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01.
arXiv (CS.CV) 2026-06-12

World Tracing: Generative Pixel-Aligned Geometry Beyond the Visible

Image-to-3D methods often trade off faithfulness and completeness: depth estimators are anchored to input pixels but stop at the visible surface, while image-to-3D models generate complete shapes that are often misaligned with the input. We introduce World Tracing, a generative pixel-aligned geometry representation that predicts 3D points aligned with observed pixels while completing geometry beyond the visible surface. For each input pixel, World Tracing predicts an ordered stack of camera-space 3D points, where the first layer represents the visible surface and subsequent layers represent front-to-back intersections with occluded surfaces. We instantiate this representation with a world-tracing diffusion transformer, WT-DiT, which treats multiple geometry layers as separate denoising tokens coupled through factorized and global attention. WT-DiT is trained with pixel-space flow matching and a mixed noise schedule that balances visible-surface reconstruction with occluded-geometry generation. World Tracing achieves strong performance on visible-surface reconstruction and complete geometry generation across object, scene, and dynamic benchmarks, outperforming both depth predictors and image-to-3D generators. It also preserves 2D-to-3D correspondence, enabling text-driven 3D scene editing, geometry-conditioned novel-view video synthesis, and training-free integration with textured-mesh generators.

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

PPDM: Pixel Puzzling Diffusion Model for Speed and Memory Efficient Volumetric Medical Image Translation

Diffusion models have demonstrated superior fidelity for medical image-to-image translation, but their extension to high-resolution 3D volumes is severely constrained by prohibitive computational cost and GPU memory requirements. Existing memory-efficient strategies often compromise global volumetric consistency or fine anatomical detail. In this work, we propose the Pixel Puzzling Diffusion Model (PPDM), a simple and effective framework for memory- and speed-efficient 3D medical image translation. PPDM introduces a reversible pixel puzzle-unpuzzle operator that trades spatial resolution for channel dimensionality, substantially reducing activation memory while preserving global context. To further improve efficiency and stability, we adopt a direct bridge diffusion formulation that starts from the conditional input rather than pure noise, enabling the model to focus on task-relevant residuals. In addition, a puzzle-gradient loss is incorporated to enforce spatial coherence and suppress grid-like artifacts introduced by spatial rearrangement. We evaluate PPDM on multiple challenging 3D medical image translation tasks, including low-count PET denoising, joint PET denoising and attenuation correction, and cross-modal MRI translation. Across all tasks, PPDM consistently matches or outperforms full 3D diffusion models while reducing training GPU memory usage by up to an order of magnitude and significantly accelerating inference, and it outperforms existing memory-efficient diffusion approaches based on latent compression or frequency decomposition. These results demonstrate that PPDM provides a practical and scalable solution for high-fidelity 3D diffusion-based medical image translation under limited computational resources.

03.
arXiv (CS.CL) 2026-06-17

A Framework for Evaluating Agentic Skills at Scale

Agent skills – structured, reusable knowledge artifacts that augment LLM agent capabilities – have been rapidly adopted in industry, yet their cross-domain impact and use across commercial and open-source models remain under-studied, and no reusable methodology exists for evaluating an individual skill. In this work, we present an evaluation framework that lets a skill author construct realistic tasks to rigorously assess the aspects of a skill that matter most to them, and that estimates skill utility by solving those tasks. Further, we apply our evaluation approach at scale to 500 real-world skills, generating 1,000 tasks derived from the skills' content, along with instruction-following and goal-completion scoring rubrics. Using these metrics, we evaluate how 19 agent-model configurations, both proprietary and open-source, perform on the tasks. Our results show that models vary widely in how closely they adhere to the instructions encoded in skills, leading to substantial differences in their performance gains. Furthermore, we show that access to a skill significantly changes model behavior compared to the no-skill setup, providing an essential mechanism for encoding opinionated workflows into LLM agents. We release our evaluation dataset to support future work on agent skills.

