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01.
medRxiv (Medicine) 2026-06-17

Real-World Effectiveness and Safety of Avacopan in ANCA-Associated Vasculitis: A Systematic Literature Review and Meta-analysis

Background: The efficacy and safety of avacopan in ANCA-associated vasculitis (AAV) has been established in randomized trials of of avacopan as a glucocorticoid (GC) sparing therapy. However, real world evidence (RWE) has an important role in confirming effectiveness and evaluating safety in more generalizable settings. This study aimed to synthesize RWE on the effectiveness and safety of avacopan in adults with AAV. Methods: A systematic literature review and meta analysis of non interventional real world studies was conducted in accordance with Preferred Reporting Items for Systematic Reviews and Meta Analyses (PRISMA) guidelines. Eligible studies included adults with AAV treated with avacopan in routine clinical practice. Pooled estimates of effectiveness and safety outcomes were calculated using random effects meta-analyses. Primary outcomes included remission at 6 and 12 months and sustained remission at 12 months. Secondary outcomes included relapse, GC use and dosing, hepatotoxicity, infections, and treatment discontinuation. Exploratory outcomes included changes in estimated glomerular filtration rate (eGFR) and dialysis related endpoints. Results: A total of 71 studies were included and contributed to quantitative analyses. Pooled remission for patients on avacopan was 87% (95% CI: 75%-94%) at 6 months and 93% (95% CI: 86%-97%) at 12 months, and sustained remission was 86% (95% CI: 74%-93%) at 12 months. Relapse at 12 months was low (7%; 95% CI: 4%-11%). GC use was 36% at both 6 and 12 months. Improvements in eGFR were observed at 6 months (18 mL/min/1.73 m2) and 12 months (18 mL/min/1.73 m2), and dialysis liberation was 66% in a limited subset. Among avacopan patients, 11% experienced any hepatotoxicity, including 7% with serious (defined as directly reported or requiring hospitalization) hepatotoxicity, while 7% experienced serious (defined as directly reported or requiring hospitalization) infection. Conclusions: In real world clinical practice, avacopan is associated with high remission rates, low relapse rates, and a consistent GC sparing effect, with effectiveness comparable to standard of care regimens. Findings support its clinical use with appropriate safety monitoring; however, the observed heterogeneity in hepatotoxicity and the limited comparative effectiveness evidence highlight areas requiring further investigation.

02.
medRxiv (Medicine) 2026-06-15

Longitudinal monitoring exposes correlated temporal protein variations in the female plasma proteome

The plasma proteome is a valuable resource for assessment of the physiological state of the donor. Containing hundreds of different proteins of variable concentrations, it displays substantial inter-donor differences in individual protein levels, making each plasma proteome highly donor-specific. Less is known about intra-donor variability in the plasma proteome over time, although such variations may even be more indicative of a changing physiological state. Here we assessed data obtained from the TIMES cohort, comprising 51 apparently healthy participants monitored monthly over 12 months, focusing especially on temporal variations in blood protein levels. Most strikingly, we observed that several women in this cohort revealed strongly correlated temporal variations in their plasma proteome, including most notably PZP, SHBG, FETUB, AGT, SERPINA6, SERPINA7, CP, APOL1 and KNG1, with levels sometimes fluctuating by more than 20-fold. In contrast, such variations were absent in men. Some of the fluctuating proteins have been known to be hormone-regulated (e.g., PZP, SHBG), but for others this was not yet fully clear. Through the tight co-variation observed for these proteins in the plasma proteome of women, we can conclude that all these proteins are similarly hormone regulated. The findings reported here not only corroborate previous studies showing estrogen-dependent regulation of several plasma proteins, but also extend this category to include also CP, APOL1, and KNG1. As these latter have been often proposed as candidate biomarkers, they should be validated in sex-balanced cohorts and interpreted with caution, especially in large-scale plasma proteomics studies wherein often only one or a few sampling time points are measured per donor.

