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01.
medRxiv (Medicine) 2026-06-11

Foundation model-based tool for automated ulcerative colitis histology scoring demonstrates non-inferiority to pathologists across multiple scoring indices

In clinical trials for ulcerative colitis (UC), pathologists assess disease severity through standardized histological indices, including the Geboes Score, Robarts Histopathology Index (RHI), and Nancy Histologic Index (NHI). Despite strong associations with clinical outcomes, histologic scoring suffers from inter- and intra-reader variability, and consensus criteria for histologic remission remain uncertain. Through a consortium approach, we developed an artificial intelligence-based measurement (AIM) tool for scoring histology in UC mucosal biopsies (AIM-HI UC). This model, trained on a large dataset of UC biopsies (N=10,230), utilizes additive multiple instance learning models leveraging PLUTO, a pathology foundation model, that predict each of the Geboes subgrades, from which the Geboes grade-level score, RHI, and NHI can be calculated. Evaluation of this model on a standalone verification set including clinical trial specimens established algorithm non-inferiority and/or superiority relative to standard qualified pathologists through comparison of algorithm-consensus and pathologist-consensus agreement metrics (non-inferior if difference >-0.1, superior if difference >0, inclusive of confidence intervals). AIM-HI UC was determined to be non-inferior to pathologists (N=3) for the prediction of all seven Geboes subgrades, grade-level Geboes, RHI, NHI, histologic improvement (GS

02.
arXiv (CS.AI) 2026-06-16

JADE: Expert-Grounded Dynamic Evaluation for Open-Ended Professional Tasks

arXiv:2602.06486v2 Announce Type: replace Abstract: Evaluating agentic AI on open-ended professional tasks faces a fundamental dilemma between rigor and flexibility. Static rubrics provide rigorous, reproducible assessment but fail to accommodate diverse valid response strategies, while LLM-as-a-judge approaches adapt to individual responses yet suffer from instability and bias. Human experts address this dilemma by combining domain-grounded principles with dynamic, claim-level assessment. Inspired by this process, we propose JADE, a two-layer evaluation framework. Layer 1 encodes expert knowledge as a predefined set of evaluation skills, providing stable evaluation criteria. Layer 2 performs report-specific, claim-level evaluation to flexibly assess diverse reasoning strategies, with evidence-dependency gating to invalidate conclusions built on refuted claims. Experiments on BizBench show that JADE improves evaluation stability and reveals critical agent failure modes missed by holistic LLM-based evaluators. We further demonstrate strong alignment with expert-authored rubrics and effective transfer to HealthBench and DR.BENCH, covering medical and 10-domain professional evaluation settings. Code and data are available at https://github.com/smiling-world/JADE.

03.
arXiv (CS.CV) 2026-06-16

Cascaded Sparse Autoencoders Learn Multi-Level Visual Concepts in Multimodal LLMs

Multimodal Large Language Models (MLLMs) have demonstrated strong performance on vision-language tasks, yet their internal visual representations remain difficult to interpret. Sparse Autoencoders (SAEs) provide a scalable way to decompose dense model activations into sparse, interpretable features. However, existing SAE architectures primarily recover flat feature dictionaries and are less suited for explicit multi-level concept organization. In this paper, we introduce cascaded sparse autoencoders (CSAEs) for learning hierarchical visual concepts in MLLMs. Rather than nesting or stacking SAE sparse activation codes, CSAEs train a second-level SAE directly on the decoder weights of the first-level SAE, treating learned low-level feature directions as inputs for higher-level abstraction. This design enables CSAEs to learn "concepts of concepts" while avoiding drawbacks from the shared-prefix coupling of nesting, Matryoshka-style hierarchies and the bottlenecks of naively stacked SAEs. Experiments across Qwen3-VL, Gemma-3, and LLaVA on multiple visual datasets show that CSAEs improve interpretability in terms of hierarchical concept coherence over state-of-the-art SAE baselines. Results on concept steering further demonstrate that the learned concept groups support effective group-level interventions in MLLM outputs.