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

Stringalign: Moving beyond summary statistics with a transparent Unicode-aware tool for evaluating automatic transcription models

Comparing text strings is crucial when evaluating and understanding the performance of various text processing tasks such as document recognition and audio transcription. With an increasingly complex landscape of AI-based handwritten text recognition (HTR), optical character recognition (OCR) and automatic speech recognition (ASR) models, there is a need for tools that facilitate evaluation in a flexible and reproducible way. This paper presents Stringalign, a Python library designed to simplify the evaluation process for automatic transcription projects and facilitate transparent evaluation. Stringalign's tools to examine and visualise both the rate of errors and the types of errors a model makes, give insights into possible improvements and help inform model selection for a particular task. Widely used string comparison metrics, such as the character and word error rates (CER and WER), although useful, can be ambiguous due to varying definitions of what constitutes a character and a word. Stringalign addresses this challenge by ensuring all preprocessing (i.e. normalisation and tokenisation) is transparent and easily replicable, and by providing tools to move beyond summary statistics and analyse common model errors. Moreover, Stringalign adheres to FAIR (Findable, Accessible, Interoperable, and Reusable) principles for research software while staying lightweight and easy to adapt into researchers existing workflows. In this paper, we discuss challenges with character and word level string comparisons and show through examples that where existing tools can yield opaque and sometimes confusing results, Stringalign provides an easy-to-use and unambiguous alternative.

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

The Simplified Stabilizer ZX-Calculus is Minimal

arXiv:2606.12383v1 Announce Type: new Abstract: The stabilizer fragment of the ZX calculus is amongst the most important fragments of the theory. The closely related Clifford+T fragment is approximately universal (arXiv:1705.11151). Additionally, the stabilizer calculus can be described by a small collection of rewrites, most of which have been shown to be necessary (arXiv:1709.08903). However, two rules, describing the red/green compact-structure coincidence and the important bialgebra law, had not been shown to be necessary. We present a countermodel-style argument showing that both of these rules are individually necessary relative to the connectivity meta-rule of Backens–Perdrix–Wang (arXiv:1709.08903), and hence establish that the rule set presented in arXiv:1709.08903 has no redundant rewrite rule.

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

VISTA: An End-to-End Benchmark for Visual Spec-to-Web-App Coding Agents

We present VISTA (VIsual Spec-To-App Benchmark), a benchmark for evaluating the end-to-end web-app generation capabilities of LLM-based agents. Unlike prior code generation benchmarks that focus on algorithmic tasks, VISTA targets realistic UI-centric development, where agents must produce functional, visually coherent applications from underspecified inputs. We define five prompt-information conditions that vary along two axes, visual/structural fidelity and stack constraint: (1) text only with free stack choice, (2) text with reference screenshots under three specified stacks, (3) text with reference screenshots under free stack choice, (4) text with screenshots and pruned Figma structure under a single specified stack, and (5) text with screenshots and pruned Figma structure under free stack choice. To enable robust evaluation, each page in the benchmark is manually annotated with interactive UI components and around three visual anchor points, addressing the well-known limitations of script-based testing tools such as Playwright in open-ended code generation settings. Evaluation combines DOM-grounded reference matching, behavior-specific browser tests, and CLIP-based visual similarity, jointly measuring structural alignment, behavioral completeness, and overall visual fidelity. We use VISTA to assess four agent systems drawn from two model families and two harnesses, finding that visual fidelity and functional correctness are partially decoupled across both input conditions and agents, and that agent editing style varies sharply but is largely orthogonal to task quality. VISTA establishes a rigorous and reproducible foundation for advancing agent-based software engineering research.