03.
arXiv (quant-ph) 2026-06-11

Shadow Engineering of Quantum Processes

arXiv:2606.12035v1 Announce Type: new Abstract: Characterizing quantum processes is essential for hardware benchmarking, error diagnosis, and algorithm verification. While recent work [PRX QUANTUM 4, 040337 (2023)] extended classical shadows from quantum state to quantum process, enabling efficient single-channel $\mathcal{E}$ property prediction, its applicability to composite processes $f(\mathcal{E}_1, \mathcal{E}_2,\cdots, \mathcal{E}_k)$ remains unexplored. We introduce shadow engineering, a framework encoding the classical shadows of processes into sparse transfer matrices to predict $f(\mathcal{E}_1, \mathcal{E}_2,\cdots, \mathcal{E}_k)$ properties with proven polynomial sample complexity, matching single-channel efficiency while exponentially lower than quantum process tomography. Crucially, this approach repurposes existing $\mathcal{E}_m$-shadow data without physical execution of $f(\mathcal{E}_1, \mathcal{E}_2,\cdots, \mathcal{E}_k)$, enabling flexible quantum process characterization with minimal hardware overhead. We demonstrate the framework's effectiveness and practicality on a superconducting quantum processor for typical applications such as error mitigation and Hamiltonian dynamical simulation. This framework unlocks new capabilities for predicting complex quantum behaviors without physical re-execution, with immediate applications in near-term device calibration and quantum simulation.

04.
arXiv (math.PR) 2026-06-12

Exact Fourier dimensions of dyadic Mandelbrot cascades under minimal integrability

arXiv:2606.08683v2 Announce Type: replace Abstract: We determine the Fourier dimension of dyadic Mandelbrot cascades under the minimal Kahane-Peyriere integrability condition. The interval theorem is proved in a vector-valued dyadic cascade model in which sibling weights may have arbitrary dependence. For every balanced energy-admissible vector law, almost surely on non-extinction, dim_F(mu)=dim_E(mu)=dim_2(mu)=D_E(X). In the canonical scalar case, under W>=0, E W=1, E[W log_2^+ W]

05.
arXiv (quant-ph) 2026-06-11

Split-Evolution Quantum Phase Estimation for Particle-Conserving Hamiltonians

arXiv:2604.14921v2 Announce Type: replace Abstract: We present a hardware demonstration and resource analysis of split-evolution quantum phase estimation (SE-QPE) on a Quantinuum System Model H2 quantum computer. SE-QPE is a modification to canonical QPE for particle-conserving Hamiltonians in which controlled time evolution is replaced by CSWAP-based interference between a target register and a reference register. For factorizations of time evolution with a shared eigenbasis, SE-QPE preserves the phase-register outcome distribution of canonical QPE and, unlike with compute–uncompute substitutions, it remains compatible with non-exact eigenstates. The substitution removes controlled-simulation overhead and enables parallel evolution on two registers, reducing the depth of each phase-kickback block. Resource analysis for Trotterized double-factorized chemistry Hamiltonians shows that the substitution becomes increasingly favorable at higher phase powers and combining QPE and SE-QPE implementations can be a useful option. Over a range of FeMoco active spaces, SE-QPE reduces time evolution resources, with asymptotic reductions of about 33% in CX count, 25% in $T$ count, and an asymptotic depth ratio of $3/N$ for CX layers. On Quantinuum H2-2, a four-qubit model ethylene demonstration with explicit inverse QFT and repeated phase-kickback steps up to 8 phase bits yields distinct energies and shows the auxiliary registers provide useful error detection filters.

06.
Nature (Science) 2026-06-10

Whole-genome duplication shaped cell-type evolution in the vertebrate brain

Authors:

The complex brains of vertebrates have more cell types than those of their closest relatives. Whole-genome duplications (WGDs) occurred during early vertebrate evolution1, but it is unclear whether the duplicated genes (ohnologues) facilitated cell-type evolution. Here using brain single-cell transcriptomes from five chordates—human2, mouse3, lizard4, lamprey5 and amphioxus—we report that many cell-type families with conserved core transcription factors in vertebrates do not show one-to-one homology with amphioxus. Moreover, ohnologues, particularly those from the first WGD, were more important than small-scale duplication paralogues for vertebrate cell-type evolution. To explore whether ohnologues are mechanistically important for this process, we predicted ancestral cell-type states and compared them to amphioxus and experimentally investigated macroglia. The findings indicate that ohnologues had a role in early vertebrate cell-type diversification. Moreover, by examining paralogue expression across cell types and species, we show that expression changes were mainly driven by dosage selection and subfunctionalization. We also link ohnologues to cellular diversity at different anatomical and cell-type scales. Our findings demonstrate the importance of WGDs for the evolution of early vertebrate brain complexity and highlight that the resultant ohnologues continued to capacitate cell-type evolution long after they were formed. Analyses of brain single-cell transcriptomes from human, mouse, lizard, lamprey and amphioxus reveal that duplicated genes (ohnologues) played a pivotal part in early vertebrate cell-type diversification.

