Academic Intelligence · Curated Daily

Explore the Frontier of Global Academia

AcademicHub aggregates real-time literature from top journals and preprint platforms. Build your personal research radar and let large language models compile cross-disciplinary analysis briefings automatically.

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

Conflict-Aware Federated Fine-Tuning of Large Language Models with Mixture-of-Experts

arXiv:2606.15625v1 Announce Type: new Abstract: The continuous scaling of large language models (LLMs) incurs prohibitive computational costs, making Mixture-of-Experts (MoE) a scalable alternative for efficient fine-tuning via sparse activation. While federated learning (FL) emerges as the paradigm for privacy-preserving collaborative optimization, integrating MoE into FL under data heterogeneity may trigger conflicting expert optimizations. Client-specific data distributions force same-indexed experts to optimize under inconsistent or even conflicting feature-label correlations. This mismatch induces destructive interference during aggregation, thus destabilizing the optimization trajectory and degrading model performance. To address this issue, we propose FC-MoE, a federated conflict-aware framework for MoE fine-tuning. It employs an importance aware weighting scheme to prioritize reliable local updates and utilizes gradient consensus projection to suppress conflicting updates, ensuring a stable global optimization path. Moreover, a local knowledge retention mechanism further preserves specialized client expertise by re-anchoring domain-specific residuals. Extensive experiments demonstrate that FC-MoE accelerates convergence and enhances both global and local model performance in non-IID federated environments.

02.
arXiv (CS.CV) 2026-06-17

Unified Multimodal Autoregressive Modeling with Shared Context-Visual Tokenizer is Key to Unification

Unified Multimodal Modeling aims to integrate visual understanding and generation within a single system. However, existing approaches typically rely on two disparate visual tokenizers, which splits the representation space and hinders truly unified modeling. We propose UniAR, a unified autoregressive framework where a single discrete visual tokenizer serves as the key bridge between understanding and generation, enabling a shared context in which the model can directly interpret its own generated visual tokens without additional re-encoding. UniAR adapts a pretrained vision encoder with multi-level feature fusion and a lookup-free bitwise quantization scheme, preserving both high-level semantics and low-level details while scaling the effective visual vocabulary at minimal cost. Building on this, the unified autoregressive model adopts parallel-bitwise-prediction to jointly predict spatially grouped, multi-level visual codes, substantially reducing visual sequence length and accelerating generation. Finally, a diffusion-based visual decoder operates on discrete visual tokens to decode high-fidelity images. Through large-scale pre-training, followed by supervised fine-tuning and reinforcement learning, UniAR achieves state-of-the-art performance on image generation and image editing while remaining competitive on multimodal understanding benchmarks. The project page is available at https://sharelab-sii.github.io/uniar-web.

03.
arXiv (CS.AI) 2026-06-25

End-to-End Voice Intent Recognition for Spontaneous Human-Drone Interaction with Naive Users

arXiv:2606.24910v1 Announce Type: cross Abstract: Voice control offers an intuitive alternative to manual drone piloting, yet most existing systems rely on rigid command vocabularies that fail to handle the spontaneous, disfluent speech of naive users. This paper addresses this gap by proposing an End-to-End Spoken Language Understanding architecture for real-time human-drone interaction in French. Our model combines a frozen Self-Supervised Learning acoustic encoder with a lightweight LSTM-based classification head, augmented by a cross-modal knowledge distillation objective that aligns acoustic representations with semantic embeddings from a text teacher, without requiring transcription at inference time. We evaluate our approach on VoiceStick, a novel French corpus of spontaneous speech collected during real teleoperation sessions with 29 nonexpert dyads. On simple voice commands, our best configuration achieves 93% accuracy at 7 ms inference latency, outperforming cascade baselines (79%, 202 ms) with a 29x speedup. On the full spontaneous speech test set, our architecture reaches 82% accuracy, with crossmodal distillation consistently improving robustness across all configurations. These results demonstrate that End-to-End architectures are not only feasible but preferable for spontaneous voice-guided UAV teleoperation, combining semantic robustness, low latency, and calibrated confidence.

