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01.
arXiv (CS.AI) 2026-06-19

FlowEdit: Associative Memory for Lifelong Pronunciation Adaptation in Flow-Matching TTS

Authors:
Harshit Singh↗Ayush Pratap Singh↗Nityanand Mathur↗

arXiv:2606.20518v1 Announce Type: new Abstract: Flow-matching text-to-speech systems achieve remarkable zero-shot quality but remain static after deployment: pronunciation errors on out-of-vocabulary proper nouns persist unless the model is retrained. We introduce FlowEdit, a life-long adaptation framework for frozen flow-matching TTS that learns pronunciation corrections as latent conditioning edits rather than weight updates. When corrective feedback is provided, FlowEdit optimizes a token-level perturbation in the text embedding space, then stores the correction in a Modern Hopfield Network serving as content-addressable episodic memory. At inference, corrections are retrieved via soft attention with a similarity gate, enabling fuzzy morphological matching. On our curated benchmark of 312 multilingual proper nouns across 18 language families, FlowEdit reduces target-word Phoneme Error Rate by 92.7% relative to the zero-shot baseline while maintaining identical general-speech quality. Corrections complete in approximately 15 seconds on a single GPU.

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02.
arXiv (CS.CL) 2026-06-11

TokenRatio: Principled Token-Level Preference Optimization via Ratio Matching

Authors:
Truong Nguyen↗Tien-Phat Nguyen↗Linh Ngo Van↗Duy Minh Ho Nguyen↗Khoa Doan↗Trung Le↗

Direct Preference Optimization (DPO) is a widely used RL-free method for aligning language models from pairwise preferences, but it models preferences over full sequences even though generation is driven by per-token decisions. Existing token-level extensions typically decompose a sequence-level Bradley-Terry objective across timesteps, leaving per-prefix (state-wise) optimality implicit. We study how to recover token-level preference optimality using only standard sequence-level pairwise comparisons. We introduce Token-level Bregman Preference Optimization (TBPO), which posits a token-level Bradley-Terry preference model over next-token actions conditioned on the prefix, and derive a Bregman-divergence density-ratio matching objective that generalizes the logistic/DPO loss while preserving the optimal policy induced by the token-level model and maintaining DPO-like simplicity. We introduce two instantiations: TBPO-Q, which explicitly learns a lightweight state baseline, and TBPO-A, which removes the baseline through advantage normalization. Across instruction following, helpfulness/harmlessness, and summarization benchmarks, TBPO improves alignment quality and training stability and increases output diversity relative to strong sequence-level and token-level baselines.

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

ORAgentBench: Can LLM Agents Solve Challenging Operations Research Tasks End to End?

Authors:
Jiajun Li↗Mingshu Cai↗Yixuan Li↗Yu Ding↗Ran Hou↗Guanyu Nie↗Xiongwei Han↗Wanyuan Wang↗

arXiv:2606.19787v1 Announce Type: new Abstract: Large language models are increasingly deployed as autonomous agents for multi-step tasks in executable environments, yet their ability to perform realistic operations research (OR) work remains unclear. Existing OR evaluations often decouple modeling from solving, rely on pre-formalized or text-only instances, and rarely test the full workflow from operational artifacts to validated decisions. In this work, we introduce ORAgentBench, an execution-grounded benchmark for evaluating autonomous agents on challenging end-to-end operations research tasks. It contains 107 human-reviewed tasks across diverse operational scenarios, each packaged in an isolated environment with a natural-language brief, multi-file data, configuration artifacts, and a required submission schema. Agents must write and run solution code, and their submissions are evaluated by hidden validators for schema validity, hard-constraint feasibility, and normalized objective quality. Experiments with fourteen frontier agent-model configurations show that current agents remain far from reliable OR practice. The best agent passes only 35.51% of all tasks and 20.59% of hard tasks, and many feasible submissions still fall below the required quality threshold. Failure analysis further shows that errors are dominated by strategic weaknesses, including missed operational rules, brittle formulations, weak feasible-solution construction, and insufficient solution improvement. OR-specific procedural skills increase hard-task feasibility, but do not reliably improve solution quality or pass rate. These results suggest that progress in OR agents requires moving beyond plausible optimization code toward dependable, high-quality operational decision-making.