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

When AUC Misleads: Polarization-Aware Evaluation of Deepfake Detectors under Domain Shift

Recent advances in generative AI, such as diffusion models and face-swapping tools, have enabled the creation of highly realistic deepfakes, leading to real-world harms including financial fraud and non-consensual explicit content. In response, deepfake detection has become an active research area, with recent methods increasingly focusing on improving generalization to unseen manipulations. This is typically evaluated using the Area Under the ROC Curve (AUC) measured separately across multiple datasets. However, such an evaluation fails to reflect real-world scenarios where detectors face a mixture of data sources and varying artifact types. To address this limitation, we introduce a novel metric, Cross-dataset AUC (Cross-AUC) that averages per-domain AUCs with a measure of prediction polarization for taking into account the robustness to domain shift. The polarization extent is quantified by the Wasserstein Distance between class score distributions. Cross-AUC not only assesses the generalization capabilities of deepfake detectors under domain shifts more realistically, but it is also interpretable as it better explains the reason behind a drop in performance. Experiments performed on seven benchmark datasets demonstrate its practical relevance.

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

ShearFuse-UNet: Hadamard, DCT, and Shearlet Transform Fusion for Next-Day Wildfire Spread Prediction

We propose ShearFuse-UNet, a lightweight and computationally efficient deep learning model for next-day wildfire spread prediction from multi-modal satellite data. The model integrates three complementary transform-domain branches inside each encoder block of a U-Net backbone: a 2D Fast Walsh-Hadamard Transform (WHT) branch, a 2D Discrete Cosine Transform (DCT) branch, and a cone-adapted digital Shearlet residual branch. The WHT and DCT branches establish orthogonal latent spaces with learnable spectral scaling and fixed soft-thresholding, while the Shearlet branch provides anisotropic, multi-directional feature decomposition that explicitly encodes the elongated edge structures characteristic of fire fronts. A learned SpectralFusion gate adaptively combines the WHT and DCT responses, and the Shearlet reconstruction is added as a residual. This three-branch design bears a loose structural analogy to transformer self-attention: the WHT and DCT branches provide complementary spectral representations that are adaptively fused, while the Shearlet branch contributes directional content through a residual pathway. Unlike self-attention, the proposed design relies on fixed mathematical transforms rather than learned projection operators, reducing parameter count and computational cost. Evaluated on the WildfireSpreadTS dataset, ShearFuse-UNet achieves an F1 score of 0.596 with only 267k parameters, outperforming a ResNet18-based U-Net (14M parameters, F1 = 0.589) and demonstrating a highly favorable accuracy-efficiency trade-off. Results on the Google Next-Day Wildfire Spread dataset further validate these findings across a different benchmark.

10.
arXiv (CS.LG) 2026-06-19

Weighted Bayesian Conformal Prediction

arXiv:2604.06464v2 Announce Type: replace Abstract: Conformal prediction provides distribution-free prediction intervals with finite-sample coverage guarantees, and recent work by Snell \& Griffiths reframes it as Bayesian Quadrature (BQ-CP), yielding powerful data-conditional guarantees via Dirichlet posteriors over thresholds. However, BQ-CP fundamentally requires the i.i.d. assumption. Meanwhile, weighted conformal prediction handles distribution shift via importance weights but remains frequentist, producing only point-estimate thresholds. We propose Weighted Bayesian Conformal Prediction (WBCP), which generalizes BQ-CP to arbitrary importance-weighted settings by replacing the uniform Dirichlet $\Dir(1,\ldots,1)$ with a weighted Dirichlet $\Dir(\neff \cdot \tilde{w}_1, \ldots, \neff \cdot \tilde{w}_n)$, where $\neff$ is Kish's effective sample size. We prove four theoretical results: (1)~$\neff$ is the unique concentration parameter matching frequentist and Bayesian variances; (2)~posterior standard deviation decays as $O(1/\sqrt{\neff})$; (3)~BQ-CP's stochastic dominance guarantee extends to per-weight-profile data-conditional guarantees; (4)~the HPD threshold provides $O(1/\sqrt{\neff})$ improvement in conditional coverage. We instantiate WBCP for spatial prediction as Geographical BQ-CP, where kernel-based spatial weights yield per-location posteriors with interpretable diagnostics. Experiments on synthetic and real-world spatial datasets demonstrate that WBCP maintains coverage guarantees while providing substantially richer uncertainty information.