04.
arXiv (CS.CV) 2026-06-12

Iterative Tool Usage Exploration for Multimodal Agents via Step-wise Preference Tuning

Multimodal agents, which integrate a controller e.g., a vision language model) with external tools, have demonstrated remarkable capabilities in tackling complex multimodal tasks. Existing approaches for training these agents, both supervised fine-tuning and reinforcement learning, depend on extensive human-annotated task-answer pairs and tool trajectories. However, for complex multimodal tasks, such annotations are prohibitively expensive or impractical to obtain. In this paper, we propose an iterative tool usage exploration method for multimodal agents without any pre-collected data, namely SPORT, via step-wise preference optimization to refine the trajectories of tool usage. Our method enables multimodal agents to autonomously discover effective tool usage strategies through self-exploration and optimization, eliminating the bottleneck of human annotation. SPORT has four iterative components: task synthesis, step sampling, step verification, and preference tuning. We first synthesize multimodal tasks using language models. Then, we introduce a novel trajectory exploration scheme, where step sampling and step verification are executed alternately to solve synthesized tasks. In step sampling, the agent tries different tools and obtains corresponding results. In step verification, we employ a verifier to provide AI feedback to construct step-wise preference data. The data is subsequently used to update the controller for tool usage through preference tuning, producing a SPORT agent. By interacting with real environments, the SPORT agent gradually evolves into a more refined and capable system. Evaluation in the GTA and GAIA benchmarks shows that the SPORT agent achieves 6.41% and 3.64% improvements, underscoring the generalization and effectiveness introduced by our method. The project page is https://SPORT-Agents.github.io.

05.
bioRxiv (Bioinfo) 2026-06-16

Accelerating String Comparison in RLZ Compressed Sequences via LCE Jumps

Relative Lempel-Ziv (RLZ) is an effective compression method for large, repetitive collections; however, the fundamental primitives required to elevate it from a passive archival format to a tractable representation for compressed construction have yet to be fully established. In this paper, we introduce an algorithmic framework for structurally comparing and lexicographically sorting sequences of RLZ factors. We characterize when direct factor comparisons are necessary and when they can be bypassed using RLZ specific shortcuts. We further introduce a method for extending truncated factors into right-maximal matches, enabling the recovery of matching statistics from the RLZ parse. Experimentally, RLZ sorting achieved speedups of up to 3.93x over character-based sorting. Together, these results advance the use of the RLZ format as a foundation for compressed construction.

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

Categorical Prior Lock-in: Why In-Context Learning Fails for Structured Data

arXiv:2606.11961v1 Announce Type: cross Abstract: Large language models (LLMs) are increasingly used as conditional generators for structured data, relying on in-context learning (ICL) to adapt to new distributions without parameter updates. We investigate the limits of ICL for structured generation under distribution mismatch, using high-cardinality tabular data as a controlled test case, and identify a structural failure mode we term categorical prior lock-in: the inability of ICL to update the model's prior over token distributions inherited from pre-training. Across two 7B-parameter open-weight models, ICL improves numerical fidelity with additional examples but exhibits a sharp ceiling on categorical distributions, failing to reproduce rare classes entirely. Parameter-efficient fine-tuning (LoRA) overcomes these limitations but introduces measurable memorization risk and, in some cases, destabilizes structured output generation, highlighting a fundamental trade-off between adaptability and privacy.

08.
arXiv (CS.CV) 2026-06-18

VGGHeads: 3D Multi Head Alignment with a Large-Scale Synthetic Dataset

Human head detection, keypoint estimation, and 3D head model fitting are essential tasks with many applications. However, traditional real-world datasets often suffer from bias, privacy, and ethical concerns, and they have been recorded in laboratory environments, which makes it difficult for trained models to generalize. Here, we introduce \method – a large-scale synthetic dataset generated with diffusion models for human head detection and 3D mesh estimation. Our dataset comprises over 1 million high-resolution images, each annotated with detailed 3D head meshes, facial landmarks, and bounding boxes. Using this dataset, we introduce a new model architecture capable of simultaneous head detection and head mesh reconstruction from a single image in a single step. Through extensive experimental evaluations, we demonstrate that models trained on our synthetic data achieve strong performance on real images. Furthermore, the versatility of our dataset makes it applicable across a broad spectrum of tasks, offering a general and comprehensive representation of human heads.