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05.
arXiv (CS.AI) 2026-06-16

Service-Induced Congestion in Memory-Constrained LLM Serving

Authors:
Ruicheng Ao↗Jing Dong↗Gan Luo↗David Simchi-Levi↗

arXiv:2606.15555v1 Announce Type: cross Abstract: In large language model (LLM) serving, each request accumulates persistent graphics processing unit (GPU) memory during service as its key-value cache grows with every generated token. Under high concurrency, aggregate memory usage therefore increases endogenously over time: the service process itself creates future capacity pressure. When memory capacity is exceeded, systems evict active requests, discarding cached state and restarting them later, which wastes computation and reduces throughput. We develop a discrete-time dynamical model of memory-constrained LLM inference that captures admission, memory growth, and eviction under continuous batching. In the saturated-input regime, the system admits both eviction-free fixed points and limit cycles with evictions. For homogeneous workloads, we show that the eviction-free equilibrium is unstable and that, except for a Lebesgue-measure-zero exact-capture set, the system converges to a unique worst-case limit cycle that is asymptotically stable outside this exceptional set, with throughput losses as large as 50%. For heterogeneous workloads, we prove a stability criterion in the two-class common-input setting and explain how the survival-polynomial mechanism generalizes to multiple classes and heterogeneous-input lengths. Under an input-dominated scaling regime, coprime decoding lengths stabilize the eviction-free equilibrium, while non-coprime lengths create synchronized modes that drive instability. These results characterize when workload heterogeneity desynchronizes completions and helps stabilize memory-constrained serving. More broadly, we identify service-induced congestion as a structural instability mechanism and derive scheduling design principles for sustaining high throughput.

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

Adaptively secure unitary designs with constant non-Clifford cost

Authors:
Lennart Bittel↗Lorenzo Leone↗

arXiv:2510.08129v2 Announce Type: replace Abstract: Randomness is a fundamental resource in quantum information, with crucial applications in cryptography, algorithms, and error correction. A central challenge is to construct unitary $k$-designs that closely approximate Haar-random unitaries while minimizing the costly use of non-Clifford operations. In this work, we present a protocol able to generate unitary $k$-designs on $n$ qubits, secure against any adversarial quantum measurement, with a system-size-independent number of non-Clifford gates. Our construction applies a $k$-design only to a subsystem of size $\Theta(k)$, independent of $n$. This ``seed'' design is then ``diluted'' across the entire $n$-qubit system by sandwiching it between two random Clifford operators. The resulting ensemble forms an $\varepsilon$-approximate unitary $k$-design on $n$ qubits. We prove that this construction achieves full quantum security against adaptive adversaries using only $\tilde{O}(k^2 \log\varepsilon^{-1})$ non-Clifford gates. If one requires security only against polynomial-time adaptive adversaries, the non-Clifford cost decreases to $\tilde{O}(k + \log^{1+c} \varepsilon^{-1})$. This is optimal, since we show that at least $\Omega(k)$ non-Clifford gates are required in this setting. Compared to existing approaches, our method significantly reduces non-Clifford overhead while strengthening security guarantees to adaptive security as well as removing artificial assumptions between $n$ and $k$. These results make high-order unitary designs practically attainable in near-term fault-tolerant quantum architectures.

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07.
arXiv (CS.AI) 2026-06-19

Rethinking Shrinkage Bias in LLM FP4 Pretraining: Geometric Origin, Systemic Impact, and UFP4 Recipe