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

Multi-Modal Attention for Automated Disaster Damage Assessment Using Remote Sensing Imagery and Deep Learning

Timely and accurate disaster damage assessment is crucial for effective emergency response, resource allocation, and recovery. Traditional methods, which often rely on manual inspections or sparse data, are typically slow and error-prone. This paper introduces a novel framework leveraging remote sensing imagery and deep learning to automate building damage classification. Using pre- and post-disaster satellite imagery, our model categorizes buildings into four damage levels: no damage, minor damage, major damage, and destroyed. The core innovation is a multi-modal attention mechanism that fuses bi-temporal features to explicitly detect and assess structural changes. We employ a lightweight ConvNeXT-Tiny backbone to ensure efficient processing without compromising performance. Key contributions include: (1) a cross-attention module for multi-modal data fusion, (2) an optimized preprocessing pipeline for large-scale datasets, and (3) robust data augmentation techniques. Experiments on a large-scale disaster dataset demonstrate an overall classification accuracy of 94.90%. The model effectively discriminates between damage categories and remains resilient to incomplete data. This system significantly improves assessment speed and accuracy, aiding emergency responders in prioritizing interventions. This work advances automated disaster damage detection by integrating multi-temporal imagery with deep learning, offering a scalable solution for real-time response.

05.
arXiv (CS.CV) 2026-06-25

In-Context World Modeling for Robotic Control

Modern Vision-Language-Action (VLA) models often fail to generalize to novel setups, such as altered camera viewpoints or robot morphologies, because they are typically conditioned only on current observations and language instructions. By ignoring the underlying system configuration as a variable, these models implicitly assume a fixed execution context encountered during training, necessitating data-intensive fine-tuning for any new environment. In this work, we introduce In-Context World Modeling (ICWM), a framework that treats system identification as an in-context adaptation problem. ICWM enables robot policies to autonomously infer essential system variables from a short history of self-generated, task-agnostic interactions. Unlike traditional In-Context Learning that uses demonstrations to specify what task to perform, ICWM leverages the context window to understand how the system operates. By processing these interactions before task execution, the model implicitly captures the world dynamics of the current system, enabling adaptation to novel configurations without parameter updates. Extensive experiments in simulation and on real-world robot platforms demonstrate that ICWM significantly outperforms standard VLA baselines on novel camera viewpoints.

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

DYNA : Dynamic Episodic Memory Networks for Augmenting Large Language Models with Temporal Knowledge Graphs in Continuous Learning

Large Language Models (LLMs) struggle to incorporate new knowledge without forgetting or costly retraining. We propose DYNA, a lightweight framework that augments a frozen LLM with a temporal knowledge graph where events are nodes and temporal relations are directed, timestamped edges. The graph serves as an external, updatable memory. At query time, DYNA retrieves relevant nodes via random walks and centrality measures, then augments the LLM's response. Evaluated on three temporal recall tasks, DYNA reduces catastrophic forgetting by ~7% compared to fine-tuning and improves temporal ordering by ~5% over standard RAG. Higher graph clustering coefficients correlate with better retrieval, showing that graph structure matters. Contributions: (1) episodic memory as temporal KG, (2) retraining-free LLM augmentation, (3) graph properties as predictors of retrieval performance.