07.
bioRxiv (Bioinfo) 2026-06-14

Structural Analysis of Prostate Cancer N-Glycans Using Graph-Based Structural Metrics

The N-linked glycans are structurally complex carbohydrate modifications that regulate protein folding, immune recognition, and cellular signaling, and their expression is extensively remodeled during cancer progression, making them promising biomarkers. In this study, prostate cancer-associated N-glycans from a range of relevant peer-reviewed studies were curated and digitized to develop a versatile computational framework that quantitatively encodes their spatial complexity across diverse biological systems. We invented two indices – the Distance & Connectivity Index (DCI) and the Position & Composition Index (PCI) – to capture the spatial information in N-glycans as layered architectures, enabling calculation of residue-level path lengths, branching structure, and compositional diversity. DCI summarizes glycan structure as both a scalar and matrix representation, while PCI does the same but also captures monosaccharide diversity, linkage heterogeneity, and cross-layer branching features. These metrics were computed with GlycoAssessor, an open-source platform that extracts information for the DCI and PCI from glycans drawn via Symbol Nomenclature for Glycans (SNFG) notation. Principal Component Analysis (PCA) was applied to evaluate whether glycans from prostate cancer tissues cluster distinctly in a disease-relevant manner. Results show that the spatial information in N-glycans: (1) increased in a multi-dimensional, non-linear manner, (2) objectively segregated structural themes, (3) could function as a potential prostate cancer biomarker that is distinct from mass-to-charge ratio and relative abundance, and (4) could objectively quantify novel subtype classifications of glycans associated with disease states and progression.

08.
PLOS Computational Biology 2026-06-01

Challenges and progress in RNA velocity: Comparative analysis across multiple biological contexts

Authors:

by Sarah Ancheta, Leah Dorman, Guillaume Le Treut, Abel Gurung, Greg Huber, Loïc A. Royer, Alejandro Granados, Merlin Lange Single-cell RNA sequencing is revolutionizing our understanding of cell state dynamics, allowing researchers to capture and quantify the transcriptomic profile of a single cell at a specific timepoint. Among the computational techniques used to predict cellular trajectories, RNA velocity has emerged as a predominant tool for modeling transcriptional dynamics. RNA velocity leverages the mRNA maturation process to generate velocity vectors that predict the likely future state of a cell, offering insights into cellular differentiation, aging, and disease progression. Although this technique has shown promise across biological fields, the performance accuracy varies depending on the RNA velocity method and dataset. We established a comparative pipeline and analyzed the performance of five RNA velocity methods on three datasets based on local consistency, method agreement, identification of driver genes, and robustness to sequencing depth. This benchmark provides a resource for scientists to understand the strengths and limitations of different RNA velocity methods.

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

Detecting High-Potential SMEs with Heterogeneous Graph Neural Networks

arXiv:2602.19591v3 Announce Type: replace-cross Abstract: Small and Medium Enterprises (SMEs) constitute 99.9% of U.S. businesses and generate 44% of economic activity, yet systematically identifying high-potential SMEs remains an open challenge. We introduce SME-HGT, a Heterogeneous Graph Transformer framework that predicts which SBIR Phase I awardees will advance to Phase II funding using exclusively public data. We construct a heterogeneous graph with 32,268 company nodes, 124 research topic nodes, and 13 government agency nodes connected by approximately 99,000 edges across three semantic relation types. SME-HGT achieves an AUPRC of 0.621 0.003 on a temporally-split test set, outperforming an MLP baseline (0.590 0.002) and R-GCN (0.608 0.013) across five random seeds. At a screening depth of 100 companies, SME-HGT attains 89.6% precision with a 2.14 lift over random selection. Our temporal evaluation protocol prevents information leakage, and our reliance on public data ensures reproducibility. These results demonstrate that relational structure among firms, research topics, and funding agencies provides meaningful signal for SME potential assessment, with implications for policymakers and early-stage investors.