Authors:
Qian Zhao↗Kunlong Chen↗Changxin Tian↗Zhonghui Jiang↗Haitao Zhang↗Chaofan Yu↗Peijie Jiang↗Mingliang Gong↗Jia Liu↗Ziqi Liu↗Zhiqiang Zhang↗Jun Zhou↗…

arXiv:2606.20381v1 Announce Type: new Abstract: FP4 training promises substantial reductions in memory and computation cost for LLM pretraining, yet current FP4 hardware paths and recipes, including NVIDIA Blackwell/Rubin-class systems and AMD MI350-series GPUs, remain centered on E2M1 data elements. In this study, we identify a fundamental limitation of that choice: non-uniform formats such as E2M1 inherently suffer from Shrinkage Bias, a systematic negative rounding error caused by the geometric asymmetry of their representable bins. We show that this bias accumulates multiplicatively across layers and is amplified by the Random Hadamard Transform (RHT), providing a unified explanation for the training instability observed in existing E2M1-based FP4 recipes. In contrast, uniform grids (E1M2/INT4) bypass this grid-geometry error and better convert the improved bucket utilization from RHT into higher quantization quality. Based on this finding, we propose UFP4, a uniform 4-bit training recipe that applies RHT to all three training GEMMs while restricting stochastic rounding to dY alone. On Dense 1.5B, MoE 7.9B, and MoE 124B long-run pretraining, UFP4 consistently achieves lower BF16-relative loss degradation than strong E2M1-based baselines, supported by scaling-law analysis and ablation studies. Our results suggest that future accelerators should support E1M2/INT4-style uniform 4-bit grids as first-class training primitives alongside E2M1.

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08.
arXiv (math.PR) 2026-06-16

Stein's method for the matrix normal distribution

Authors:
Robert E. Gaunt↗Fr\'ed\'eric Ouimet↗Donald Richards↗

arXiv:2601.11422v2 Announce Type: replace-cross Abstract: This work presents the first systematic development of Stein's method for matrix distributions. We establish the basic essential ingredients of Stein's method for matrix normal approximation: we derive an extended-generator-based Stein identity from a matrix Ornstein-Uhlenbeck diffusion with two-sided scales, provide an explicit semigroup representation for the solution of the Stein equation, and obtain regularity estimates for the solution. The new methodology is demonstrated in three examples: (i) smooth Wasserstein distance bounds to quantify the matrix central limit theorem (a didactic example), (ii) a Wasserstein distance bound for the matrix normal approximation of the centered matrix $T$ distribution, and (iii) a Stein's method-of-moments approach to estimating the row and column covariance factors of the matrix normal, yielding a flexible class of weighted flip-flop Stein estimators that generalize Dutilleul's classical flip-flop algorithm and naturally accommodate row/column importance weights, systematic missingness, and projection onto structured covariance families. The latter two examples are intrinsically matrix-valued and cannot be treated using naive vectorization.

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09.
arXiv (quant-ph) 2026-06-16

Reconstruction of detector error model for quantum error correction

Authors:
Cheng Ye↗Pan Zhang↗

arXiv:2606.16288v1 Announce Type: new Abstract: Fault-tolerant quantum computing fundamentally relies on the accurate characterization of circuit-level noise to optimize decoding algorithms. However, extracting complex multi-body error correlations remains challenging. Contemporary greedy inference algorithms can suffer from statistical distortion, discarding true physical mechanisms while introducing many unphysical false positives. Here, we introduce the Correlation-Analysis-based Hypergraph Reconstruction (CAHR) algorithm, a globally consistent framework to invert experimental syndrome statistics directly into discrete physical hypergraphs. By coupling exact algebraic correlation equations with a top-down concurrent-pruning strategy, CAHR recovers the fault topology without false positives for both $d=5$ rotated surface codes and dense 8-body 2D color codes in our benchmark settings. Furthermore, we show that exact continuous parameter extraction in dense codes is limited by a variance cascade, where absolute statistical variance accumulates linearly from high- to low-degree mechanisms. This motivates a two-stage inference paradigm: utilizing CAHR to extract the fault topology, followed by continuous probability optimization. This provides a practical approach for characterizing and decoding highly correlated noise in realistic quantum hardware.