07.
arXiv (CS.AI) 2026-06-12

Cross-Model Disagreement as a Label-Free Correctness Signal

arXiv:2603.25450v2 Announce Type: replace Abstract: Detecting when a language model is wrong without ground truth labels is a fundamental challenge for safe deployment. Existing approaches rely on a model's own uncertainty – such as token entropy or confidence scores – but these signals fail critically on the most dangerous failure mode: confident errors, where a model is wrong but certain. In this work we introduce cross-model disagreement as a correctness indicator – a simple, training-free signal that can be dropped into existing production systems, routing pipelines, and deployment monitoring infrastructure without modification. Given a model's generated answer, cross-model disagreement computes how surprised or uncertain a second verifier model is when reading that answer via a single forward pass. No generation from the verifying model is required, and no correctness labels are needed. We instantiate this principle as Cross-Model Perplexity (CMP), which measures the verifying model's surprise at the generating model's answer tokens, and Cross-Model Entropy (CME), which measures the verifying model's uncertainty at those positions. Both CMP and CME outperform within-model uncertainty baselines across benchmarks spanning reasoning, retrieval, and mathematical problem solving (MMLU, TriviaQA, and GSM8K). On MMLU, CMP achieves a mean AUROC of 0.75 against a within-model entropy baseline of 0.59. These results establish cross-model disagreement as a practical, training-free approach to label-free correctness estimation, with direct applications in deployment monitoring, model routing, selective prediction, data filtering, and scalable oversight of production language model systems.

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

Priors Persist Through Suppression: A Stroop Paradigm for Lexical Override

Authors:

Glossaries, technical specifications, and system prompts routinely ask language models to use familiar words in unfamiliar ways. When this works, the local rule does not install the new meaning on top of the old one; the pretrained prior keeps operating underneath, and its strength still shows through. We test this with a Stroop-style paradigm: a remapping rule (doctor means forest) pitted against the query word's lexical-prior distractor (hospital), with matched neutral controls. Across 11 open-weight models spanning four families and 1B-9B parameters, lexical-prior strength predicts interference even after item-level controls for answer prior, frequency, tokenization, and prompt wording. Activation patching on five aligned models locates a source-position triplet (definition subject, definition target, query word) that nearly fully recovers the conflict effect (aggregate $R \in [0.92, 1.06]$); a definition-target swap shows the triplet performs binding rather than identity matching. Dissociation experiments isolate target preservation as the binding-specific signature: distractor suppression occurs under matched, swap, and item-mismatched conditions alike, whereas target logit collapse occurs only when the definition-target position is corrupted. Behavior and mechanism converge on the same channel: the prior's strength both predicts which overrides fail and marks where the causal repair lands.

09.
arXiv (CS.AI) 2026-06-19

Science Earth: Towards A Planet-Scale Operating System for AI-Native Scientific Discovery

arXiv:2606.01316v2 Announce Type: replace Abstract: Scientific discovery demands intelligence, perseverance, and serendipity across vast search spaces. Today, top scientific capabilities remain siloed–one AI system for biological analysis, another for clinical reasoning, mathematical derivation, or materials simulation–and no pre-designed team can anticipate every skill a question will need. Science Earth is a planet-scale scientific runtime in which any capability–a simulation cluster, a wet-lab robot, a proof engine, a single-cell pipeline–can connect to any other, with collaboration structure emerging from the question itself. Its underlying EACN protocol lets capabilities discover one another, negotiate task ownership, and adjudicate across incompatible evidentiary standards without prior knowledge of who will meet whom. This shifts the organizing challenge from workflow design to open-ended connectivity. Two runs validate this under structurally distinct conditions. In a trans-Pacific higher-order Kuramoto synchronization study, agents identified and corrected a closure-ratio assumption in Ott-Antonsen analytic theory that fails outside the Lorentzian limit, within thirty minutes. In an eight-agent single-cell run on the 4.88M-cell Kang 2024 pan-cancer atlas, heterogeneous capabilities coupled over a 64.9-hour window with one structural external instruction, producing three new result layers and anchoring findings against an independent wet-lab study on an adjacent CCR8- TIGIT+ Treg subset. These cases are a first empirical reading, not a benchmark sweep. They show that when AI capabilities are truly connectable and coordination emerges from the problem, scientific reasoning becomes a distributed, self-correcting process–a step towards scaling AI-native discovery to the planet.