11.
arXiv (quant-ph) 2026-06-16

Preparation of Fractional Quantum Hall States on Quantum Computers

arXiv:2606.16548v1 Announce Type: new Abstract: The realization of fractional quantum Hall (FQH) states, characterized by fractional charge and intrinsic topological order, on quantum computers represents a central challenge at the interface of condensed matter physics and quantum information science. Current methods are grouped into two types: methods based on (quasi-)adiabatic evolution of complex parent Hamiltonians to yield target states, and circuit-based approaches for direct state preparation, which are confined to effectively one-dimensional systems near the thin cylinder or torus limit. We introduce a complementary scheme relying on direct quantum circuit construction, which works for arbitrary geometries. Specifically, we present a method to precisely prepare the $\nu=1/3$ Laughlin state on the sphere geometry and demonstrate that it significantly reduces the required number of two-qubit gates and circuit depth, compared to variational quantum circuit approaches. In addition, we employ optimal control techniques to design control pulses for both superconducting and Rydberg atom platforms, identifying experimentally feasible protocols for state preparation. Our results provide an efficient and hardware-relevant pathway for realizing generic FQH states on both noisy intermediate-scale and fault-tolerant quantum devices.

12.
arXiv (math.PR) 2026-06-16

The existence of invariant sublinear expectations for $G$-SDEs

arXiv:2606.15203v1 Announce Type: new Abstract: In this paper, we study the existence of invariant sublinear expectations of Markovian semigroups on sublinear expectation spaces. To achieve this, we establish a complete metric space of sublinear expectations, on which we extend Harris' method to the nonlinear setting on the convergence of sublinear semigroups. We then explore two cases of $G-$diffusions by studying the Lyapunov function and the local Doeblin condition. One is the $G-$Brownian motion on the unit circle which is the case studied in Feng and Zhao [Zhaonon], but with the new method. Another is the multidimensional $G-$SDEs on the whole space $\mathbb{R}^d$. We establish, for the first time in the literature, the existence of the invariant sublinear expectation for $G-$SDEs under the non-degenerate and weakly dissipative assumption. For this, we prove that for a class of $G-$SDEs, the $G-$expectation can be represented as the supremum of the semigroup of a family of SDEs, of which the regularity is obtained by considering the Bismut-Elworthy-Li formula and the Denis-Hu-Peng representation for the distribution of $G-$Brownian motions.

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

BaltiVoice: A Speech Corpus and Fine-tuned Whisper ASR System for the Balti Language

作者:

We present BaltiVoice, a 16.8-hour read-speech corpus for Balti (ISO 639-3: bft), a Tibetic language spoken in Gilgit-Baltistan, Pakistan, with no prior publicly available ASR resources. The corpus contains 10,060 validated utterances in native Nastaliq script, derived from Mozilla Common Voice recordings. Fine-tuning OpenAI Whisper-small yields a Word Error Rate (WER) of 26.74% and a Character Error Rate (CER) of 8.67% on a 538-utterance speaker-disjoint validation set, down from a zero-shot baseline of 159.19% WER and 152.52% CER. A Whisper-base fine-tuned on the same data achieves 44.54% WER and 15.61% CER, confirming that model capacity matters for this low-resource setting. The dataset, fine-tuned model, and a live transcription demo are publicly available on HuggingFace.

14.
arXiv (CS.LG) 2026-06-19

An adaptive framework for the axisymmetric pulsar magnetosphere using physics-informed Kolmogorov-Arnold networks

arXiv:2606.10686v2 Announce Type: replace-cross Abstract: The pulsar magnetosphere has only recently been addressed using Physics-Informed Neural Networks (PINNs), by deploying a domain-decomposition approach and treating the separatrix and equatorial current sheet as infinitesimally thin discontinuities. However, this baseline requires extensive manual hyperparameter tuning, achieves limited final accuracy and demands several hours of training. We refine this framework by introducing domain-specific neural architectures based on Kolmogorov-Arnold networks, an automated adaptive training pipeline and a physics-based convergence criterion that eliminate the need for manual calibration. The proposed methodology delivers self-consistent axisymmetric magnetosphere solutions with mean squared errors of the PDE residuals at O(1e-6) in double precision - an improvement of two orders of magnitude over the baseline - while achieving convergence in under 20 minutes in single precision. Importantly, the method reliably resolves stellar radii reduced by up to 80% compared to the baseline, overcoming the severe spatial scale disparities that also challenge traditional solvers. Furthermore, by varying the flux that opens to infinity, we provide a correction to the equation that connects it to the equatorial T-point's position. The complete framework is released as the open-source library PulsarX.