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10.
arXiv (CS.AI) 2026-06-17

ParkingTransformer: LLM-Enhanced End-to-End Trajectory Planning for Autonomous Parking

Authors:
Hauteng Wu↗Xu Li↗Dong Kong↗Zihang Wang↗Xieyuanli Chen↗Benwu Wang↗Wenkai Zhu↗

arXiv:2606.17082v1 Announce Type: cross Abstract: End-to-end autonomous parking has emerged as a critical task within the realm of autonomous driving. However, existing methods suffer from black-box characteristics, lacking high-level semantic understanding and interpretability, which impedes the realization of seamless long-distance autonomous parking from the road to the target spot. To address these limitations, we propose ParkingTransformer, a novel framework that leverages multi-view perception and the scene understanding capability of Large Language Models (LLMs). By combining trajectory queries with LLMs implicit state features, our method interacts directly with historical information and raw sensor data to output planning trajectories, eliminating the need for dense Bird's-View (BEV) representations. To compensate for the inadequate spatial reasoning ability of LLMs, we introduce 3D positional encoding to explicitly inject spatial geometric awareness. Furthermore, a fixed-window streaming mechanism is designed for historical information processing, significantly improving long-term temporal processing efficiency and inference speed. Additionally, a coarse-to-fine decoding strategy is employed to progressively enhance trajectory precision. Extensive closed-loop experiments are conducted on the CARLA simulator and real-world vehicle platforms. The results demonstrate that our method achieves a driving score of 61.32 in CARLA simulator and an average success rate of 88.70% in real-world experiments, validating the feasibility and effectiveness of the proposed algorithms.

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

Sentinel: Decoding Context Utilization via Attention Probing for Efficient LLM Context Compression

Authors:
Yong Zhang↗Heng Li↗Yanwen Huang↗Ning Cheng↗Yang Guo↗Yun Zhu↗Yanmeng Wang↗Shaojun Wang↗Jing Xiao↗

Retrieval-augmented generation (RAG) often suffers from long and noisy retrieved contexts. Existing context compression methods typically rely on heuristic relevance estimation or supervised compression models rather than on how LLMs utilize retrieved context during inference. We propose Sentinel, a lightweight sentence-level compression framework that decodes inference-time contextual utilization behaviors from head-wise attention patterns of frozen LLMs. To ground supervision in retrieval-dependent answering behavior, Sentinel trains a lightweight probe using QA examples where the model succeeds only when retrieved context is available. Sentinel performs compression using only a single non-autoregressive forward pass without dedicated compression training or autoregressive scoring. Empirically, we find that effective contextual utilization signals remain accessible even in compact proxy models. On LongBench, Sentinel with a 0.5B proxy model achieves up to 5$\times$ compression while attaining question-answering performance competitive with compression methods built on 7B-scale models. Despite being trained only on English QA data, Sentinel also generalizes effectively to Chinese and out-of-domain settings.

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12.
arXiv (CS.CV) 2026-06-11

Exploring Adaptive Masked Reconstruction for Self-Supervised Skeleton-Based Action Recognition

Authors:
Shengkai Sun↗Zhiyong Cheng↗Zefan Zhang↗Jianfeng Dong↗Zhihui Li↗Meng Wang↗

Recently, masked skeleton reconstruction models have emerged as strong action representation learners, driving significant progress in self-supervised skeleton-based action recognition. However, existing state-of-the-art methods must predict an exceedingly large number of spatiotemporal patches, significantly prolonging training time. Besides, by treating all spatiotemporal regions equally during reconstruction, these models are distracted from learning the critical motion patterns that underlie action semantics. To address these challenges, we propose Adaptive Masked Reconstruction (AMR), a faster and stronger pre-training framework. We first decouple the decoder from the encoder, enabling flexible prediction of larger spatiotemporal patches and dramatically reducing reconstruction complexity. Given that larger patches contain more complex information, which is challenging to predict and consequently degrades performance, we accordingly introduce an adaptive guidance module. This module identifies regions of high motion informativeness, guiding the model to focus on the most discriminative parts of each patch and alleviating reconstruction difficulty. Experiments on NTU RGB+D 60, NTU RGB+D 120, and PKU-MMD datasets demonstrate that AMR not only accelerates pre-training substantially but also improves downstream recognition accuracy, surpassing current state-of-the-art approaches.