09.
arXiv (math.PR) 2026-06-12

A mathematical study of the excess growth rate

arXiv:2510.25740v2 Announce Type: replace-cross Abstract: The excess growth rate, defined as the gap in Jensen's inequality for the logarithm, is a fundamental functional in portfolio theory. In this paper, we present a mathematical study motivated by information theory. We begin by establishing its properties and showing that it has rich connections with information theoretic concepts such as the Helmholtz free energy, L. Campbell's measure of average code length and large deviations. Our main results consist of three axiomatic characterization theorems of the excess growth rate, in terms of (i) the relative entropy, (ii) the gap in Jensen's inequality, and (iii) the logarithmic divergence that generalizes the Bregman divergence. Furthermore, we study maximization of the excess growth rate and compare it with the growth optimal portfolio. Our results not only provide theoretical justifications of the significance of the excess growth rate, but also establish new connections between information theory and quantitative finance.

10.
arXiv (CS.CL) 2026-06-18

Montreal Forced Aligner and the state of speech-to-text alignment in 2026

The Montreal Forced Aligner (MFA) was released in 2016 and has since become the most widely used tool for forced alignment in research and industry. In the decade since, MFA has undergone substantial development, including expanded coverage across more languages and dialects using larger open-source datasets, harmonized IPA dictionaries, model adaptation, cross-language phone remapping, and support utilities. This paper documents MFA 3.0's developments since version 1.0 and evaluates MFA's performance across English, Japanese, and Korean, benchmarked against classic and neural forced aligners. MFA 3.0 achieves state-of-the-art or near state-of-the-art performance across all four benchmark datasets with mean boundary errors below 15 ms. Adaptation and cross-language remapping are effective for languages outside MFA's training distribution, and pronunciation probability modeling and phonological rules provide gains in specific conditions.

11.
medRxiv (Medicine) 2026-06-11

Impact of Out-Migration and Remittances on Food Consumption Outcomes among Rural Households in Tigray, Ethiopia

作者:

This study examines the effects of rural out-migration and remittance inflows on food consumption outcomes among rural households in the Tigray region of Ethiopia. Utilizing household survey data collected from 521 rural households across three distinct Weredas (districts) (Tahtay Maichew, Kola Tembien, and Kilte-awlaelo). A Binary Probit model was employed to identify factors influencing migration decisions, while an Endogenous Switching Regression (ESR) model was used to estimate the impact of migration on food consumption outcomes while controlling for selection bias and unobserved heterogeneity. Food security was measured using the Food Consumption Score (FCS) and dietary diversity indicators. The empirical results reveal that severe food insecurity is widespread, with over 60% of all surveyed households falling into the "Poor" food consumption category. Descriptive baseline comparisons show that migration and remittance transfers marginally shift the raw average FCS upward from 23.86 to 25.48. However, this impact is profoundly nuanced: remittances serve as an immediate consumption-smoothing safety net but run parallel to a "labor-lost" constraint that reduces own-production capacities, forcing households to rely increasingly on market purchases for staple foods. The findings reveal that migration creates short-term labor shortages in agricultural production; however, remittance inflows substantially improve household food consumption frequencies, particularly for pulses, vegetables, and other nutrient-rich foods. After accounting for self-selection bias and unobserved traits, the rigorous ESR estimates indicate that migration increases the Food Consumption Score of participating households by an average Treatment Effect on the Treated (ATT) of 10.75 points, shifting them into more secure dietary tiers. Moreover, remittances help households mitigate the adverse effects of drought and other shocks by relaxing liquidity constraints and supporting both food purchases and agricultural investments. The study recommends establishing target food security safety nets for non-remittance households, promoting scale-appropriate labor-saving agricultural technologies, expanding traditional communal labor-sharing innovations, and boosting irrigation and agricultural input support programs to enhance rural food security and livelihood resilience.

