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01.
arXiv (CS.CV) 2026-06-18

Splaxel: Efficient Distributed Training of 3D Gaussian Splatting for Large-scale Scene Reconstruction via Pixel-level Communication

3D Gaussian Splatting (3DGS) enables high-fidelity and real-time 3D scene reconstruction, but scaling training to large-scale scenes requires optimizing hundreds of millions of Gaussians across multiple GPUs. Existing distributed approaches either partition scenes into isolated regions, causing global inconsistency, or rely on global Gaussian-level exchanges, which lead to substantial growth in inter-GPU communication and quickly dominate iteration time. We propose Splaxel, a communication-efficient distributed 3DGS training framework based on pixel-level local rendering and global composition. Instead of synchronizing Gaussians, each GPU renders its local subset and exchanges only partial pixel values, maintaining mathematical consistency while keeping communication cost stable as the scene size increases. Splaxel further reduces pixel-level redundancy through geometric and transmittance visibility prediction and improves GPU utilization via conflict-free camera-view consolidation. Evaluated on large-scale datasets with up to 120M Gaussians, Splaxel achieves up to 7.6$\times$ speedup over the state-of-the-art distributed 3DGS framework while preserving high reconstruction quality.

02.
Nature (Science) 2026-06-17

Cortical development dynamics across autism spectrum disorder mouse models

Despite the functional diversity of over 100 causal genes1–3, phenotypic convergence across models may reveal common neurobiological processes in autism spectrum disorder (ASD). Here we profiled 251 samples from 11 monogenic mouse models of ASD using single-nucleus multi-omic sequencing across three developmental stages, both sexes and two brain regions. Despite genetic heterogeneity, ASD-linked mutations converged on perturbations of the radial glial cell lineage. These alterations reflect a transient developmental delay rather than lasting lineage misspecification and resolve by postnatal stages. Molecularly, the largest transcriptional differences emerged in neurons at early postnatal stages. These changes included downregulation of synaptic and ion channel-related genes, consistent with homeostatic adaptation or delayed maturation. Network analysis showed molecular convergence across models within each developmental stage, suggesting that diverse mutations linked to ASD impinge on common, stage-specific processes. Convergence becomes less pronounced by postnatal day 14, highlighting the dynamic nature of ASD-associated changes. Cross-genotype heterogeneity is superimposed on stage-specific effects. Electrophysiology corroborated this pattern: mutants generally showed altered neuronal excitability and synaptic properties with model-specific nuances. Our study also highlighted sex-specific gene expression alterations, with female mice often displaying larger effect sizes than male mice. Together, our findings provide a comprehensive view of developmental cellular and molecular dynamics across models of ASD. Using single-nucleus multi-omic sequencing, diverse autism spectrum disorder-linked gene mutations converge on transient, stage-specific disruptions in early brain development, and highlight sex-specific gene expression alterations.

03.
arXiv (CS.CV) 2026-06-19

ReA-OVCD: Reliability-Aware Open-Vocabulary Change Detection via Semantic and Spatial Refinement

Unlike traditional remote sensing change detection that relies on predefined categories, Open-Vocabulary Change Detection (OVCD) identifies land cover changes flexibly using arbitrary text prompts. However, existing methods suffer from an inherent trade-off when modeling changes: instance-level comparison overlooks fine-grained semantic variations (e.g., partial building extensions), while direct pixel comparison proves unreliable, yielding unstable responses and boundary artifacts due to semantic ambiguity and spatial inconsistency. To this end, we propose an efficient training-free Reliability-Aware Open-Vocabulary Change Detection (ReA-OVCD) framework. It first derives candidate change regions from pixel-wise semantic discrepancies to ensure flexible and detailed localization. To ensure reliability, it subsequently introduces a collaborative refinement strategy to explicitly model change validity from both semantic and spatial perspectives. Specifically, we develop a Semantic Change Reasoning (SCR) module that reassesses changes by jointly analyzing distributional divergence and response variation, enabling the suppression of incidental inconsistencies while preserving reliable semantic shifts. In addition, a Boundary-aware Change Refinement (BCR) module is designed to mitigate artifacts stemming from boundary misalignment and uncertainty through validating whether candidate regions are supported by reliable interior pixels. Extensive experiments across multiple datasets (LEVIR-CD, WHU-CD, DSIFN, and SECOND) demonstrate that our method consistently outperforms state-of-the-art approaches, achieving $\mathrm{F}_{1}^{C}$ improvements of 2.13\% to 9.75\% with higher computational efficiency. The code is publicly available at \https://github.com/Funny0101/ReA-OVCD