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

Scalable anomaly detection via a univariate Christoffel function

Authors:
Florian Grivet↗Didier Henrion↗Jean-Bernard Lasserre↗Louise Trav\'e-Massuy\`es↗

arXiv:2606.12483v1 Announce Type: new Abstract: Anomaly detection plays a critical role in identifying unusual patterns across domains such as fraud detection, network intrusion, and system fault diagnosis. Recently, Christoffel function-based methods, rooted in polynomial optimization, have emerged as promising alternatives to deep learning due to their strong mathematical foundations and computational frugality. However, their practical applicability is hindered by the need to invert a matrix whose size grows exponentially with the data dimension, rendering the method intractable even for moderate-dimensional datasets. This paper addresses the dimensionality limitations of Christoffel function-based anomaly detection while preserving its key theoretical properties, i.e., the on-off support dichotomy behavior and the accurate support shape capture. We introduce UCF, a univariate Christoffel function which is based on the squared distance between the query point and the support points. Extensive experiments on the ADBench benchmark demonstrate that UCF consistently outperforms 14 state-of-the-art baselines in terms of Average Precision. By resolving the scalability bottleneck of the Christoffel Function, this work expands the toolkit of anomaly detection methods with a robust, theoretically grounded, and universally applicable approach.

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14.
arXiv (quant-ph) 2026-06-16

Ultracold atomic lattice systems for simulating topological phases: A review

Authors:
Bei-Bei Wang↗Xiao-Dong Lin↗Jinyi Zhang↗Long Zhang↗

arXiv:2606.16598v1 Announce Type: cross Abstract: Owing to rapid recent progress, ultracold atomic lattice systems for simulating topological phases are now at a pivotal stage, evolving from established paradigms into increasingly versatile and programmable quantum simulators. In this review, we survey recent experimental advances across four major classes of platforms: optical lattices, including optical lattices with laser-assisted tunneling and optical Raman lattices; synthetic lattices in momentum or internal-state space; Floquet-engineered lattices; and optical tweezer arrays, all of which offer distinct capabilities for realizing and probing topological matter. For each class, we highlight representative experimental breakthroughs, the topological models that have been realized, and the advanced detection and characterization techniques employed, emphasizing how these complementary approaches collectively expand the frontier of quantum simulation. We also discuss emerging directions in strongly correlated and nonequilibrium topological phases, and conclude with an outlook on future prospects.

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15.
arXiv (quant-ph) 2026-06-16

On-chip semi-device-independent quantum random number generator exploiting contextuality

Authors:
Maddalena Genzini↗Caterina Vigliar↗Mujtaba Zahidy↗Hamid Tebyanian↗Andrzej Gajda↗Klaus Petermann↗Lars Zimmermann↗Davide Bacco↗Francesco Da Ros↗

arXiv:2601.08392v2 Announce Type: replace Abstract: We present a semi-device-independent quantum random number generator (QRNG) based on the violation of a contextuality inequality, implemented by the integration of two silicon photonic chips. Our system combines a heralded single-photon source with a reconfigurable interferometric mesh to implement qutrit state preparation, transformations, and measurements suitable for testing a KCBS contextuality inequality. This architecture enables the generation of random numbers from the intrinsic randomness of single-photon interference in a complex optical network, while simultaneously allowing a quantitative certification of their security without requiring entanglement. We observe a contextuality violation exceeding the classical bound by more than 10{\sigma}, unambiguously confirming non-classical behavior. From this violation, we certify a conditional min-entropy per experimental round of Hmin = 0.077 +- 0.002, derived via a tailored semidefinite-programming-based security analysis. Each measurement outcome therefore contains at least 0.077 +- 0.002 bits of extractable genuine randomness, corresponding to an asymptotic generation rate of 21.7 +- 0.5 bits/s. These results establish a viable route towards general-purpose, untrusted quantum random number generators compatible with practical integrated photonic quantum networks.