12.
arXiv (quant-ph) 2026-06-11

Mixed-State Topological Order under Coherent Noise

arXiv:2411.03441v2 Announce Type: replace Abstract: Mixed-state phases of matter under local decoherence have recently garnered significant attention due to the ubiquitous presence of noise in current quantum processors. One of the key issues is understanding how topological quantum memory is affected by realistic coherent noise, such as random rotation noise and amplitude-damping noise. In this work, we investigate the intrinsic error threshold of the two-dimensional toric code (TC), a paradigmatic topological quantum memory, under these types of coherent noise by employing both analytical and numerical methods based on the doubled-Hilbert-space formalism. A connection between the mixed-state phase of the decohered TC and a non-Hermitian Ashkin-Teller-type statistical-mechanics model is established, and the mixed-state phase diagrams under the coherent noise are obtained. We find remarkable stability of mixed-state topological order under random rotation noise with axes near the $Y$-axis of qubits. We also identify intriguing extended critical regions at the phase boundaries, highlighting a connection with non-Hermitian physics. We argue that these phase boundaries provide upper bounds for the intrinsic error threshold, beyond which quantum error correction becomes impossible. We complement these findings by estimating the error thresholds for random rotation noise under standard quantum error correction, thereby providing lower bounds on the intrinsic error threshold.

13.
arXiv (CS.AI) 2026-06-12

Intelligence as Managed Autonomy: Failure, Escalation, and Governance for Agentic AI Systems

arXiv:2605.27628v2 Announce Type: replace Abstract: As autonomous and agentic AI systems scale in robotic and human-machine environments, managing hallucination and persistent but unjustified action remains an open challenge. Rather than attributing these failures solely to model or alignment limitations, this paper explores the architectural vulnerability of unbounded autonomy - the presumption that an agent should continue operating regardless of rising uncertainty. It introduces a theory of managed autonomy that defines intelligent behavior through the formal capacity to detect epistemic drift, suspend reasoning, attempt recovery, and ultimately surrender control when reliability diminishes. We instantiate this theory via the SMARt (Self-Managing Multi-tier Autonomous Reasoning with Regulated/Revoked transitions) model, a four-layer framework featuring Stable, Meta-cognitive, Assisted, and Regulated states. By developing a timed, guarded Petri net formulation, we establish theoretically bounded properties for the system, demonstrating how architecture can formally mandate escalation, constrain invalid outputs, and ensure governance reachability under specified conditions. We further analyze how incorporating domain-specific trigger sets across varied operational settings (e.g., healthcare, robotics, etc.) can systematically preserve safety, assuming completeness and soundness criteria are met. Because these triggers are designed to be adaptive, the SMARt model accommodates the safe, controlled expansion of an agent's operational scope over time. We conclude that formalizing failure management within the autonomy lifecycle is a crucial step toward realizing reliable and governed artificial intelligence.

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

A Complexity Measure for Active Learning in Multi-group Mean Estimation

arXiv:2606.14690v1 Announce Type: new Abstract: We study a max-risk objective for active learning in a multi-group mean estimation $d$-armed bandits: a learner adaptively allocates a budget of $T$ samples across $d$ groups to minimize the worst-case uncertainty index $\max_{k\in[d]}\sigma_k^2/n_k$, where $\sigma_k$ is the standard deviation of the distribution of arm $d$, and $n_k$ is the number of times arm $d$ is sampled. We develop a local minimax framework and prove the first general lower bound for this objective, valid for any finite-variance hypothesis class. The bound separates difficulty into three orthogonal factors: a budget term, a heteroscedasticity index measuring how unevenly the uncertainty is spread across arms, and a model-dependent complexity measure, the Variance Local Curvature ($\mathrm{VLC}$), which captures how much information a local change of variance creates inside the hypothesis class. For smooth classes, the $\mathrm{VLC}$ is a reparametrization of a variance–Fisher information, with closed-form values for common families. Benchmarking against the strongest available upper bound shows near-optimality up to logarithmic factors in broad regimes, and pinpoints a systematic gap in highly heterogeneous instances. Our proof introduces two key ingredients: a loss-induced $\ell_1$ geometry on the decision space, and a representation-based instance generator that reduces hard-instance construction to an explicit random matrix calculation.