04.
arXiv (CS.LG) 2026-06-19

Representing Piecewise-Linear Functions by Functions with Minimal Arity

arXiv:2406.02421v2 Announce Type: replace-cross Abstract: Any continuous piecewise-linear function $F\colon \mathbb{R}^{n}\to \mathbb{R}$ can be represented as a linear combination of $\max$ functions of at most $n+1$ affine-linear functions. In our previous paper [``Representing piecewise linear functions by functions with small arity'', AAECC, 2023], we showed that this upper bound of $n+1$ arguments is tight. In the present paper, we extend this result by establishing a correspondence between the function $F$ and the minimal number of arguments that are needed in any such decomposition. We show that the tessellation of the input space $\mathbb{R}^{n}$ induced by the function $F$ has a direct connection to the number of arguments in the $\max$ functions.

05.
arXiv (CS.CL) 2026-06-12

Detect, Remask, Repair: Diffusion Editing for Faithful Summarization of Evolving Contexts

Summaries of real-world events can become outdated as contexts evolve and new information arrives. A common response is to generate a new summary from the updated context, but full regeneration discards the previous draft, can obscure what changed, and may be unnecessary when only a few claims are unsupported. We study localized faithfulness repair: updating outdated spans in an existing summary while preserving supported content. We propose DETECT-REMASK-REPAIR, a diffusion-based framework that identifies, remasks, and repairs outdated regions with masked diffusion language models. To evaluate evolving-context summarization, we introduce StreamSum, a benchmark of synthetic event timelines. Experiments on DialogSum and StreamSum show that localized diffusion repair provides a controllable alternative to full rewriting: faithfulness-steered repair improves early drafts, one-step repair reduces repair cost to under half a second, with the framework enabling faithfulness-speed-preservation tradeoffs across datasets. We also find that the framework can provide a post-hoc correction step that improves faithfulness for autoregressive systems.

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

Veriphi: Attack-Guided Neural Network Verification with Dataset-Dependent Training Methods

arXiv:2606.18454v1 Announce Type: cross Abstract: We present Veriphi, a GPU-accelerated neural network verification system that combines fast adversarial attacks with formal bound certification using alpha,beta-CROWN methods. Through systematic experiments on MNIST and CIFAR-10 using three training methodologies (standard, adversarial, certified), we demonstrate that training method effectiveness is fundamentally dataset-dependent. Interval Bound Propagation (IBP) achieves 78% certified accuracy on simple MNIST (784 dimensions) but provides negligible certification performance on the more complex CIFAR-10 dataset, where PGD adversarial training dominates with 94% certification at small perturbations. We achieve 5x verification speedup through attack-guided falsification and scale our approach to production-size models (105.8M parameters) for real-world aerospace logistics optimization. Our results challenge the assumption that certified training universally outperforms adversarial training, showing context matters critically for verification strategy selection.

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

CONCORD: Asynchronous Sparse Aggregation for Device-Cloud RAG under Document Isolation

arXiv:2606.15179v1 Announce Type: new Abstract: Retrieval-augmented generation (RAG) has emerged as a pivotal technique for improving language models by incorporating external knowledge at inference time. As device-cloud collaborative inference makes it feasible to deploy small language models on edge devices, a new setting arises in which private documents remain on the device and public knowledge resides in the cloud. Privacy and policy constraints often forbid raw document exchange, creating a document-isolated dual-end RAG setting. However, existing methods rely on frequent remote synchronization and dense evidence transfer, limiting throughput under realistic latency and bandwidth conditions. To address this issue, we propose CONCORD, an asynchronous sparse aggregation framework for dual-end RAG under document isolation. CONCORD treats the cloud as an asynchronously arriving evidence source rather than a continuously synchronized co-generator. Specifically, we introduce waiting debt control to decide whether each decoding step should continue waiting for remote participation based on the observed return of waiting. We also design a certificate-guided minimal supplementation mechanism that requests only the remote evidence needed to determine the current greedy decision. Steps that consult the cloud preserve the same greedy token as dense dual-end aggregation, while the remaining steps commit locally without remote evidence. Experiments on Natural Questions and WikiText-2 show that CONCORD improves end-to-end throughput over baselines by $1.66\times$ and $2.15\times$, respectively, while reducing per-token communication by over two orders of magnitude and maintaining comparable answer quality and perplexity.