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

Constraining the outputs of ReLU neural networks

Authors:
Yulia Alexandr↗Guido Mont\'ufar↗

arXiv:2508.03867v2 Announce Type: replace-cross Abstract: We introduce a class of algebraic varieties naturally associated with ReLU neural networks, arising from the piecewise linear structure of their outputs across activation regions in input space, and the piecewise multilinear structure in parameter space. By analyzing the rank constraints on the network outputs within each activation region, we derive polynomial equations that characterize the functions representable by the network. We further investigate conditions under which these varieties attain their expected dimension, providing insight into the expressive and structural properties of ReLU networks.

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

BrainWorld: A Structural-Prior-Conditioned Generative Model for Whole-Brain 4D fMRI Dynamics

Authors:
Junfeng Xia↗Wenhao Ye↗Junxiang Zhang↗Xuanye Pan↗Mo Wang↗Quanying Liu↗

Whole-brain 4D fMRI generation is valuable for modeling functional brain dynamics, yet existing fMRI foundation models mainly target representation learning and downstream prediction rather than conditional predictive generation. We introduce BrainWorld, a structural-prior-conditioned generative model for whole-brain 4D fMRI dynamics. BrainWorld uses sMRI as subject-level anatomical context to guide future fMRI generation, integrating structural information into the denoising process rather than treating it as a parallel modality. Evaluated on 22 datasets spanning diverse cohorts and brain states, BrainWorld generates stable 4D fMRI trajectories up to 400 frames, improves downstream performance through generated-example augmentation, and learns transferable multimodal representations that outperform baselines. Together, these results establish BrainWorld as a condition-aware generative framework for long-horizon brain dynamics modeling and multimodal representation learning.

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

PostDeg: Placement Beats Parameterization in LayerNorm GNNs

Authors:
Yash Tomar↗Aryav Das↗

arXiv:2606.14022v1 Announce Type: new Abstract: LayerNorm-based GNNs routinely erase the topology signals (degree, centrality, $k$-core) that node-selection policies should depend on, but the literature has not located where in the residual block the erasure happens. We answer that question: a positive per-node scalar inserted before LayerNorm is divided out up to a stabilizer term, while the same scalar inserted after LayerNorm reaches the score head as representation magnitude. The surviving slot is the post-LayerNorm position. We instantiate it with PostDeg, a parameter-free post-LayerNorm inverse-degree scale, and pre-register four falsifiers (graphwise scalars, extra LayerNorm, expressive same-slot capacity, backbone-agnostic source) that would reject the rule. PostDeg gains $+3.5\%/+2.5\%/+5.6\%$ over the LN backbone on influence maximization, network dismantling, and maximum independent set, with $10/10$ paired-seed wins per task; none of the four falsifiers fires. The takeaway is that placement, not parameterization, carries the gain – a small invariance check that generalizes to any positive topology scalar in any normalized residual stack.

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

UniECG: Understanding and Generating ECG in One Unified Model

Authors:
Jiarui Jin↗Haoyu Wang↗Xiang Lan↗Jun Li↗Hongyan Li↗Shenda Hong↗

Electrocardiogram (ECG) interpretation is a fundamental skill in medical education, yet students often need more than static examples to connect waveform evidence with diagnostic reasoning. This paper presents UniECG as a step toward interactive ECG education. UniECG supports two complementary learning interactions: given an ECG signal or image, it generates an evidence-based explanation; given a textual learning objective, it generates a corresponding ECG signal example for case-based learning. The model follows a two-stage design. First, it learns grounded ECG explanation from ECG signal–image–text data. Second, it introduces special ECG generation tokens and aligns their hidden representations with a pretrained text-conditioned ECG diffusion model, enabling controllable signal-level ECG generation. We evaluate UniECG through grounded ECG explanation and generation-oriented qualitative analysis, examining its potential to support explanation and case-based learning. UniECG is intended as an educational aid and a research step toward interactive AI-assisted ECG learning, rather than a clinically validated diagnostic system.