15.
arXiv (CS.AI) 2026-06-17

Quantum Cinema: An Interactive Cinematic Exploration of Quantum Computing Hardware via Generative World Models

arXiv:2606.17102v1 Announce Type: cross Abstract: Quantum computing promises transformative advances across science and industry, yet the physical hardware that enables these computations remains invisible to the public: quantum processors operate inside sealed dilution refrigerators at temperatures near absolute zero, making direct observation impossible. This "imagination gap" between quantum computing's growing societal impact and the public's ability to visualize it represents a significant barrier to quantum literacy and workforce development. We present Quantum Cinema, an open-source, browser-based interactive application that closes this gap by transforming invisible quantum hardware into explorable, cinematic experiences using generative world models. Quantum Cinema guides users through a four-act narrative – from the foundational Nobel Prize-winning science of quantum entanglement, through curated video introductions to three major quantum computing architectures (trapped-ion, neutral-atom, and superconducting systems), into immersive three-dimensional generative worlds that make invisible quantum phenomena observable, and finally to interactive radar-chart comparisons grounded in real quantum device specifications. All three-dimensional environments are generated using WorldLabs' generative world model platform and are scientifically grounded in curated metrics from Amazon Web Services (AWS) Braket quantum hardware. Quantum Cinema requires no installation, no specialized hardware, and no quantum computing background. It is designed to serve two distinct communities: scholars and developers seeking to replicate or extend the platform, and educators, researchers, and science communicators seeking an intuitive tool for explaining quantum hardware to diverse audiences. This paper describes the system architecture, the generative world model pipeline, use cases for both communities, and directions for future work.

16.
arXiv (CS.CV) 2026-06-19

SketchKeyAnime: Reference-anchored Sparse Key-Sketch Animation Synthesis

Traditional animation production relies heavily on manual drawing and iterative refinement, particularly for key-pose design, in-betweening, and character coloring. While existing animation and video generation methods have made notable progress, they typically depend on RGB boundary frames, dense frame-wise conditions, or complete sketch sequences, limiting their applicability under low-cost input conditions. We present SketchKeyAnime, a video diffusion framework for generating structurally controllable, appearance-consistent, and temporally coherent animations from sparse key-sketch inputs. Given a single reference RGB image and a few temporally indexed key sketches, SketchKeyAnime introduces a dual-branch conditioning mechanism to encode local geometric constraints alongside semantic-temporal context. It leverages Sketch Cross Attention to fuse reference image and sketch conditions with learnable gating, and incorporates an Adaptive Weighted Loss to strengthen supervision on key-sketch frames and line-art regions. Experimental results on the Aesthetic subset of Sakuga-42M show that our approach consistently outperforms representative animation interpolation and sketch-guided generation baselines. Compared to the best-performing baseline, SketchKeyAnime reduces EDMD by 31.9\% and FVD by 9.5\%, demonstrating superior sketch fidelity and temporal coherence, while achieving the best overall performance across most quantitative metrics. These results validate the proposed framework and highlight its potential for low-cost, highly controllable animation creation.

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

Query-Efficient Video Adversarial Attack with Stylized Logo on Service Computing

In service computing, video classification has become fundamental to many intelligent applications. While Deep Neural Networks (DNNs) have demonstrated excellent performance in recognizing video content, recent studies have shown that DNNs are highly vulnerable to adversarial examples. Thus, understanding adversarial attacks can better respond to emergency situations. In order to improve attack performance, many style-transfer-based attacks and patch-based attacks have been proposed. However, the global perturbation of the former will bring unnatural global colors, while the latter is difficult to achieve success in targeted attacks due to the limited perturbation space. Moreover, compared to a plethora of methods targeting image classifiers, video adversarial attacks remain relatively underexplored. Therefore, to generate adversarial examples with a low budget and to provide them with a higher verisimilitude, we propose a novel black-box video attack framework, called Stylized Logo Attack (SLA). SLA is conducted through three stages. The first stage involves building a style reference set for logos, which can not only make the generated examples more natural, but also carry more target class features in targeted attacks. Then, Reinforcement Learning is employed to determine the style reference and position parameters of the logo within the video, which ensures that the stylized logo is placed in the video with optimal attributes. Finally, perturbations are optimized in a step-by-step manner so as to improve the fooling rate. Experimental results indicate that SLA can achieve better performance than state-of-the-art methods and still maintain good deception effects when facing various defense methods. We believe SLA can raise awareness among the security community about the reliability and security of video classification systems and serve as a memorandum of possible attack methods.