10.
arXiv (quant-ph) 2026-06-11

Super-Link Fragility in Asymmetric W-Class States under Quantum Noise

arXiv:2606.12307v1 Announce Type: new Abstract: The asymmetric three-qubit W-class state $|\overline{W_3^L}\rangle$ defines an isosceles entanglement-network geometry, (a) two vertex-base (VB) links form stronger bipartite connections, (b) while the base-base (BB) link is weaker. This suggests that concentrating entanglement into a super-link may be advantageous for quantum-network tasks. Here, we show that this intuition is incomplete. We analytically compare the bipartite concurrence dynamics of the symmetric |W> state and the asymmetric $|\overline{W_3^L}\rangle$ state, which differ both in entanglement-network geometry and excitation sector under standard noise models. In the absence of noise, the concurrence hierarchy is C_{VB} > C_W > C_{BB}$. Under phase damping, this hierarchy is preserved for all noise strengths and no entanglement sudden death occurs. Under amplitude damping, however, the hierarchy is reordered. The symmetric |W> state becomes the most robust, while the base-base concurrence of $|\overline{W_3^L}\rangle$ vanishes at the finite threshold of parameter $\gamma$. We term this reordering as the Super-Link Fragility Effect. The same structural asymmetry that produces a stronger vertex-base link also makes it more vulnerable to energy dissipation when coupled with multi-excitation amplitudes. Under depolarization, the asymmetry advantage is erased, with $C_W$ and $C_{VB}$ sharing the same sudden-death threshold for some value of the parameter p, while $C_{BB}$ disappears earlier at some other value of the parameter p. The generalized amplitude damping channel continuously connects the damping-dominated regime to the pure-excitation limit, where the initial hierarchy is restored. These results show that entanglement robustness in $W$-class resources is controlled not by initial concurrence alone, but by the joint structure of entanglement-network geometry, excitation sector, and noise symmetry.

11.
arXiv (quant-ph) 2026-06-24

How Events Separated by a Timelike Interval Can Help Us Understand Quantum Nonlocality

arXiv:2604.03744v2 Announce Type: replace Abstract: Quantum entanglement plays a fundamental role in quantum cryptography and computation. An important example of quantum entanglement can be found in the correlations of Einstein, Podolsky, and Rosen (EPR). However, despite the plethora of articles related to the topic, different interpretations of the EPR correlations coexist, and a consensus has not yet been reached. In this article, we seek to demonstrate, through the simple and direct application of quantum formalism, how events separated by timelike intervals can, strangely enough, help us better understand some aspects of the so-called "quantum nonlocality" associated with EPR correlations.

12.
bioRxiv (Bioinfo) 2026-06-19

Simulation-based Bayesian deep learning enables uncertainty-aware tumor fraction estimation in cell-free DNA

Background: Estimating tumor fraction from whole-genome cell-free DNA sequencing is critical for liquid biopsy, but is hampered by weak signals and baseline noise at low tumor fractions. Existing computational methods often require matched controls or large labeled datasets for training and lack uncertainty quantification. To address these gaps, we developed purNPE, a Bayesian deep-learning framework trained without labeled cancer cell-free DNA samples. Specifically, purNPE leverages a two-part generative model: one component simulates diverse tumor copy-number profiles based on evolutionary genealogies, while a second, data-driven component learns and replicates realistic sequencing background patterns from cancer-free cell-free DNA. By training a Neural Posterior Estimator on synthetic tumor profiles augmented with learned noise, purNPE performs amortized inference in milliseconds without needing a reference sample set at inference. Results: In a real-world pan-cancer cohort, purNPE achieved comparable performance with existing methods against orthogonal mutant-allele-fraction validation (MAE = 0.066). In silico and semi-synthetic experiments suggested analytical sensitivity around 1% tumor fraction under the evaluated conditions and showed strong classification accuracy in low tumor fractions (AUC = 0.98 for TF [≤] 3% versus controls). Conclusions: This work provides a framework for using simulation-based inference to derive calibrated, uncertainty-aware TF estimates, offering a potential alternative to traditional data-dependent methods.