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20.
arXiv (CS.AI) 2026-06-19

Improving End-to-End Speech Recognition for Dysarthric Speech through In-Domain Data Augmentation

Authors:
Paban Sapkota↗Hemant Kumar Kathania↗Sudarsana Reddy Kadiri↗Shrikanth Narayanan↗

arXiv:2606.19797v1 Announce Type: cross Abstract: Dysarthric speech recognition is crucial for facilitating effective communication among individuals with dysarthria. However, accurately recognizing dysarthric speech poses significant challenges due to varying severity levels and limited data availability. In this paper, we explore data augmentation techniques for dysarthric automatic speech recognition (ASR) systems by fine-tuning the End-to-End pre-trained Wav2Vec2 model, with a specific focus on severity levels. To address the challenges of data scarcity and the need for extensive data in fine-tuning pre-trained ASR systems for dysarthric speech, we investigate four prominent data augmentation methods: Speaking-Rate Modification (SRM), Pitch Modification (PM), Formant Modification (FM), and vocal tract Length Perturbation (VTLP), tailored to different aspects of dysarthria. The study uses individually fine-tuned Wav2Vec2 models for each severity class as baseline systems. Additionally, we conducted severity-specific fine-tuning of the ASR model using augmented data. Results demonstrate distinct efficacy patterns for each augmentation technique across severity levels. The best WERs were achieved with SRM ($s$=0.8) for low (9.02\%) and medium (38.11\%) severities, and with PM ($\tau$=0.8) for high severity (55.15\%), reflecting relative improvements of 30.02\%, 16.64\%, and 15.47\%, respectively. These results confirm the effectiveness of the augmentation methods in improving dysarthric ASR performance.

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21.
bioRxiv (Bioinfo) 2026-06-12

Generalisable tissue-wide molecular reconstruction from histology

Authors:
Zhang↗Yu↗Bian↗Cao↗Ye↗Han↗Robertson↗Dong↗Mao↗Liu↗Patrick↗Kim↗…

Spatial transcriptomics technologies measure gene expression within intact tissues but remain difficult to scale across large tissue sections and patient cohorts. Consequently, many studies rely on tissue microarrays (TMAs) or sparse spatial profiling designs, where molecular measurements are available for only limited tissue regions and are often generated using heterogeneous gene panels. Existing H&E to spatial gene expression prediction methods remain challenged by sparse molecular measurements, partially overlapping gene panels and tissue-wide reconstruction across heterogeneous spatial datasets. Here, we present GHIST+, a framework for tissue-wide reconstruction of single-cell molecular states from H&E histology. GHIST+ integrates cellular morphology, local tissue context and shared tissue representations to extend sparse molecular measurements into tissue-wide molecular maps across heterogeneous spatial datasets. Across multiple cancer types and GTEx breast tissues, GHIST+ reconstructs biologically meaningful tissue-wide molecular organisation from sparse TMA-derived measurements while preserving spatial tissue structure, cell-type organisation and age-associated tissue states across cancer and non-cancer settings. GHIST+ establishes a scalable framework for transforming sparse spatial profiling experiments into tissue-wide molecular maps, enabling cohort-scale molecular reconstruction from routine histology under heterogeneous spatial transcriptomic settings.

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22.
bioRxiv (Bioinfo) 2026-06-11

Revealing trajectories of multi-modal voxel-level changes in neurodegenerative diseases using latent event mapping

Authors:
Pinnawala↗Hartanto↗Jairamani↗Simpson↗I. J. A↗Wijeratne↗P. A↗

Neurodegenerative diseases are driven by pathological mechanisms that can be indirectly measured in vivo using multi-modal neuroimaging. However, current computational methods that aim to reconstruct trajectories of voxel-level changes in the brain are either not computationally scalable or fully interpretable, limiting their ability to reveal associations between disease progression and underlying mechanisms. Here we introduce Latent Event Mapping (LEMING), a generative unsupervised modelling technique that learns a latent map of disease events along a common pseudo-timeline of events. We apply LEMING to amyloid PET and structural MRI data from the Alzheimer's Disease Neuroimaging Initiative to reveal the first voxel-level trajectories of events in Alzheimer's disease. Notably, we show how LEMING can provide new insights into progression-dependent disease mechanisms. We find that acetylcholine receptor density is significantly positively associated with both late-stage amyloid and atrophy events, suggesting that either these receptors are targeted later in disease progression, or that amyloid does not play an active role. This has strong implications for therapeutics that target acetylcholine receptors, particularly for early-stage intervention strategies.