10.
arXiv (CS.CV) 2026-06-11

From Nominal Intensity to Equivalent Rainfall: A Path-Based Credibility Evaluation Framework for Simulated Rainfall in Autonomous-Driving Perception Tests

Credible simulated-rainfall conditions are essential for identifying perception-system boundaries and supporting SOTIF-oriented risk assessment in automated driving. However, closed-field tests are often described only by nominal rainfall intensity or single-point measurements, making it difficult to align simulated rain fields with real rainfall and map test results to real-world scenarios. This paper proposes a path-based credibility evaluation method for simulated rainfall in autonomous-driving perception tests. Using the drop size and velocity joint distribution of real rainfall as the reference, each candidate path is represented by path-equivalent rainfall intensity, an uncertainty band, and a path-averaged Realism of Raindrop Distribution (RRD) score. Lidar target point-cloud count and mean reflectivity are further used for perception-consistency correction, quantifying the proxy capability of each simulated-rainfall path for real-rainfall perception effects. Experiments are conducted using about 10,000 real-rainfall raindrop-spectrum samples, 728 RainSense perception samples, and 45 spatial sampling points in a 2.4 m x 7.2 m simulated-rainfall area. Results show that spatial non-uniformity remains under the same nominal condition, confirming the need for path-based evaluation. The method identifies Path IV and Path VI as preferable candidates, with results of 11.54 +/- 0.31 mm/h, RRD = 0.43, and 8.28 +/- 0.34 mm/h, RRD = 0.46, respectively. These paths show more balanced performance in rainfall-intensity stability, raindrop-spectrum realism, and perception consistency. The proposed method supports path selection, condition description, and credible interpretation of autonomous-driving perception tests under rainfall.

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

Korzhinskii-Net: Physics-Informed Neural Network for Sub-Surface Mineral Prospectivity Modelling

Authors:

arXiv:2606.13695v1 Announce Type: cross Abstract: Mineral prospectivity modelling (MPM) underpins exploration economics, yet most operational pipelines reduce to data-driven classifiers trained on shallow surface proxies. Such models are blind to the subsurface physics that actually localises ore: heat advection, fluid flow, and lithology-dependent precipitation. We present Korzhinskii-Net, a 2-D radial physics-informed neural network (PINN) that couples Darcy flow, advective-diffusive heat transport, and a softplus-saturated reaction rate into a single differentiable forward model, weakly supervised by surface and remote-sensing proxies. The network is named after Dmitri S. Korzhinskii (1899-1985), whose theory of infiltration metasomatism provides the physical scaffold. We evaluate Korzhinskii-Net on five ore provinces spanning four commodity classes – Norilsk (Ni-Cu-PGE), Pechenga (Ni-Cu sulphide), Udokan (sandstone-hosted Cu), Sukhoi Log (orogenic Au), and Mirny (kimberlitic diamond) – under a fair, leakage-controlled 5-fold cross-validation protocol with hard ring-shaped negatives. Korzhinskii-Net attains a mean PR-AUC of 0.885 versus 0.281 for the strongest classical baseline (gradient boosting), and a mean fractional rank of 0.019 versus 0.413. The improvement is consistent across all five provinces and four commodity systems, suggesting that physics-informed differentiable simulators, even when constrained only by global open-data proxies, can recover localisation patterns that pure feature-based learners systematically miss. We release the full pipeline and evaluation harness as open source.

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

Retrospective Progress-Aware Self-Refinement for LLM Agent Training

LLM-based agents trained with reinforcement learning optimize step-wise action prediction but lack metacognitive awareness of task progress, inducing a gap that hinders long-horizon scaling. A pilot study reveals that online progress prompting hurts performance while retrospective demonstrations help, yet this capability cannot emerge from outcome-reward training alone. We present RePro, Retrospective Progress-Aware Training, a framework that trains agents to self-generate progress signals via a forward-then-reflect rollout paradigm: the agent executes actions online, then retrospectively reassesses its step-wise progress given the completed trajectory and known outcome. RePro initializes with a Retrospection Warmup that teaches reflection format from minimal external demonstrations, then further trains through RePro-PO with a composite reward that produces self-generated signals without continuous external supervision. Experiments on WebShop, ALFWorld, and Sokoban show that RePro enhances the Qwen family's performance, with up to $12\%$ absolute success rate gains.