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

Budget-Aware Adaptive Adversarial Patches for Black-Box Object Detection

Adversarial patches pose a practical threat to modern object detectors. Prior work shows vulnerability, but three gaps limit actionable insight: (i) few score-based black-box attacks jointly optimize patch location, texture, and size under tight query budgets; (ii) success is rarely tied to the patch's visual footprint; and (iii) evaluations often conflate EOT robustness with plain-view suppression. We present \method{}, a query-efficient, budget-adaptive black-box attack that couples a lightweight Contextual Thompson-Sampling placer with NES-style pixel updates, growing the patch only when progress stalls. Reporting is anchored by a strict plain-image suppression test; EOT is audited but never used as a substitute for success, and optional appearance/printability weights expose strength–visibility trade-offs. Across YOLOv5, Faster R-CNN, and YOLOS, \method{} achieves strong suppression on CNN-based detectors and substantial suppression on the transformer-based detector, using compact patches and exposing clear query–footprint trade-offs relative to fixed-size and heuristic baselines. A print–capture pilot further shows transfer across unseen physical objects and viewpoints.

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

The Pound-Drever-Hall Method for Superconducting-Qubit Readout

arXiv:2512.03138v3 Announce Type: replace Abstract: Scaling quantum computers to large sizes requires the implementation of many parallel qubit readouts. Here we present an ultrastable superconducting-qubit readout method using the multi-tone self-phase-referenced Pound-Drever-Hall (PDH) technique, originally developed for use with optical cavities. In this work, we benchmark PDH readout of a single transmon qubit, using room-temperature heterodyne detection of all tones to reconstruct the PDH signal. We demonstrate that PDH qubit readout is insensitive to microwave phase drift, displaying $0.73^\circ$ phase stability over 2 hours, and capable of single-shot readout in the presence of phase errors exceeding the phase shift induced by the qubit state. We show that the PDH sideband tones do not cause unwanted measurement-induced state transitions for a transmon qubit, leading to a potential signal enhancement of at least $14$~dB.

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

A homotopy-type-theoretic generalization of neurosymbolic inference

arXiv:2606.17851v1 Announce Type: new Abstract: A wide range of neurosymbolic (NeSy) systems compute one functional: a belief-weighted sum of a logical quantity over a space of $\sigma$-structures, of which weighted model counting, fuzzy logic, and probabilistic logic are special cases. This account is built on sets, and a set deliberately forgets two things that are important for NeSy: when two $\sigma$-structures are the same up to a symmetry of the theory, and how many distinct proofs witness a query. Replacing the underlying sets by types, in the sense of homotopy type theory, preserves this information, and turns this functional into a belief-weighted homotopy cardinality, a notion of size that counts each object in inverse proportion to its symmetries. We develop the framework from scratch for NeSy systems, prove a conservativity theorem that recovers the classical functional when symmetries are trivial, and show that the symmetry our framework exposes is exactly the one behind reasoning shortcuts. The payoff is concrete: the shortcut-aware concept posterior that recent methods reach by ensembling or expressive density estimation is the only symmetry-invariant point of the confusion-set simplex, computable in closed form by averaging a single model over the symmetry group. On MNIST reasoning-shortcut benchmarks this single-model wrapper is better calibrated than a diversity-trained ensemble, while leaving label accuracy and identifiable concepts untouched. Code is freely available at https://github.com/bio-ontology-research-group/hott-nesy.