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

Circuit Tracing in Autoregressive Protein Language Models

Authors:
Darin Tsui↗William Deinzer↗Daniel Saeedi↗Amirali Aghazadeh↗

arXiv:2606.16044v1 Announce Type: new Abstract: Protein language models (pLMs) can generate novel protein sequences with properties beyond those observed in nature, yet the mechanisms underlying protein generation remain poorly understood. Existing mechanistic interpretability methods based on sparse autoencoders and transcoders primarily focus on protein representation learning models and do not capture the computation required for autoregressive generation. Here, we introduce ProGenMech, a mechanistic interpretability framework for generative protein language models that extends cross-layer transcoders (CLTs) to ProGen3, a sparse Mixture-of-Experts model trained for both causal generation and span infilling. Unlike per-layer approaches, CLTs reconstruct each layer using sparse latent variables from all preceding layers, enabling faithful recovery of inter-layer generative computation. We further develop a zero-shot circuit discovery framework to identify sparse latent circuits responsible for protein generation and fitness prediction. In causal generation and zero-shot fitness estimation tasks, ProGenMech outperforms local transcoder baselines in recovering ProGen3's probability distribution and functional scoring behavior, while matching the original model's generative distribution in span infilling tasks. Moreover, the recovered circuits reveal biologically meaningful motifs and functional regions associated with conserved sequence patterns and protein fitness landscapes, establishing a foundation for interpretable and steerable protein generation.

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24.
PLOS Medicine 2026-06-12

Placenta accreta spectrum in the 21st century: Challenging dogma and redefining disorder

Authors:
Eric Jauniaux↗

by Eric Jauniaux, Helena C. Bartels, Yalda Afshar Placenta accreta spectrum (PAS) is a serious pregnancy complication caused by abnormal placental attachment to the uterus. In this Perspective, Eric Jauniaux and colleagues discuss emerging evidence that challenges our long-held pathophysiological understanding of PAS, and argue that a critical reassessment of definition, diagnosis, and management is overdue. In this Perspective, Jonathan Evans and colleagues discuss why restricting access to joint replacement surgery based on BMI alone is not supported by evidence, and highlight how such rest rictions risk exacerbating stigma, inequity and avoidable harm to those who would benefit from surgery.

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25.
Nature Medicine 2026-06-08

Post-adjuvant chemotherapy in ctDNA-positive patients with resected colorectal cancer: a randomized phase 3 trial

Authors:
Hideaki Bando↗

Tumor-informed circulating tumor DNA (ctDNA) enables detection of molecular residual disease (MRD) after curative resection of colorectal cancer (CRC), but whether early intervention improves outcomes remains uncertain. ALTAIR was a randomized, double-blind, phase 3 trial embedded in the CIRCULATE-Japan platform evaluating a post-adjuvant ctDNA surveillance strategy with treatment initiation upon molecular recurrence. Patients with resected stage 0–IV CRC who became ctDNA positive after completion of standard-of-care therapy and had no radiological evidence of disease were randomly assigned (1:1) to receive trifluridine/tipiracil (FTD/TPI) or placebo for 6 months. The primary endpoint was investigator-assessed disease-free survival (DFS). Between July 2020 and June 2023, 243 patients were randomized to FTD/TPI (n = 122) or placebo (n = 121). Median DFS was 9.30 months with FTD/TPI and 5.55 months with placebo (hazard ratio = 0.79, 95% confidence interval: 0.60–1.05, P = 0.107), and the primary endpoint was not met. FTD/TPI increased grade 3 or higher hematologic adverse events (73.0% versus 3.3%) without new safety signals. These findings indicate that post-adjuvant intervention with FTD/TPI did not significantly improve DFS in ctDNA-positive patients without radiological disease. ClinicalTrials.gov identifier: NCT04457297 . In the randomized, double-blind phase 3 ALTAIR trial, patients with resected colorectal cancer who became positive for circulating tumor DNA during post-adjuvant surveillance received trifluridine/tipiracil hydrochloride therapy, which did not significantly prolong disease-free survival compared with placebo.

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