13.
arXiv (CS.CV) 2026-06-15

WAM4D: Fast 4D World Action Model via Spatial Register Tokens

World action models (WAMs) have recently shown promise in jointly modeling future observations and executable robot actions. However, most existing WAMs still operate in 2D video or latent spaces, where visually plausible rollouts miss the 3D spatial constraints and occluded contact geometry required for precise manipulation. While geometric foundation models offer strong priors for recovering dense 3D structure and motion from visual observations, forcing WAMs to predict the dense 4D representation introduces costly geometric decoding and slows down causal action generation. To address the trade-off, we present WAM4D, a fast 4D world action model that uses lightweight spatial register tokens as training-time future-depth readouts to transfer pretrained geometric priors into a causal video-action transformer, then removes the register branch for lightweight action inference. To prevent non-causal shortcuts, we further design causal mixture attention for the Mixture-of-Transformers (MoT) WAM backbone, defining modality-specific visibility among video, action, and geometry tokens. Comprehensive experiments on RoboTwin 2.0 and challenging real-world manipulation tasks show that WAM4D improves spatial consistency and achieves competitive action prediction while maintaining efficient inference.

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

All Smoke, No Alarm: Oracle Signals in Agent-Authored Test Code

arXiv:2606.18168v1 Announce Type: cross Abstract: Software practitioners increasingly use AI coding agents that generate test code alongside production code in open source pull requests (PRs). Recent studies report more than 932,000 agent-authored PRs across more than 116,000 repositories, yet whether their test files contain meaningful verification logic remains underexplored. Test files lacking explicit assertions execute code without verifying behavior, so quality gates based on test-file presence overestimate verification strength. The goal of this paper is to help practitioners assess the verification strength of agent-authored patches by characterizing oracle signals and their link to merge outcomes and review effort. We conduct an empirical study of 86,156 test-file patches from 33,596 agent-authored PRs across 2,807 GitHub repositories produced by five coding agents: OpenAI Codex, GitHub Copilot, Devin, Cursor, and Claude Code. A qualitative analysis of 384 stratified patches informs a syntactic taxonomy of eight oracle signal categories. Applied at scale, 80.2% of test patches contain weak or no explicit oracle signals. While raw merge rates are lower for strong-oracle PRs, a regression analysis adjusting for agent, PR size, repository popularity, task type, and language shows strong oracles significantly improve merge likelihood (OR = 1.28, p < 0.001). Our findings suggest that test file counts substantially overestimate verification strength and that practitioners can adopt oracle-aware quality checks to more accurately evaluate agent-authored contributions.

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

CHORUS: Decentralized Multi-Embodiment Collaboration with One VLA Policy

arXiv:2606.12352v1 Announce Type: cross Abstract: Multi-robot collaboration allows robots to efficiently take on a wide range of tasks, from moving a couch through a doorway to assembling structures on a construction site. However, achieving such coordination in mobile multi-robot settings remains challenging: centralized methods conditioned on the combined observations of a team scale poorly with team size, and decentralized methods that train one policy per robot often require explicit alignment procedures or information sharing at inference time to overcome partial observability. Our key insight is that the visuomotor priors of pretrained vision-language-action (VLA) models should enable reactive, decentralized collaboration from each robot's local observations alone, without these inference-time assumptions. We propose CHORUS, a framework that adapts a single VLA backbone to control diverse, multi-robot teams. At inference time, each robot runs an independent copy of CHORUS, conditioned only on its own observations and a robot-identifying prompt. In real-world experiments including mobile tape measurement, library book handovers, and laundry basket lifting, CHORUS achieves a 64% point improvement over decentralized, from-scratch models, improves reactivity to teammate behavior by 40% points, and outperforms centralized baselines. Together, these results show that a shared VLA backbone is capable of achieving decentralized multi-robot collaboration, without per-robot policies or inter-robot communication at inference.