15.
medRxiv (Medicine) 2026-06-12

Effect of tenofovir on the outcomes of COVID-19 in persons with chronic hepatitis B: a nationwide cohort study in Sweden.

Background: Patients with chronic hepatitis B (CHB) may have an increased risk of severe COVID-19. Tenofovir has been hypothesized to confer protection against severe disease, but evidence is inconclusive. We evaluated the risk of severe COVID-19 among CHB patients treated with tenofovir compared with other nucleos(t)ide analogues (NAs). Methods and findings: In this nationwide, registry-based cohort study, we included all adults with CHB and laboratory-confirmed COVID-19 in Sweden between February 2020 and July 2022. Data from national health and socioeconomic registers were linked using unique personal identification numbers (PINs). Patients with HIV, hepatitis C, or hepatitis D coinfection were excluded. Exposure was defined as tenofovir versus other NA therapy. The primary outcome was severe COVID-19, defined as hospitalization >2 days or death within 30 days of diagnosis. Logistic regression was used to estimate adjusted odds ratios (aOR) with 95% confidence intervals (CI), controlling for age, sex, comorbidities, vaccination, socioeconomic status, and region of birth. Among 5,877 CHB patients with COVID-19, 672 were receiving NA therapy (437 tenofovir, 235 other NAs). Severe COVID-19 occurred in 8.0% of tenofovir-treated patients and 14.5% of those receiving other NAs (unadjusted OR 0.52; 95% CI, 0.31-0.85). After adjustment, the association was attenuated and no longer significant (aOR 0.72; 95% CI, 0.39-1.31). Older age, comorbidities, and unvaccinated status were strongly associated with severe disease. Conclusions: The apparent protective effect of tenofovir against severe COVID-19 in unadjusted analyses was largely explained by confounding factors. The risk of severe disease was primarily driven by age, comorbidities, and vaccination status. Prevention of severe COVID-19 in patients with CHB should instead focus on vaccination and management of comorbidities.

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

Findings of the MAGMaR 2026 Shared Task

This overview paper presents the results of the shared task for the second workshop on Multimodal Augmented Generation via Multimodal Retrieval (MAGMaR). In this shared task participants submitted systems focused on either (i) video retrieval or (ii) grounded generation of articles given retrieved videos. Teams could submit to either task. For the retrieval task, we had 2 participating teams that submitted a total of 17 systems – all of which beat a baseline derived from the winner of last year's shared task. On the generation side, we had 4 teams submit 16 systems. All teams had at least one generated report that was labeled the best by a human annotator.

17.
arXiv (math.PR) 2026-06-24

Optimal Couplings of Levy Processes in the Class of Immersion Couplings

arXiv:2606.24290v1 Announce Type: new Abstract: We study the optimal coupling problem for Levy processes on R^d with respect to the quadratic cost. For any two such processes with finite second moments, we prove that the optimal Levy coupling constructed in Kang and Lim (2025), which was previously shown to be optimal among Feller couplings, is in fact optimal among the larger class of immersion couplings. The proof makes use of a characterization of immersion couplings, which is equivalent to the classical martingale preservation definition but more convenient for our purposes. The construction is based on two fundamental ingredients: the existence of an optimal coupling within the class of Levy couplings, and a dual formulation of the associated optimization problem. While both results were previously established in Kang and Lim (2025), we provide here simpler and more transparent proofs relying only on optimal transport between infinitely divisible measures and a generalized minimax principle. These arguments are self-contained and may be of independent interest.