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

Efficient Online 3D Multi-Camera Multi-Object Tracking and Pose Estimation

This paper proposes a fast and online method for jointly performing 3D multi-object tracking and pose estimation using multiple monocular cameras. Our algorithm requires only 2D bounding box and pose detections, eliminating the need for costly 3D training data or computationally expensive deep learning models. Our solution is an efficient implementation of a Bayes-optimal multi-object tracking filter, enhancing computational efficiency while maintaining accuracy. We demonstrate that our algorithm is significantly faster than state-of-the-art methods without compromising accuracy, using only publicly available pre-trained 2D detection models. We also illustrate the robust performance of our algorithm in scenarios where multiple cameras are intermittently disconnected or reconnected during operation.

22.
PLOS Computational Biology 2026-06-22

Ten simple rules for making the supplement increase your paper’s impact

作者:

by Volker Grimm, Uta Berger, Stefano Mammola Have you ever lost hours navigating supplementary materials—clicking between the main text and dozens of auxiliary files only to encounter broken links, illegible figures, and undefined variables and acronyms? If so, you’re not alone. What should support scientific communication has instead become an obstacle: supplementary information (SI) increasingly suffers from inconsistent formatting, poor accessibility, and fragmented organization that impedes rather than advances understanding. This is disheartening since the SI, if used effectively, has the power to enhance transparency, credibility, and reproducibility of research. Therefore, we propose 10 simple rules to help authors design SI that genuinely increase the impact of their research. The rules emphasize treating SI with the same care as the main text, using it strategically to support the scientific narrative while preserving clarity and focus. Key recommendations include creating a single, well-structured, self-contained SI master document; ensuring explicit cross-referencing between the main text and SI; making SI machine-readable; and avoiding the misuse of SI as a substitute for proper data repositories. We also highlight the importance of creativity in choosing appropriate formats and strict adherence to journal-specific guidelines. Finally, when available, we advocate the use of standardized templates to improve consistency, readability, and reuse across studies. By following these rules, authors can substantially increase the scientific impact of their work while at the same time contributing to more sustainable research practices.

23.
medRxiv (Medicine) 2026-06-17

Macrophage-targeted glucocorticoid prodrug resolves acute inflammation while preserving HPA axis function: mechanistic, preclinical, and Phase II/III clinical evidence

Glucocorticoids (GCs) remain the fastest-acting anti-inflammatory agents but are constrained by systemic exposure that suppresses the hypothalamic pituitary adrenal (HPA) axis, silences adaptive immunity, and drives chronic toxicities. Chronic inflammatory diseases are sustained by long-lived CD206+ macrophages containing immune-resistant pathogenic material not cleared physiologically. We developed 101-PGC-005 ('005), a macrophage-targeted type 1a dexamethasone prodrug engineered for low-affinity, recycling-compatible uptake via CD206, with intracellular release triggered by acidic endosomes. We evaluated '005 in mechanistic assays, pathogen-diverse preclinical models, three human pharmacokinetic (PK) studies, and an adaptive-design randomized Phase II/III trial in 309 hospitalized patients with moderate COVID-19. In two completed Phase I human studies, a first-in-human dose-escalation and repeated-dose study and a dedicated single/multiple-dose PK and safety study; '005 circulated as intact prodrug with rapid systemic clearance (Tmax ~0.5 h; terminal half-life ~1.9 h), with no measurable free dexamethasone after single dosing and only low, clinically non-significant free dexamethasone after repeated dosing, and intact prodrug recovered unchanged in urine. Morning cortisol and ACTH were preserved after 30 mg once daily for three consecutive days (1.5 times the intended therapeutic dose). A cerebrospinal fluid PK study is evaluating central-compartment penetration. In the Phase II/III trial, powered for non-inferiority, conducted across six sites in India under GCP with Ministry of Health approval and independent DSMB oversight; '005 (20 mg IV daily for 3 days) was superior to dexamethasone (6 mg IV daily for 3 -10 days) on the primary endpoint of time to > a 2-point improvement on the WHO ordinal scale (HR 2.31; 95% CI 1.83-2.93; p < 0.0001; median 3 vs. 4 days). '005 was also superior on viral clearance (HR 1.47; 95% CI 1.17-1.84; p = 0.0001), hospital discharge rate, SpO2; recovery, and fever resolution. Zero patients in the '005 arm received investigator-initiated corticosteroid supplementation despite protocol allowance. All 309 randomized patients completed the study (ITT = per-protocol). Safety profiles were equivalent (TEAEs 54.8% vs 54.5%; p = 0.958), with no Grade 3+ events, SAEs, deaths, or discontinuations in either arm. Mechanistically, '005 delivered dual benefit: acute debulking of inflammatory macrophages and selective depletion of chronically activated pathology-sustaining macrophages, while preserving CXCL10 antiviral signaling and physiologic HPA control. Critically, HPA preservation is not merely a safety feature, it is a core efficacy mechanism: by clearing the pathogenic macrophage burden that was overriding HPA regulation, '005 restores the conditions for endogenous cortisol to resume its pulsatile, demand-responsive anti-inflammatory role across all GR-expressing cells, lymphocytes, endothelial cells, neurons, and newly differentiated macrophages, that '005 itself cannot reach. These findings support regulatory-grade evidence for macrophage-targeted corticosteroid therapy and provide the foundation for further development across acute inflammatory indications (sepsis, viral pneumonia, cytokine-release syndromes) and chronic macrophage-driven diseases (atherosclerosis, metabolic steatohepatitis, neurodegeneration, tumor-associated macrophages).