16.
arXiv (CS.AI) 2026-06-17

Patients With Personality: Realistic Patient Simulation through Controlled Diversity and Selective Disclosure

arXiv:2606.17441v1 Announce Type: cross Abstract: Simulating realistic patient interactions is a key requirement to testing clinical applications of LLMs at scale without time-consuming and expensive user studies. However, existing approaches often lack realism and controllability, often oversharing information unprompted, and failing to capture the wide variability of patient behavior. Here, we introduce PatientsWithPersonality (PWP), a patient simulation framework that generates realistic yet diverse virtual patient responses through explicit personality parametrization over a latent patient state. Grounded in HEXACO, a six-dimensional personality space used to quantify and parameterize human behavioral traits, our approach enables fine-grained control over conversational style, cooperativeness, and information disclosure within a unified framework. In a clinician evaluation, PWP is judged nearly as realistic as recorded human actors and clearly ahead of prior simulators, while being flagged as "too informative" far less often. Conditioning on HEXACO axes yields personas whose configured traits are recoverable by both clinicians and an autorater, span a substantially wider behavioral footprint than the closest baseline, and prevent oversharing. Altogether, our framework paves the way for more accurate and informative LLM benchmarking through our realistic and steerable patient simulator.

17.
arXiv (CS.CV) 2026-06-16

V2P-Manip: Learning Dexterous Manipulation from Monocular Human Videos

Achieving autonomous robotic dexterous manipulation requires precise, human-like action sequences at scale. As a scalable supplement to costly teleoperation data, extracting trajectories with both visual fidelity and physical plausibility from monocular videos represents a promising frontier in embodied AI. To this end, we introduce V2P-Manip, an efficient framework designed to learn dexterous manipulation policies directly from human demonstration videos. We establish an efficient, integrated pipeline encompassing 3D asset acquisition, trajectory estimation, and dexterous policy learning. To bridge the gap between visual perception and physical constraints, we introduce a two-stage refinement process to enforce spatial alignment and physical consistency. Evaluations on the TACO and OakInk benchmarks demonstrate that our approach significantly outperforms previous methods in pose accuracy, adaptability to unstructured environments, and training efficiency. Ultimately, experimental results confirm an average success rate of over 75% across multiple synthetic manipulation tasks and validate the adaptability of the extracted manipulation priors across diverse dexterous hand embodiments.

18.
arXiv (CS.LG) 2026-06-19

Quantum ring all-reduce: communication and privacy advantages for distributed learning

arXiv:2606.20344v1 Announce Type: cross Abstract: Machine learning models have scaled to unprecedented sizes, making training across distributed devices the de facto standard in the field. In this work, we explore how quantum communications can make distributed training both more communication-efficient and information-theoretically private, for both classical and quantum learning models. Ring all-reduce is the foundational communication primitive for large-scale distributed training. We present a quantum version that reduces per-link online communication by a provably optimal factor of two using pre-shared entanglement and superdense coding, without requiring the learning model or gradient computation to change. Beyond bandwidth, the primitive enables privacy guarantees that are information-theoretically impossible for any classical protocol, achieving composable {\epsilon}-secure aggregation, via verified entanglement, at a 2x overhead in GHZ copies. Our hybrid quantum-classical communication architecture yields simultaneous communication and security advantages for large scale distributed training, regardless of whether the learning itself is quantum or classical. Finally, we characterise quantum advantages in gradient conflict detection for server-to-client communication under bandwidth constraints, a setting that arises after ring all-reduce is completed, when full gradient broadcast to external clients is infeasible. Two variants of the problem admit different separations. For margin-based alignment testing (\textsc{GapIP}_{\tau}), the quantum advantage is quadratic in the margin parameter: \widetilde{O}({\tau}^{-1}\log P) qubits versus \widetilde{O}(\min(\{\tau}^{-2},P)) bits. For sign-consistency auditing against a private parameter matching (\textsc{TieAudit}_{\epsilon}), the advantage represents an exponential separation in communication complexity: \Omega(\sqrt{P}) bits whereas O({\epsilon}^{-2}\log P) qubits suffice.

19.
arXiv (CS.CL) 2026-06-15

AgentSpec: Understanding Embodied Agent Scaffolds Through Controlled Composition

LLM agents are increasingly built not as single model calls, but as scaffolded systems that combine reasoning, memory, reflection, action execution, and learning. While such scaffolds often improve performance, they are often embedded in tightly coupled pipelines, making it difficult to isolate component contributions, compare alternative designs, or understand how module interactions shape agent behavior. We introduce AgentSpec, a modular specification framework that represents embodied agents as typed compositions of reusable policy components with standardized interfaces. AgentSpec standardizes the interfaces among perception, memory, reasoning, reflection, action, and optional learning, enabling components to be swapped and recombined under controlled conditions. We instantiate this framework across DeliveryBench, ALFRED, MiniGrid, and RoboTHOR, and analyze reasoning, memory, reflection, and reinforcement-learning modules across model backbones. Our results show that agent performance is governed by scaffold compatibility and interaction effects rather than isolated module strength. In particular, structured multi-granularity memory improves long-horizon state tracking, reasoning and memory interact non-uniformly across environments, reflection trades off correction and cost, and RL-trained policies compose best when optimized with deployment-time scaffold structure. AgentSpec provides a controlled foundation for studying, comparing, and designing composable LLM agents. Our code, baselines and interactive playground are publicly available at https://agentspec-embodied.github.io.