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

Quantized Stochastic Primal-Dual Methods for Distributed Optimization under Relaxed Global Geometry

arXiv:2606.11339v1 Announce Type: cross Abstract: We study distributed optimization with stochastic gradients and finite-bit communication modeled by random (unbiased) quantization. We propose q-PDGD, a quantized stochastic primal-dual method, and analyze it under relaxed global geometry. Under restricted secant inequality (RSI), a constant step-size yields linear contraction to an explicit neighborhood determined by gradient noise, quantization distortion, and network connectivity, while a diminishing step-size achieves O(1/k) convergence without shared-minimizer assumptions. Under Polyak-Lojasiewicz (PL) inequality, we obtain linear-to-neighborhood convergence in the same stochastic quantized setting. Our results match the best-known centralized stochastic rates in oracle complexity, and are supported by experiments demonstrating the predicted tradeoffs between quantization level, step-size choice, and graph structure.

14.
arXiv (CS.CL) 2026-06-11

Augmenting Molecular Language Models with Local $n$-gram Memory

Transformer-based language models for SMILES strings suffer from a locality gap: standard character-level tokenization fragments chemically meaningful motifs, forcing models to repeatedly learn local syntax at the expense of long-range dependencies. To address this without disrupting standard tokenizers, we propose MolGram, which integrates a conditional $n$-gram memory module into molecular language models. MolGram maps local string patterns to learned embeddings via scalable hash lookups and dynamically injects this regional context into hidden states. Evaluations across three tasks, including unconditional molecule generation, forward reaction prediction, and single-step retrosynthesis, show that MolGram consistently improves performance. Crucially, our analyses demonstrate that MolGram outperforms baselines with 3$\times$ more parameters, establishing explicit local pattern memory as a highly efficient inductive bias.

15.
arXiv (CS.AI) 2026-06-25

Rational Neural Networks have Expressivity Advantages

arXiv:2602.12390v2 Announce Type: replace-cross Abstract: We study neural networks with trainable low-degree rational activation functions and show that they are more expressive and parameter-efficient than modern piecewise-linear and smooth activations such as ELU, LeakyReLU, LogSigmoid, PReLU, ReLU, SELU, CELU, Sigmoid, SiLU, Mish, Softplus, Tanh, Softmin, Softmax, and LogSoftmax. For an error target of $\varepsilon>0$, we establish approximation-theoretic separations: Any network built from standard fixed activations can be uniformly approximated on compact domains by a rational-activation network with only $\mathrm{poly}(\log\log(1/\varepsilon))$ overhead in size, while the converse provably requires $\Omega(\log(1/\varepsilon))$ parameters in the worst case. This exponential gap persists at the level of full networks and extends to gated activations and transformer-style nonlinearities. In practice, rational activations integrate seamlessly into standard architectures and training pipelines, allowing rationals to match or outperform fixed activations under identical architectures and optimizers.

16.
Nature Medicine 2026-06-11

Microglia at a key inflection point in Alzheimer’s disease

Authors: Unknown Author

We analyzed brains from octogenarians and cognitively resilient centenarians to understand why some individuals with substantial Alzheimer’s disease pathology develop dementia whereas others remain cognitively intact. Spatial transcriptomics revealed gene expression changes in discrete tissue domains surrounding amyloid plaques and tau pathology that distinguish early, clinically silent, disease from later stages associated with cognitive decline.