18.
arXiv (CS.LG) 2026-06-15

Neither Parallel Nor Sequential: How DiffusionGemma Actually Commits Tokens

arXiv:2606.14620v1 Announce Type: new Abstract: Open diffusion language models are marketed as parallel, non-autoregressive decoders, yet the order in which a shipped checkpoint actually commits its tokens is almost never measured. We instrument DiffusionGemma 26B, a masked discrete-diffusion mixture-of-experts model built on Gemma 4, hooking its sampler's accept step to record which canvas positions commit, when, and at what confidence. Across a 686-prompt, six-regime probe suite we find that its decoding is neither parallel nor block-autoregressive: it follows a partial left-to-right commit bias whose apparent strength depends almost entirely on the granularity at which you look. Order is weak token by token and strengthens smoothly as the analysis is coarsened, so the model's "block size" turns out to be an artifact of the measuring ruler rather than the architecture. The model commits in large simultaneous batches, leaving much of the within-batch order genuinely undefined rather than merely unobserved. The behaviour is regime-dependent: structured JSON is committed in essentially arbitrary order, and a position's commit confidence tracks correctness on mathematical reasoning but carries no signal on factual recall. Commitment is aggressive, finishing in a short late burst well inside the step budget, while task accuracy matches the model's autoregressive Gemma-4 sibling. Beyond these findings, our central contribution is methodological: measuring decoding order honestly demands handling trailing-EOS padding, within-regime confounding, commit non-monotonicity, block-size sensitivity, and large commit-batch ties, each of which can otherwise manufacture a decoding-order result that is not really there.

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

On Aligning Hierarchical Standardized Embedding for Audio-visual Generalized Zero-shot Learning

Audio-visual Generalized Zero-shot Learning (AV-GZSL) is a challenging task that aims to classify both seen and unseen objects or scenes by integrating data from audio and visual modalities. Recent studies primarily focus on fusing or aligning audio and visual features to generate more informative audio-visual embeddings. Also, aligning the audio-visual and textual features of most existing methods relies solely on the optimization objectives. However, those methods neglect the inherent distributional and structural differences between audio-visual and textual modalities. To address this limitation, we propose a method termed Aligning Hierarchical Standardized Embedding (AHSE), which enables hierarchical alignment of standardized audio-visual and textual embeddings within a shared embedding space. Specifically, we first apply Z-score standardization to the fused audio-visual and textual embeddings to reduce distributional mismatches. We then introduce a hierarchical alignment strategy that minimizes discrepancies at the semantic, class, and batch levels, thereby constructing a more robust and well-structured embedding space. This strategy not only preserves semantic and inter-class relationships but also maintains spatial consistency within each batch. Extensive experiments on three benchmark datasets: VGGSound-GZSL, UCF-GZSL, and ActivityNet-GZSL, demonstrate that AHSE achieves competitive performance in zero-shot learning.

20.
arXiv (CS.CL) 2026-06-11

Vector Quantized Latent Concepts: A Scalable Alternative to Clustering-Based Concept Discovery

Large language models (LLMs) encode rich semantic information in their hidden states, yet it remains difficult to understand what information these internal representations capture. Latent concepts extracted from hidden states offer a promising direction for interpreting LLMs, but existing clustering-based methods face a trade-off: hierarchical clustering produces coherent concepts but is limited to small datasets due to its quadratic memory cost, while K-Means scales efficiently but may yield less semantically coherent concepts. We propose Vector Quantized Latent Concept (VQLC), a discrete concept learning framework that learns a codebook of latent concepts on frozen hidden states. Across 12 dataset-model settings, VQLC stays close to K-Means in computational cost, scales better than hierarchical clustering, and remains competitive in faithfulness, with the clearest gains on decoder-only models. LLMs-based evaluation, qualitative analysis, and a Sparse Autoencoder (SAE) comparison demonstrate that the learned concepts are interpretable and task-relevant.