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

LLMs+Graphs: Toward Graph-Native, Synergistic AI Systems

arXiv:2606.11560v1 Announce Type: cross Abstract: Large Language Models (LLMs) have advanced rapidly, but their limitations in structured and multi-hop reasoning underscore the need for graph-native, synergistic artificial intelligence (AI) systems. Graph-structured data underpins critical applications across social, biological, financial, transportation, web, and knowledge domains, making it essential to understand how LLMs can leverage graph computation for grounded, context-rich inference. Three complementary synergies are emerging: LLMs augmented with graph computation for retrieval and reasoning; bidirectional integration between LLMs and knowledge graphs (KGs), where LLMs support KG construction and curation while KGs enforce semantic constraints and factual consistency; and AI agents strengthened by graph algorithms for planning, decision making, and multi-step reasoning. In parallel, LLMs introduce new capabilities for graph data management and graph machine learning (ML) through natural language interfaces and hybrid LLM-graph neural network (GNN) pipelines. This tutorial synthesizes the algorithms, systems, and design principles driving these converging directions, offering data science and data mining researchers a unified perspective on integrating LLMs, graph data management, graph mining, graph ML, and agentic computation into next-generation graph-native AI systems.

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

D2H-AD: A Hybrid Model Utilizing Hyperdimensional Computing for Advanced Anomaly Detection

arXiv:2606.13754v1 Announce Type: new Abstract: Anomaly detection is a fundamental component of intelligent systems with applications in healthcare, cybersecurity, smart grids, and IoT environments. Although conventional machine learning and deep learning methods have demonstrated effectiveness in identifying anomalies, they often rely on large labeled datasets, incur high computational costs, and face scalability challenges in edge and high-dimensional settings. This paper presents D2H-AD, a novel anomaly detection framework based on Hyperdimensional Computing (HDC), a brain-inspired paradigm that represents information using high-dimensional distributed vectors. Unlike existing HDC-based methods, D2H-AD integrates distance-based similarity and density-aware encoding within a unified framework, improving anomaly representation and detection performance. Ablation studies show that hyperdimensional encoding alone yields up to 5.4% higher ROC-AUC than applying the same density-distance scoring directly in the original feature space. Furthermore, D2H-AD consistently outperforms five established baselines, namely HDAD, ODHD, One-Class SVM, Isolation Forest, and Autoencoders, across all evaluated datasets. The framework is lightweight, interpretable, and computationally efficient, making it suitable for resource-constrained and real-time applications. We validate D2H-AD on five benchmark datasets and demonstrate superior F1-score and ROC-AUC performance, together with robustness to class imbalance, noise, and data complexity. In addition to improved accuracy, D2H-AD offers scalability, a small memory footprint, and low-latency operation enabled by binary computations and a compact design. These properties make it particularly attractive for TinyML and edge AI deployments. The proposed framework highlights the potential of HDC for accurate, interpretable, and energy-efficient anomaly detection in dynamic environments.