict continuous arm trajectories and the scalar grasp intent; the second stage freezes this spatial backbone and leverages an intent-conditioned denoising diffusion head to decode fine-grained joint articulations for multi-fingered end-effectors. Extensive simulation benchmarks across a suite of multi-stage, contact-rich dexterous manipulation tasks demonstrate that InDex effectively masters intricate skills with minimal demonstration data, substantially outperforming monolithic baselines while preserving the robust spatial generalizability of the original VLA prior.

19.
arXiv (CS.CV) 2026-06-11

Image Quality Assessment of Identity Cards Using Measures from Open Face Image Quality

This paper addresses the challenge of assessing image quality in ID cards in remote verification systems by applying capture-related quality measures from the Open Face Image Quality (OFIQ) standard to ID card images. Our preprocessing pipeline includes corner detection, perspective normalization, and comprehensive foreground masking to ensure accurate and unbiased quality measure computation. We evaluate the effectiveness of these measures by analyzing their correlation with the performance of three presentation attack detection (PAD) algorithms across four diverse ID card datasets, where two datasets contain bona fide, i.e. pristine, images and two contain printed mock ID cards. Our results suggest that quality assessment based on some OFIQ measures can significantly improve PAD performance.

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

WOMBET: World Model-Based Experience Transfer for Robust and Sample-efficient Reinforcement Learning

arXiv:2604.08958v3 Announce Type: replace-cross Abstract: Reinforcement learning (RL) in robotics is often limited by the cost and risk of data collection, motivating experience transfer from a source task to a target task. Offline-to-online RL leverages prior data but typically assumes a given fixed dataset and does not address how to generate reliable data for transfer. We propose World Model-Based Experience Transfer (WOMBET), a framework that jointly generates and utilizes prior data. WOMBET learns a world model in the source task and generates offline data via uncertainty-penalized planning, followed by filtering trajectories with high return and low epistemic uncertainty. It then performs online fine-tuning in the target task using adaptive sampling between offline and online data, enabling a stable transition from prior-driven initialization to task-specific adaptation. We show that the uncertainty-penalized objective provides a lower bound on the true return and derive a finite-sample error decomposition capturing distribution mismatch and approximation error. Empirically, WOMBET improves sample efficiency and final performance over strong baselines on continuous control benchmarks, demonstrating the benefit of jointly optimizing data generation and transfer.

21.
arXiv (CS.AI) 2026-06-15

Elastic Queries Reinforcement Learning: Self-Aware Policy Execution for VLA Models

arXiv:2606.14375v1 Announce Type: cross Abstract: Vision-language-action (VLA) models are powerful action generators for robot manipulation, but they are typically executed with fixed inference and replanning schedules. This rigidity ignores the uneven difficulty of robot control: contact-rich or uncertain states may need more computation and fresher feedback, while easier states can often be handled with fewer inference steps and longer open-loop execution. We propose Elastic Queries Reinforcement Learning (EQRL), a framework that makes each VLA policy query elastic. A lightweight latent-schedule adaptor jointly selects the latent input, denoising budget, and action chunk length, without fine-tuning the underlying VLA model. To make scheduling difficulty-aware, EQRL trains a critic over the joint latent-schedule action and derives a state difficulty signal from critic ensemble disagreement. This signal guides compute toward difficult states, while a learned residual allows task-driven correction. We formulate variable chunk execution as query-level macro-action RL with chunk-dependent discounting and an amortized number-of-function-evaluations (NFE) budget. Across simulation and real-robot manipulation, EQRL reduces amortized inference cost while preserving or improving task success.

22.
arXiv (CS.LG) 2026-06-11

Tree-Structured Orthonormal Decomposition of the Aitchison Simplex

arXiv:2606.11646v1 Announce Type: new Abstract: Compositional data – vectors encoding relative proportions – arise across scientific domains, including ecology, geochemistry, and genomics. The features in these data often come with known hierarchical structure (e.g., taxonomies, phylogenies, ontologies), yet existing methods either ignore this structure, discard the intrinsic Aitchison geometry, are designed for binary trees, or yield incomplete coordinate systems. We describe PolyILR, a canonical orthonormal decomposition of the Aitchison tangent space aligned with any tree topology. Our construction defines a weighted local geometry at each internal node capturing full branching structure, then lifts these to a global orthonormal basis where every coordinate corresponds to a specific tree location. On microbiome and single-cell benchmarks, PolyILR yields stable, interpretable features and enables inference at multiscale tree resolution. We also establish a novel theoretical connection to softmax classifiers, suggesting possible applications to probabilistic modeling.