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

Decoupling Reconnaissance and Exploitation: Measuring the Capability Boundaries of LLM-Based Web Penetration Testing

arXiv:2606.25332v1 Announce Type: cross Abstract: Large Language Models (LLMs) have shown promise for automated penetration testing, yet existing end-to-end black-box evaluations are highly susceptible to error cascading: failures in early reconnaissance can mask an agent's actual ability to exploit vulnerabilities. To more accurately characterize these capabilities, we propose a two-stage decoupled evaluation framework that separates exploit execution from reconnaissance. Using ground-truth injection and knowledge-driven ablation across 70 high-fidelity web vulnerability testbeds, our framework isolates exploitation performance from reconnaissance noise. We empirically evaluate five open-source penetration-testing agents, covering multiagent, monolithic, and graph-driven architectures, on a strictly aligned subset of 50 representative vulnerabilities. The results reveal a substantial capability gap. With accurate vulnerability context, agents achieve a functional success rate of up to 90.0%, whereas autonomous reconnaissance, measured by targeted vulnerability recall, plateaus at approximately 50.0%, primarily due to failures in parsing unstructured telemetry. Cross-architectural analysis further reveals distinct capability niches: multi-agent isolation is more effective for long-sequence interactions such as de-serialization, while monolithic and graph-driven designs perform better on short-chain injections and cross-session access-control vulnerabilities, respectively. This decoupled evaluation work provides a fine-grained benchmarking protocol and an empirical basis for designing next-generation automated offensive security agents.

18.
arXiv (quant-ph) 2026-06-15

Efimov Effect in Ultracold Microwave-Shielded Polar Molecules

arXiv:2602.21433v2 Announce Type: replace-cross Abstract: A quantum-mechanical description is presented for the three-body physics of shielded dipolar molecules, including a prediction of observable Efimov physics. Despite the anisotropic and long-range nature of the interaction, shielding enables a regime in which universality emerges already at the two-body level and extends to the three-body sector, where Efimov physics emerges. On the negative side of the scattering-length resonance, computed trimer binding energies display the characteristic scaling expected for Efimov resonances. Finally, the sudden approximation can be used to create trimer bound states, starting from positive energy trap states as a way to create or detect these molecular trimers. Moreover, the three-body parameter expressed in dipolar units is found to be universal.

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

ALIGNBEAM : Inference-Time Alignment Transfer via Cross-Vocabulary Logit Mixing

Domain fine-tuning degrades the safety of large language models: fine-tuned specialists readily comply with harmful prompts framed in domain language. Existing inference-time defenses that mix logits from a safe anchor model require both models to share a vocabulary, which rules them out for the cross-family specialists where safety is most degraded. We present ALIGNBEAM, a training-free method that lifts this restriction by translating anchor logits into the target model's vocabulary token-by-token at each decoding step; a small LLM judge then selects the safest among K candidate continuations. No weights are changed, and the safety-utility trade-off can be tuned at deployment without retraining. Across both cross-vocabulary and same-vocabulary evaluation pairs, ALIGNBEAM substantially raises refusal on adversarial benchmarks while keeping task accuracy and inference overhead within practical bounds. The results show that safety alignment can be transferred between model families at inference time, without touching either model's weights.

20.
arXiv (CS.AI) 2026-06-17

Kolmogorov Regression for Robust Diffusion Policies

Authors:

arXiv:2606.18186v1 Announce Type: cross Abstract: Finite-dimensional (FD) diffusion policies exhibit temporal drift owing to discretization artifacts that degrade long-horizon performance (when deployed on physical systems). We introduce a backward Kolmogorov equation that lifts diffusion policies to a Cameron-Martin space – a subset of the Hilbert space. Essentially, replacing stochastic score matching with a deterministic boundary-value PDE problem. Our core innovation thrives on Gaussian measure theory whereupon the diffusion noise covariance operator is realized from a colored noise distribution which prescribes a notion of regularity on samples from the model at inference time. We train the diffusion model with a derived precision-weighted Cameron- Martin loss and a Kolmogorov residual is introduced as a PDE diagnostic during inference. These substitutions yield (i) convergence guarantees where the bound's constants depend on the effective rank of the kernel rather than action dimension, (ii) improved trajectory regularity via spectral weighting, and (iii) a deterministic failure detector without reward signals. Validation across two application domains demonstrates substantial improvements: on the PushT manipulation benchmark, the Cameron-Martin loss achieves a 17% improvement in maximum episode reward (0.95 vs. 0.78 for MSE) and 67.6% reduction in inter-step drifts during inference via the introduced residual magnitude. Similarly, on a 6-station manufacturing line with constant work-in-process (CONWIP) flow control, we achieve 28.4% lower RMSE than classical LSTM baselines; a high starvation-event recall (1.0 in test cycles), and effective bottleneck identification (Precision@1 = 1.0 in test set, 13x signal-to-noise ratio). We then certify the dispatch policies with Hamilton-Jacobi reachability theory which reduces deadlock events by 96% compared to uncontrolled dispatch over 100 simulated runs (351 events prevented).