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

Vision-language models for chest radiography do not always need the image

Medical vision-language models report strong chest radiograph accuracy, and this is increasingly read as evidence that they use the image. That inference is unsafe: a model exploiting finding-name priors scores like one that reads the scan, and no standard benchmark separates them. We introduce a causal audit that intervenes on the image, occluding the relevant region, occluding an irrelevant one, and swapping in another patient's same-label scan, and combines three behavioral metrics to test whether a correct answer depends on the image. Across nine systems, a text-only model with no image access reaches within 5.7 accuracy points of the best multimodal one, and a 119-billion-parameter multimodal model is statistically indistinguishable from a 7-billion text-only baseline. The audit splits the cohort into three models that ignore the image, one that is unstable, and five that use it selectively, for a subset of findings; the categories hold across a second dataset, resolution, and prompt phrasing. Against board-certified radiologists, a text-only model is statistically indistinguishable from a radiologist's accuracy while grounding at zero, whereas the image-using models ground at radiologist-comparable rates. Reported confidence flags ungrounded answers only when a model uses the image. Grounding audits, not accuracy, should gate clinical deployment.

09.
arXiv (CS.CV) 2026-06-16

MoECa: Aligning Feature Reuse with Expert Decomposition in Diffusion Transformers

Diffusion Transformers with Mixture-of-Experts (DiT-MoE) improve model capacity under sparse activation, but diffusion inference is still bottlenecked by redundant computation across timesteps. Existing caching methods mainly operate at the token level, which becomes suboptimal in DiT-MoE because each token update is internally decomposed into multiple routed expert branches. Our analysis shows that cross-timestep redundancy in DiT-MoE is better characterized at the expert-branch level than at the whole-token level. Based on this observation, we propose MoECa, a fine-grained caching framework that performs branch-level feature reuse across timesteps. MoECa further introduces expert-aware adaptive control and synchronized cache updates across MoE and attention paths to maintain stable intermediate states. Experiments on multiple DiT-MoE models show that MoECa consistently achieves a better speed-quality trade-off than prior caching methods, with up to 2.83$\times$ inference speedup and minimal quality degradation.

10.
arXiv (CS.CV) 2026-06-16

Power Battery Detection

Power batteries are essential components in electric vehicles, where internal structural defects can pose serious safety risks. We conduct a comprehensive study on a new task, power battery detection (PBD), which aims to localize the dense endpoints of cathode and anode plates from industrial X-ray images for quality inspection. Manual inspection is inefficient and error-prone, while traditional vision algorithms struggle with densely packed plates, low contrast, scale variation, and imaging artifacts. To address this issue and drive more attention into this meaningful task, we present PBD5K, the first large-scale benchmark for this task, consisting of 5,000 X-ray images from nine battery types with fine-grained annotations and eight types of real-world visual interference. To support scalable and consistent labeling, we develop an intelligent annotation pipeline that combines image filtering, model-assisted pre-labeling, cross-verification, and layered quality evaluation. We formulate PBD as a point-level segmentation problem and propose MDCNeXt, a model designed to extract and integrate multi-dimensional structure clues including point, line, and count information from the plate itself. To improve discrimination between plates and suppress visual interference, MDCNeXt incorporates two state space modules. The first is a prompt-filtered module that learns contrastive relationships guided by task-specific prompts. The second is a density-aware reordering module that refines segmentation in regions with high plate density. In addition, we propose a distance-adaptive mask generation strategy to provide robust supervision under varying spatial distributions of anode and cathode positions. The source code and datasets will be publicly available at \href{https://github.com/Xiaoqi-Zhao-DLUT/X-ray-PBD}{PBD5K}.