23.
medRxiv (Medicine) 2026-06-22

Longitudinal multi-omics characterization of the malignant evolution in multirelapsing glioblastoma

Linking glioblastoma (GBM) evolution to clinical progression is challenged by multiple factors, including tumor location for repeated sample collection, and short patient survival. In a single individual, we collected and analysed samples from 11 operations distributed across 31 months of multi-relapsing and multifocal GBM, including terminal leptomeningeal progression. All samples shared genomic ancestry of the retinoblastoma protein 1 (RB1) and neurofibromin 1 (NF1) mutations while advanced progression and extracranial metastases featured mutations of tuberous sclerosis complex 2 (TSC2), PBRM1, CD22 and Fanconi anemia supplementation group I (FANCI), correlated with clinical resistance to immunotherapies and DNA-damaging agents. Single-cell analytics revealed distinct yet reversible shifts in response to the precision medicine arsenal. GBM parenchymal dissemination and extracranial progression were associated with strengthening of neuron-like cell phenotypes. Our multidimensional study describes GBM evolution over a rarely reported time scale, and provides a valuable resource linking genetic, molecular, cellular and clinical progressions.

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

Learning to Share: Selective Memory for Efficient Parallel Agentic Systems

arXiv:2602.05965v2 Announce Type: replace-cross Abstract: Agentic systems solve complex tasks by coordinating multiple agents that iteratively reason, invoke tools, and exchange intermediate results. To improve robustness and solution quality, recent approaches deploy multiple agent teams running in parallel to explore diverse reasoning trajectories. However, parallel execution comes at a significant computational cost: when different teams independently reason about similar sub-problems or execute analogous steps, they repeatedly perform substantial overlapping computation. To address these limitations, in this paper, we propose Learning to Share (LTS), a learned shared-memory mechanism for parallel agentic frameworks that enables selective cross-team information reuse while controlling context growth. LTS introduces a global memory bank accessible to all teams and a lightweight controller that decides whether intermediate agent steps should be added to memory or not. The controller is trained using stepwise reinforcement learning with usage-aware credit assignment, allowing it to identify information that is globally useful across parallel executions. Experiments on the AssistantBench and GAIA benchmarks show that LTS significantly reduces overall runtime while matching or improving task performance compared to memory-free parallel baselines, demonstrating that learned memory admission is an effective strategy for improving the efficiency of parallel agentic systems. Project page: https://joefioresi718.github.io/LTS_webpage/

25.
arXiv (CS.CL) 2026-06-11

Fanar-Sadiq: A Multi-Agent Architecture for Grounded Islamic QA

Large language models (LLMs) can answer religious knowledge queries fluently, yet they often hallucinate and misattribute sources, which is especially consequential in Islamic settings where users expect grounding in canonical texts (Qur'an and Hadith) and jurisprudential (fiqh) nuance. Retrieval-augmented generation (RAG) improves grounding, however, a single retrieve-then-generate pipeline is insufficient for diverse Islamic queries, including verbatim scripture, citation-grounded guidance, and rule-constrained computations such as zakat and inheritance. To address these challenges, we present Fanar-Sadiq, a bilingual Arabic-English Islamic QA system built on a multi-agent, tool-augmented architecture. It is a core component of the Fanar AI platform. Fanar-Sadiq routes Islamic queries to specialized modules within an agentic tool architecture. It supports intent-aware routing, retrieval-grounded fiqh answers with normalized citations and verification traces, exact verse lookup with quotation validation, and deterministic Sunni zakat and inheritance calculators with madhhab-sensitive branching. We evaluate the end-to-end system on public Islamic QA benchmarks and show strong effectiveness and efficiency. It is publicly accessible through an API and Web application and has received over 1.9M accesses in less than a year (https://api.fanar.qa/docs).