21.
arXiv (math.PR) 2026-06-12

Conditional means, vector pricings, amenability and fixed points in cones

Authors:

arXiv:2512.13829v4 Announce Type: replace Abstract: We develop a generalization of conditional probability for arbitrary ordered vector spaces. A related problem is that of assigning a numerical value to one vector relative to another. We characterize the groups for which these generalized probabilities can be stationary, respectively invariant. Our results deviate from the setting of classical probability and lead to a new criterion for amenability and for fixed points in cones.

22.
medRxiv (Medicine) 2026-06-15

Two Blood-based Endotypes Reveal Divergent Clinical Outcomes of Fibrotic Hypersensitivity Pneumonitis

Rationale: Fibrotic hypersensitivity pneumonitis (fHP) is an antigen-driven, life-threatening interstitial lung disease characterized by heterogeneous radiologic features, clinical outcomes, and treatment responses. Objectives: To identify blood-based fHP endotypes that inform mechanism, prognosis and therapeutic response. Methods: We performed integrative analyses of multi-compartment transcriptomic data derived from whole blood, peripheral blood mononuclear cells, bronchoalveolar lavage, and surgical lung biopsies, alongside circulating plasma proteomics. Multiple clustering algorithms were cross-compared to ensure robustness and reproducibility of endotypes identification. Immune cell composition was inferred using bulk RNA-seq deconvolution and annotated with BAL single-cell RNA-seq. Pathway activities were characterized using Gene Set Enrichment Analysis. Transplant-free survival (TFS) was evaluated for endotype and corticosteroid exposure by Kaplan-Meier methods, with hazard ratios analyzed using multivariable Cox proportional hazards models. Results: Two molecular endotypes, lymphocytic-associated (L-fHP) and non-lymphocytic-associated (N-fHP), were identified and validated. L-fHP showed enrichment of adaptive immune signaling and lymphocyte predominance, whereas N-fHP demonstrated myeloid-cell activation with neutrophil and macrophage predominance. Corticosteroid exposure was associated with worse TFS in L-fHP but not in N-fHP after adjusting for age, sex, and baseline pulmonary function. Compared to L-fHP, N-fHP had poorer baseline pulmonary function, faster 12-month FVC decline, and shorter TFS. N-fHP also exhibited elevated neutrophil-associated markers, including matrix metalloproteinase-9, across paired transcriptomic and proteomic datasets, supporting a neutrophil-driven, cross-compartment disease process. Conclusion: Multi-omic, multi-compartment analysis identifies two reproducible fHP endotypes with distinct clinical outcomes and corticosteroid responses, supporting a precision medicine approach beyond current clinical and radiologic classification.

23.
PLOS Computational Biology 2026-06-12

Ten simple rules for executing an inherited research plan in computational biology