11.
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.

12.
PLOS Computational Biology 2026-06-09

Evolution of phenocopying in a dynamical model of developmental trajectories

by Yuuki Matsushita, Archishman Raju Developmental trajectories are known to be canalized, or robust to both environmental and genetic perturbations. However, even when these trajectories are decanalized by an environmental perturbation outside the range of conditions to which they are robust, they often produce phenotypes similar to known mutants, called phenocopies. This correspondence between the effects of environmental and genetic perturbations has received little theoretical attention. Here, we study an abstract regulatory model that is evolved to follow a specific trajectory. We then study the effects of small and large perturbations to the trajectory, both by changing parameters and by perturbing the state at specific times. We find that the phenomenon of phenocopying emerges in evolved trajectories and is not present in a null model of randomly sampled trajectories. Our results suggest that, in this class of dynamic models, evolution can allow high-dimensional phenotypic landscapes to simultaneously exhibit robustness and phenocopying.

13.
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.

14.
arXiv (CS.AI) 2026-06-16

Shachi: A Modular, Controllable Framework for LLM-Based Agent-Based Modeling of Emergent Collective Behavior

arXiv:2509.21862v3 Announce Type: replace Abstract: How collective behaviors emerge from the interactions of individual LLM-driven agents is a central question in artificial life, yet controlled study of these emergent dynamics has been hindered by the lack of a principled simulation framework for systematic experimentation. To address this, we introduce Shachi, a principled methodology and modular framework that decomposes an agent's cognition into core components: Configuration for intrinsic identity, Memory for contextual continuity, and Tools for extended capabilities, all orchestrated by an LLM reasoning engine. This decomposition treats each cognitive component as an independently controllable variable, enabling perturbation studies that trace how micro-level cognitive traits propagate into population-level dynamics. We investigate behavioral patterns across a 10-task benchmark spanning three levels of collective complexity. Shachi enables memory transfer across environment transitions, producing history-dependent behavioral shifts, and allows agents to simultaneously inhabit multiple environments, revealing cross-environment interference invisible in single-environment studies. Furthermore, in a real-world U.S. tariff shock case study, locally interacting agents with individually controlled cognitive components produce macro-level market dynamics directionally consistent with observed real-world outcomes. Our work provides a rigorous, open-source simulation framework for LLM-based ABM, aimed at fostering cumulative scientific inquiry into the emergent collective behaviors of interacting artificial agents.

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

How Linear Is a Transformer Feed-Forward Block? Per-Block Linear Recoverability Is Learned, Not Architectural

作者:

Transformer feed-forward networks (FFNs) are often treated as nonlinear stores of computation, yet how nonlinear a trained FFN block actually is has rarely been measured. We treat each FFN as a position-wise input-to-output map and split it into the exact least-squares linear approximation plus a residual. The held-out variance the closed-form linear map explains defines a block's linear recoverability (R^2_lin), an optimiser-free measure of its linearity. Across all twelve blocks of GPT-2, Pythia-160m, and llama-160m, R^2_lin is highly heterogeneous and non-monotone with depth, ranging from near-linear (>0.99) to strongly nonlinear (

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

GIST-CMTF: Goal-State Inference for Causal Minimal Tool Filtering in LLM Agents

arXiv:2606.16813v1 Announce Type: new Abstract: Tool-augmented LLM agents rely on runtime filtering to decide which tools should be visible at each step. Causal Minimal Tool Filtering (CMTF) reduces tool-choice confusion by exposing only the next causally necessary tool frontier, but it assumes that the user request has already been mapped to a symbolic goal state. In practice, requests such as "handle my appointment" or "take care of this email" may correspond to multiple possible goals. This creates wrong-goal execution, where an agent follows a valid causal tool path for an unintended objective. We introduce GIST-CMTF, a goal-state inference layer that predicts candidate symbolic goals over the same state-transition vocabulary used by CMTF, estimates ambiguity, and either applies CMTF or exposes clarification as a causal action that produces missing goal or state variables. We evaluate GIST-CMTF across seven model backends, six filtering methods, and 120 controlled tool-use tasks. GIST-CMTF achieves 97.0% task success, compared with 80.1% for top-goal CMTF and 82.9% for semantic-goal CMTF. It reduces wrong-goal execution from 19.4% under top-goal CMTF to 2.5%, while preserving the one-tool exposure of causal filtering and using substantially fewer tokens than all-tools exposure. These results suggest that reliable tool-augmented agents should validate goal state, not only tool relevance, before exposing external actions.