20.
Nature (Science) 2026-06-10

Gene ancestries reveal diverse microbial associations during eukaryogenesis

The origin of eukaryotes remains a central enigma in biology1. Continuing debates agree on the pivotal role of a symbiosis between an alphaproteobacterium and an Asgard archaeon2,3. However, the nature, timing and contributions of other potential bacterial partners4–6 and the role of interactions with viruses7–9 remain contentious. To address these questions, we used advanced phylogenomic approaches and comprehensive datasets spanning the known diversity of cellular life and viruses. Our analysis provided a revised reconstruction of the last eukaryotic common ancestor (LECA) proteome, in which we traced the phylogenetic origin of each protein family. We found compelling evidence for multiple waves of horizontal gene transfer from diverse bacterial donors, with some likely to have preceded mitochondrial endosymbiosis. We inferred plausible traits of the major donors and their functional contributions to the LECA. Our findings support a contribution of horizontal gene transfers to shaping the proteomes of pre-LECA ancestors and suggest a facilitating role of Nucleocytoviricota viruses. Taken together, our results suggest that ancient eukaryotes may have originated within complex microbial ecosystems through a succession of diverse associations that left a footprint of horizontally transferred genes. Phylogenomic reconstruction of the proteome of the last eukaryotic common ancestor sheds light on the origin of eukaryotes, indicating an important role of horizontal transfer of genes from diverse bacterial and viral donors.

21.
arXiv (CS.AI) 2026-06-19

Scaling Generative Foundation Models for Chest Radiography with Rectified Flow Transformers

arXiv:2606.19460v1 Announce Type: cross Abstract: We introduce the first generative foundation model for chest radiograph synthesis trained from scratch at the billion-parameter scale. Existing radiographic AI models often suffer from poor generalisation across patient subpopulations, institutions, and acquisition settings, resulting in limited real-world clinical utility. Controlled, high-fidelity synthesis of chest radiographs is a promising path toward diversifying clinical datasets and evaluating the robustness of diagnostic models. Therefore, we present the largest specialist generative foundation model for chest radiographs to date, with over 1.3B parameters, trained for 1.6T tokens on a curated, heterogeneous dataset comprising 1.2M radiographs and clinical expert-guided metadata. Our model supports controllable radiograph generation and editing across multiple demographic subgroups, acquisition views, and a dozen pathologies. Moreover, we significantly advance the state of the art in radiograph synthesis fidelity, producing images that are indistinguishable from real radiographs to clinical experts.

22.
arXiv (CS.AI) 2026-06-19

ELVA: Exploring Ranking-Driven Universal Multimodal Retrieval

arXiv:2606.20280v1 Announce Type: cross Abstract: Leveraging Multimodal Large Language Models (MLLMs) via contrastive learning has become a mainstream paradigm for improving the performance of Universal Multimodal Retrieval (UMR). However, previous works have ignored the grain blindness when adapting the contrastive paradigm into retrieval tasks. Grain blindness refers to the tendency of the model to overlook grain-level information contained in the query, which is crucial for effectively handling complex queries. This stems from contrastive learning treating samples as a binary classification (positive/negative), while ignoring the different information carried by each negative sample. To address this, we argue that negatives should be treated differently according to their similarity to the positive sample, enabling the model to learn distinct grain information from each negative. In this paper, we introduce a simple but effective framework, called ELVA, a novel rule-based RL framework that mitigates grain blindness through ranking-driven MLLMs. 1) Instead of relying on reward models, we extend Reinforcement Learning with Verifiable Rewards (RLVR) to retrieval tasks, allowing the model to explore new ranking behaviors without explicit ranking labels. 2) By utilizing rule-based rewards, our approach jointly optimizes the ranking of negative samples while enlarging the similarity gap between positive and negative. To more precisely measure grain blindness, we further introduce MRBench, a new benchmark specifically designed for multi-grain query scenarios. ELVA achieves state-of-the-art results across standard retrieval benchmarks, and its notable 13.1% improvement on MRBench further demonstrates its effectiveness in alleviating grain blindness.