by Sahar Javaheri Tehrani, Toni Ingolf Gossmann Trainees in computational biology frequently inherit research plans whose aims, datasets, analytical strategies, and technical constraints were defined before their arrival. These plans often emerge from grants, collaborations, legacy codebases, shared high-performance computing environments, or partially completed analyses. While such plans provide a useful scaffold, they rarely specify all implementation details, prior assumptions, evaluation criteria, or dependencies needed for reliable execution. The transition from inheriting a partially articulated plan to producing reproducible results therefore creates an execution gap: a phase in which trainees must reconstruct what the project is, which elements are fixed, which remain negotiable, and which technical or organizational assumptions need to be tested before full-scale analysis begins. In this Ten Simple Rules article, we provide a practice-oriented framework for stabilizing inherited computational biology projects before workflows, benchmarks, and decision paths become entrenched. We do not claim that the individual practices described here are novel in isolation. Rather, our contribution is to organize familiar practices into a sequenced framework for a recurrent but under-articulated phase of computational research: inherited-plan execution. Computational biology makes this phase especially important because projects often combine heterogeneous datasets, fragile software environments, undocumented preprocessing choices, benchmarking assumptions, distributed collaborators, and asymmetrical access to contextual knowledge. By making this transition visible and operational, the rules aim to help trainees, supervisors, and collaborators reduce ambiguity, test feasibility, document decisions, and support reproducible and equitable project execution under real-world constraints.

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

Detecting AI Coding Agents in Open Source: A Validated Multi-Method Census of 180 Million Repositories

arXiv:2606.24429v1 Announce Type: cross Abstract: Generative AI coding agents are entering the open-source supply chain, yet their diverse and often invisible traces leave their prevalence poorly understood. We introduce a multi-layered detection framework that integrates configuration-file scanning, commit-message analysis, author-identity matching, and bot-signature lookup across World of Code (180M+ Git repositories), classifying agent traces into four behavioral types. No single method captures more than a fraction of activity: multi-method detection identifies 850,157 Claude Code commits in one snapshot, of which bot-account lookup_the signal most adoption studies rely on_recovers only 28,154 (3.3%), a 30x relative-recall gap, so single-signal prevalence estimates are biased low by at least this factor. Every detection pattern is hand-validated (495 labels) with per-cell precision and Wilson confidence intervals. Across snapshots from December 2024 to April 2026, commit-attributed agents generate over 320,000 commits per month; Claude Code leads (886,122 commits across 17,295 projects) and dominates silent, configuration-file-only adoption (21,078 projects). Compared against an independent pull-request census (AIDev), the two channels capture nearly disjoint agent populations_a PR census misses 79% of commit-detected Claude Code adopters and essentially all Codex adopters_and different kinds of work: PR-deployed cloud agents (Codex, Cursor) surface as feature work, while commit-deployed in-editor agents (Claude Code, OpenHands, Aider) surface as maintenance. The observed work profile follows deployment and detection mode rather than the tool itself, so no single channel is representative.

25.
arXiv (CS.CV) 2026-06-18

Sensor Configuration Matters: A Systematic Evaluation of Multimodal SLAM on Quadruped Robots

Autonomous navigation of quadrupedal robots in diverse environments fundamentally relies on resilient Simultaneous Localization and Mapping (SLAM). While visual-inertial SLAM has matured across wheeled, handheld, and aerial platforms, a critical evaluation gap remains regarding how hardware-level sensor configurations affect performance under the aggressive dynamics of legged locomotion. Quadrupeds introduce distinct embodiment-induced sensory challenges, including foot-impact shocks, high-frequency mechanical vibrations, and rapid angular rotations, which degrade standard perception pipelines. To address this gap, we present a systematic evaluation of state-of-the-art visual, visual-inertial, and LiDAR-visual-inertial SLAM methods using the GrandTour dataset recorded on an ANYmal D quadruped. We isolate and quantify the impacts of camera modalities, shutter techniques, and inertial sensor tiers, analyzing their trade-offs across localization accuracy, algorithmic robustness, and computational resource utilization. Our empirical findings demonstrate that hardware selection has substantial influence on system resilience: stereo configurations consistently outperform monocular and RGB-D modalities, global shutter cameras significantly mitigate motion-induced tracking failures compared to rolling shutter cameras, and, crucially, standard inertial integration can degrade the performance of primarily vision-based frameworks under harsh legged locomotion. These insights additionally offer concrete design guidelines for tailoring custom sensor payloads to achieve dependable perception on agile legged systems.