17.
PLOS Computational Biology 2026-06-01

A statistical framework for comparing epidemic forests

by Cyril Geismar, Peter J. White, Anne Cori, Thibaut Jombart Inferring who infected whom in an outbreak is essential for characterising transmission dynamics and guiding public health interventions. However, this task is challenging due to limited surveillance data and the complexity of immunological and social interactions. Instead of a single definitive transmission tree, epidemiologists often consider multiple plausible trees forming epidemic forests. Various inference methods and assumptions can yield different epidemic forests, yet no formal test exists to assess whether these differences are statistically significant. We propose such a framework using a chi-square test and permutational multivariate analysis of variance (PERMANOVA). We assessed each method’s ability to distinguish simulated epidemic forests generated under different offspring distributions. While both methods achieved perfect specificity for forests with 100+ trees, PERMANOVA consistently outperformed the chi-square test in sensitivity across all epidemic and forest sizes. Implemented in the R package mixtree, we provide the first statistical framework to robustly compare epidemic forests.

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

ReNikud: Audio-Supervised Hebrew Grapheme-to-Phoneme Conversion

Grapheme-to-phoneme (G2P) conversion for Modern Hebrew is needed for applications like text-to-speech (TTS), but is challenging due to the language's abjad writing system, which leaves vowels largely unwritten, creating substantial ambiguity. Standard approaches first predict vowel diacritics (nikud) to produce International Phonetic Alphabet (IPA) transcriptions, but this is limited: vocalization data is scarce and laborious to produce, it does not specify features such as lexical stress, and it reflects formal grammatical rules rather than everyday spoken pronunciation. Direct sequence-to-sequence IPA prediction, meanwhile, struggles on limited data and fails to exploit the character-level alignment characteristic of abjads. Our method, ReNikud, overcomes these limitations with two key insights: (1) Weak audio supervision via a phoneme-based automatic speech recognition (ASR) pseudo-labeling pipeline on thousands of hours of unlabeled Hebrew audio, yielding phonemic transcriptions that reflect natural spoken norms without manual annotation. (2) A pseudo-vocalization architecture that predicts IPA phonemes at each character position, enforcing character-level alignment as an inductive bias. Results on existing Hebrew G2P benchmarks and the new targeted MILIM benchmark for spoken Hebrew show that ReNikud surpasses previous state-of-the-art methods. We will release our code and trained models to support further work on Hebrew TTS and speech technologies.

19.
arXiv (quant-ph) 2026-06-15

Quantum Simulation of Spin-Dependent Electron Transfer in a Synthetic Chiral Lattice with a Trapped Ion

arXiv:2606.13930v1 Announce Type: new Abstract: Electron transfer through chiral structures can exhibit spin asymmetry, known as the chiral-induced spin selectivity effect, whose microscopic origin remains an open question. While path-interference within the chiral moiety has been proposed as a key mechanism, its experimental validation requires precise and versatile tunability of system parameters. Here we implement a programmable quantum simulation of spin-dependent electron transfer in a donor–chiral-bridge–acceptor model using a trapped ion. The bridge is encoded in internal states of the ion with tunable nearest- and next-nearest-neighbor couplings, while donor and acceptor states are coupled via a spectator bosonic motional mode. We observe spin-dependent interference within the bridge, and further reveal spin-dependence in donor-to-acceptor transfer dynamics, controlled by amplitude and phase of the coupling parameter. Our results identify interference among spin-dependent pathways as a microscopic origin of spin-dependent transfer, and open a route toward quantum simulations of complex chiral lattices with multi-level and bosonic degrees of freedom.