23.
arXiv (CS.AI) 2026-06-16

Quantum Machine Learning for Industrial Applications

arXiv:2606.14822v1 Announce Type: cross Abstract: Recent advances in Machine Learning have transformed numerous industrial sectors, yet classical paradigms face fundamental limitations: rapidly growing data volumes, rising computational costs, significant energy consumption, and the physical scaling limits of conventional hardware architectures. Quantum computing has emerged as a promising computational paradigm to address these challenges, giving rise to the field of Quantum Machine Learning (QML). In this thesis, the theoretical foundations of QML are investigated, with a focus on near-term and future practical applications. Three central challenges are addressed: the trainability of variational quantum circuits, their expressivity, and their resistance to efficient classical simulation. The trainability of Hamming-weight preserving variational quantum circuits is first studied, and theoretical guarantees are established that resolve an open conjecture on the absence of barren plateaus for this circuit family. Subspace-preserving QML algorithms are then introduced, including photonic circuits and quantum convolutional neural networks, and are designed to mimic classical ML subroutines while offering polynomial quantum advantage. Finally, variational quantum circuits are analyzed as quantum Fourier models, and a framework is derived to jointly characterize expressivity and trainability, from which conditions are obtained under which quantum models provably separate from their classical counterparts. These contributions are intended to advance the theoretical roadmap for harnessing near-term and future quantum technologies in real-world applications.

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

Afrispeech Semantics: Evaluating Audio Semantic Reasoning in Spoken Language Models Across Domains and Accents

Audio language models (ALMs) are increasingly used for speech-based understanding, yet their ability to perform semantic reasoning beyond transcription, Text-to-Audio Retrieval, Captioning, and Question-Answering accuracy remains insufficiently benchmarked. In particular, the effects of accent variation, domain shift, and semantic over-inference on audio reasoning are poorly understood. We evaluate audio language models across five semantic and paralinguistic reasoning tasks: entailment, consistency, plausibility, accent drift, and accent restraint. Collectively, these tasks assess a model's ability to reason over spoken audio as the primary evidence source, including whether a textual hypothesis can be inferred, contradicted, or left undetermined by the audio, whether statements align or conflict with spoken content, whether claims are plausible given the discourse, and whether model predictions remain stable or appropriately constrained across accent variation. These findings highlight critical limitations in current audio reasoning evaluations and hope to provide guidance for more robust and equitable ALM design and assessment

25.
bioRxiv (Bioinfo) 2026-06-13

ProtAff: Protein Binding Affinity Prediction via LoRA-Finetuned ESM-2

Predicting the binding affinity of protein–protein interactions remains a central challenge in computational biology. Structure prediction models such as AlphaFold3 (AF3) and Boltz-2 can produce high-quality docking poses, and their confidence scores indicate structure quality, but these same scores fail to rank binding affinity among confirmed binders. Here we present ProtAff, a sequence-only affinity prediction model built on ESM-2 (650M parameters) with low-rank adaptation (LoRA) fine-tuning and a cross-attention module. ProtAff is trained using a margin ranking loss on 362,567 affinity measurements spanning 20 heterogeneous data sources, and we removed all training samples whose target sequence exceeds 50% similarity to the test target EGFR. On the AdaptyvBio EGFR benchmark (N = 55), ProtAff achieves a Spearman correlation coefficient {rho} = 0.413, outperforming the best AF3 metric ({rho} = 0.054), the best Boltz-2 metric ({rho} = -0.046), and ML-based predictors MINT ({rho} = 0.242) and CrossAffinity ({rho} = 0.216). Applied to the AdaptyvBio Nipah virus binder design competition, a pipeline incorporating ProtAff for affinity ranking produced a design with KD = 0.132 nM (2 of 5 designs confirmed binding), a 2.8-fold improvement over the competition winner. On a cross-target discrimination benchmark of 91 VHH-antigen crystal structures, ProtAff underperforms structural methods for distinguishing cognate from non-cognate pairings, indicating that sequence-based affinity models are effective for within-target ranking but not for cross-target specificity.