21.
Nature (Science) 2026-06-24

Zero-shot design of drug-binding proteins via neural iterative selection−expansion

作者:

The design of proteins that bind to small molecules has been challenging because it requires simultaneous optimization of the protein sequence, protein structure and ligand conformation1–7. Current deep-learning algorithms have struggled to navigate this landscape, precluding the zero-shot design of binders. Here we show that by combining two neural networks in an iterative design algorithm, small-molecule binding proteins can be created from scratch with high accuracy. We trained a graph neural network—ligand-aware sequence engineering message-passing neural network (LASErMPNN)—to design compatible protein sequences for an input protein backbone and docked ligand. We paired  LASErMPNN with a structure predictor that models a three-dimensional protein–ligand complex for an input protein sequence and ligand identity. The closed-loop iteration of these reciprocal networks optimized sequence–structure–ligand compatibility, and outperformed a comparable design loop using a physics-based energy function. We used our strategy, termed neural iterative selection–expansion (NISE), to design proteins that, using different folds, specifically bind to two chemically distinct small-molecule drugs, exatecan and apixaban, with success rates of 100% and 83%, respectively. The tightest NISE binders had nanomolar-to-picomolar affinities, surpassing those of the next-leading method by 70-fold for exatecan and nearly 10,000-fold for apixaban. LASErMPNN then suggested two amino-acid substitutions that improved the affinity of the tightest exatecan binder by 100-fold without any experimental input. The optimized binder protected the labile lactone ring of exatecan from hydrolysis for days. Our work describes a general recipe for using neural networks to automate the design of small-molecule binding proteins for applications in drug delivery, sensing and catalysis.  By pairing two neural networks in an iterative optimization algorithm, small-molecule binding proteins can be designed from scratch with high accuracy, affinity and success rates, showing promise for applications in drug delivery and sequestration.

22.
bioRxiv (Bioinfo) 2026-06-23

EnrichViz: An Interactive R Shiny Application for Visualization of Pathway Enrichment Results from Omics Data

Pathway and functional enrichment analysis is a cornerstone of omics data interpretation, enabling researchers to map differentially expressed proteins or genes onto curated biological processes, signaling cascades, and molecular functions. While tools such as Ingenuity Pathway Analysis (IPA), g:Profiler, and Enrichr are widely used to generate ranked enrichment results, translating these tabular outputs into clear, publication-ready figures remains a time-consuming step that typically requires custom scripting and familiarity with visualization libraries, a significant barrier for researchers without a computational background. Here we present EnrichViz, a self-contained, browser-based R Shiny application that enables interactive, code-free visualization of pathway and functional enrichment results from quantitative proteomics, transcriptomics, and metabolomics experiments. EnrichViz accepts three standard CSV files as input, a normalized abundance matrix, a sample annotation or metadata file, and enrichment results from any platform that exports tabular output, and produces six complementary, publication-ready visualizations: bar and bubble plots for ranking enriched terms by significance, chord diagrams for exploring pathway-molecule connectivity, clustered heatmaps for displaying Z-score normalized expression patterns across experimental groups, and boxplots or violin plots for examining the abundance distribution of individual proteins, genes, or metabolites. The application supports both raw p-values and pre-transformed -log10(p) values through automatic detection, and all plot parameters are adjustable in real time through a graphical sidebar. Every figure can be exported as a high-resolution PNG file at 300 dpi. EnrichViz is implemented in R using the Shiny, ggplot2, pheatmap, and circlize packages, and is freely available at https://rgmilian.shinyapps.io/EnrichViz/

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

Focus, Align, and Sustain: Counteracting Gradient Dilution in Incremental Object Detection