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

GF-DiT: Scheduling Parallelism for Diffusion Transformer Serving

arXiv:2606.13501v1 Announce Type: cross Abstract: Diffusion Transformers (DiTs) have become the dominant architecture for image and video generation, creating growing demand for efficient DiT serving. Existing systems assign each request a fixed parallel configuration throughout its lifetime. However, DiT workloads exhibit substantial heterogeneity across requests, execution stages, and system conditions, making static parallelism inefficient and often leading to poor GPU utilization and degraded service quality. This paper argues that DiT serving should treat GPU parallelism as a first-class schedulable resource. We present GF-DiT, a policy-programmable runtime for elastic DiT serving that dynamically adapts the parallelism of running requests according to workload demands and service objectives. GF-DiT introduces an asynchronous execution abstraction that decomposes requests into independently schedulable trajectory tasks and enables online GPU reallocation. To make elastic parallelism practical, GF-DiT further proposes group-free collectives, a lightweight communication abstraction that supports low-overhead online formation and reconfiguration of arbitrary execution groups. We implement GF-DiT in vLLM-Omni and evaluate it on representative image and video diffusion workloads. Compared with fixed-pipeline execution with static parallelism, GF-DiT improves throughput by up to 6.01$\times$, reduces mean latency by up to 95%, lowers SLO violation rates by up to 90%, and reduces communication-group setup overhead from 778 ms to approximately 60 $\mu$s.

21.
arXiv (CS.AI) 2026-06-16

Guiding Federated Graph Recommendation with LLM-encoded knowledge

arXiv:2606.15277v1 Announce Type: cross Abstract: Graph-based recommender systems are highly effective at extracting collaborative signals from user–item interactions, and federated learning (FL) allows these models to be trained while preserving user privacy. However, aggregating graph representations across distributed, non-IID clients remains a challenge; structural embeddings learned locally often misalign, and naive averaging fails to capture meaningful cross-client relationships. Most existing federated graph methods rely exclusively on structural aggregation, neglecting the rich, global semantic context available in large language models (LLMs). In this paper, we propose a novel framework that uses LLM-encoded knowledge to guide federated graph recommendation. Specifically, clients learn structural representations from local graphs while simultaneously summarizing their typical interaction patterns into compact semantic vectors via a frozen LLM. The central server then uses these LLM-encoded semantic signals to discover related preference patterns across clients, guiding the selective aggregation of their structural representations. This enables semantically informed cross-client collaboration without exposing raw data. Extensive experiments on standard benchmarks show that guiding structural alignment with LLM-encoded knowledge consistently improves recommendation accuracy over existing federated graph baselines.

22.
bioRxiv (Bioinfo) 2026-06-12

PeptiDIA: A Machine Learning Framework for Enhanced Peptide Identification in Fast-Gradient Data-Independent Acquisition Proteomics

Data-independent acquisition (DIA) mass spectrometry has become increasingly prevalent in proteomics as advances in instrumentation, chromatography, and computational analysis have enabled robust proteome identification across complex biological samples. However, analytical depth achieved with fast chromatographic gradients remains lower than that obtained using long-gradients, reflecting a throughput-depth trade-off. Here, we present PeptiDIA, a machine learning framework that enhances peptide identification in fast-gradient DIA data by leveraging paired fast and long-gradient acquisitions from identical samples. PeptiDIA processes DIA-NN outputs generated at relaxed false discovery rate thresholds to obtain expanded candidate peptide pools and trains gradient-boosted decision tree models using long-gradient identifications as reference labels. The model integrates DIA-NN features with engineered peptide descriptors and applies isotonic regression to calibrate probabilities, enabling controlled peptide recovery relative to the long-gradient reference. Applied to human and murine datasets spanning six tissues acquired on an Orbitrap Exploris 480, PeptiDIA increased peptide identifications by 25-34% at 1% target reference-discordance rate (RDR) and increased the number of protein groups containing at least one rescued peptide by 15-17%. Overall, PeptiDIA improves the identification depth of fast-gradient DIA-NN workflows without altering acquisition strategies. The framework is available as a web application and command-line tool at https://github.com/Jordano700/PeptiDIA.