Adapting Detection Transformers to Incremental Object Detection (IOD) poses a systemic challenge, as set-based optimization is inherently destabilized by sequential learning. In this work, we identify Gradient Dilution as the root cause of performance degradation, wherein optimization signals required to preserve old knowledge are progressively weakened. This phenomenon manifests as a cascading erosion of preservation gradients in magnitude, direction, and support coverage, driven by three tightly coupled factors: Signal Dispersion, where foreground gradients are overwhelmed by background noise; Assignment Drift, where stochastic query-target matching induces inconsistent gradient trajectories; and Support Attrition, where gradients from retained samples insufficiently cover the old-class feature space, weakening decision boundaries under interference from new classes. To counteract this, we propose FAS, a unified framework that Focuses, Aligns, and Sustains gradient flow throughout incremental learning. Specifically, we introduce prior-injected queries to focus discriminative signals by filtering background interference at the source. We further propose deterministic anchor distillation to align query-target assignments and enforce semantic consistency across stages under unstable matching. Finally, we devise manifold-support replay to sustain distributional support of old classes, counteracting representational erosion induced by continual updates. Extensive experiments show that FAS restores robust optimization dynamics and outperforms state-of-the-art methods, achieving over 5.0 AP improvement in the challenging 40+10x4 incremental setting.

24.
medRxiv (Medicine) 2026-06-15

Pulmonary extracellular vesicles drive alveolar macrophage dysfunction via microRNA transfer in Acute Respiratory Distress Syndrome

Background: Alveolar macrophage (AM) dysfunction contributes to Acute Respiratory Distress Syndrome (ARDS) pathogenesis. We investigated the role of extracellular vesicles (EVs) in mediating this dysfunction. Methods: Pulmonary EVs were isolated from broncho-alveolar lavage and non-directed bronchial lavage samples of ventilated sepsis patients with and without ARDS, and post-operative control patients via ultracentrifugation. AMs were isolated from lung tissue resections of lobectomy patients. AMs were treated with pooled EVs for 24 hours prior to functional, metabolic and autophagy profiling. EV cargo was profiled via small RNA transcriptomics and proteomics. Mechanistic role of EV microRNAs was assessed via mimic / antagomir transfection. Results: Pulmonary EVs from sepsis patients with ARDS impaired AM efferocytosis, and control EVs had no effect. ARDS EV treatment enhanced AM mitochondrial-linked respiration, but not glycolysis. ARDS EV treatment impaired LC3B-II and LAMP1 expression, indicating dysregulated AM autophagy-lysosomal machinery. Proteomics revealed downregulation of innate immune pathways in ARDS EVs. Transcriptomics revealed enrichment of 24 microRNAs in ARDS EVs; miR-652-3p was the most enriched, validated by RT-qPCR. EV miR-652-3p was associated with 90-day mortality (9.20 vs 0.59 RQ, p=0.0295) and inversely correlated with oxygenation (PaO2/FiO2). AM transfection with miR-652-3p mimic induced similar dysregulation of function and autophagy as ARDS EVs. Transfection of ARDS EVs with antagomirs to miR-652-3p prior to AM treatment partially rescued efferocytosis and autophagy. Conclusions: Targeting EV miR-652-3p may restore alveolar macrophage function and reduce excessive inflammation, thus offering a novel therapeutic strategy for patients with ARDS.

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

MCompassRAG: Topic Metadata as a Semantic Compass for Paragraph-Level Retrieval

Retrieval-augmented generation (RAG) systems depend critically on how documents are chunked and searched. Fine-grained chunks can improve retrieval precision but expand the search space, increasing latency and cost; larger chunks reduce the number of candidates but make dense similarity less reliable, as the representation for each chunk mixes multiple topics and introduces more semantic noise. This trade-off becomes especially limiting in deep research tasks, where retrieval must be both fast and precise across large, heterogeneous corpora. We introduce MCompassRAG, a metadata-guided retrieval framework that uses topic-level signals as a semantic compass for selecting relevant evidence. Instead of relying only on cosine similarity between queries and noisy chunk embeddings, MCompassRAG enriches chunk representations with topic metadata in the same embedding space and trains a lightweight retriever through LLM-teacher distillation. At inference time, MCompassRAG performs topic-aware retrieval without additional LLM calls, improving both efficiency and evidence quality. Across six complex retrieval benchmarks, MCompassRAG improves information efficiency (IE) by 8.24% on average with over 5 times lower latency than the strongest efficient RAG baselines. Code is available on https://github.com/AmirAbaskohi/MCompassRAG.