23.
PLOS Computational Biology 2026-06-23

CARGO: A cytometry analysis framework via Regularized graph optimal-transport

by Abida Sanjana Shemonti, Grzegorz B. Gmyrek, Katrien L. A. Quintelier, Sofie Van Gassen, Yvan Saeys, Marcella Willemsen, Joachim G. J. V. Aerts, Eva V. E. Madsen, J. Paul Robinson, Alex Pothen, Bartek Rajwa Conventional data visualization techniques in single-cell analysis (such as two-dimensional dot plots, SPADE, PCA, t-SNE, or UMAP) often fall short in enabling an intuitive understanding of high-parameter flow cytometry data. These methods tend to oversimplify complex biological relationships, lack biologically meaningful interpretations, and offer no principled framework for downstream quantitative analysis. To address these limitations, we present a graph-based (network-based) visualization framework grounded in optimal transport theory. In this framework, cell populations are defined by their marker-expression profiles, and inter-population similarity is quantified using an efficiently computable optimal transport formulation known as the Sinkhorn distance. Our approach produces biologically consistent two-dimensional graph layouts using a phenotype-aware Hamming distance. Structural differences between sample graphs are characterized through a customized graph-edit distance that captures changes in population size, marker expression, and relationships between populations. We demonstrate our methods on two flow cytometry datasets: one from a clinical trial of dendritic cell-based immunotherapy in malignant peritoneal mesothelioma, involving 14 patients sampled at three time points with 14-color panels, and another from FlowCAP-II, which involved 43 acute myeloid leukemia patient samples analyzed with 7-color panels. Our framework produces robust, quantitative visual summaries of cell populations and supports statistical analysis based on graph edit distances, thereby offering new insights into disease progression and treatment response. Ultimately, our method bridges the gap between flow cytometry data visualization and biological interpretation.

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

Model-Based and Data-Driven Hierarchical Control and Topology Co-Design for Robust Networked Systems

arXiv:2606.11596v1 Announce Type: cross Abstract: In this paper, we consider a class of networked systems comprising an interconnected set of linear subsystems, disturbance inputs, and performance outputs. Using dissipativity theory, we first propose a model-based hierarchical control design strategy to ensure the closed-loop networked system is dissipative from its disturbance inputs to performance outputs. This involves designing local controllers for each subsystem to enforce local dissipativity guarantees, which are then exploited to co-design distributed global controllers and the interconnection topology to enforce global dissipativity guarantees while optimizing interconnection topology costs. The overall design process requires only solving a sequence of linear matrix inequality (LMI) problems, thereby retaining compositionality and decentralizability while avoiding non-convex, iterative design processes that are inefficient and centralized. This model-based hierarchical control design strategy assumes the knowledge of the subsystem dynamics, which may not hold in many real-world networked systems. Motivated by this, we also propose a data-driven hierarchical control design strategy that assumes only the availability of rich input-state-output trajectory data from the subsystems. The proposed data-driven design process assumes that the unknown disturbances affecting the subsystem dynamics are bounded by a quadratic matrix inequality (relaxing conventional bounds) and accounts for this by using the matrix S-lemma. Finally, the effectiveness of the proposed model-based and data-driven hierarchical control designs is illustrated for a networked system representing a DC microgrid, with the aim of enforcing robust (dissipative) voltage regulation and current sharing.

25.
arXiv (quant-ph) 2026-06-16

Interaction and non-Hermiticity controlled transmission in extended Su-Schrieffer-Heeger models

arXiv:2606.15245v1 Announce Type: cross Abstract: We study the transport characteristics of an extended version of the Su-Schrieffer-Heeger (SSH) model with next-nearest-neighbor (NNN) interactions and non-Hermitian onsite energies. We observed that transport in such a system is significantly modified by the NNN interaction and the non-Hermitian terms. The transmission coefficient exhibits oscillatory behavior as the strength of the NNN interaction varies in a fixed-length chain. Moreover, the transmission coefficient also shows oscillation with system size for a fixed strength of the NNN interaction. We find that novel oscillatory behavior of the transmission coefficient, arising form the NNN interaction, is a unique feature of such a model and has not been reported previously. The presence of the non-Hermitian terms also enhances/reduces the transmission coefficient depending on the values of the other system parameters like intra-, inter- and NNN hopping. It appears from our study that both the NNN interaction and the non-Hermiticity introduce significant changes in the transport properties of the extended SSH chain, which are not observed in the standard Hermitian nearest-neighbour variant of the SSH model.