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01.
medRxiv (Medicine) 2026-06-17

A non-invasive liquid biopsy resolves the diagnostic blind spot in chronic kidney disease

Chronic kidney disease is a major global health burden, and its early detection is critical for delaying progression to kidney failure using recently developed targeted therapies. However, current diagnostic screening relies heavily on blood markers that are confounded by muscle mass, and on urine tests that frequently miss structural damage occurring without protein leakage. This creates a critical diagnostic blind spot that hinders timely intervention. Here we show a non-invasive liquid biopsy platform that quantifies a specific protein marker, MUC1, on urinary extracellular vesicles to accurately assess renal parenchymal integrity. By bypassing the systemic metabolic noise of traditional blood tests, our assay provides a remarkably stable, person-specific functional signature. Following extensive validation across diverse cohorts, our longitudinal analysis demonstrated that the discrepancy between this novel urine-based readout and standard blood tests unmasks hidden renal vulnerability, successfully predicting rapid functional decline. By comprehensively evaluating both tubular and glomerular integrity from a single spot urine sample, these findings establish a completely non-invasive, highly scalable prescreening tool that resolves the diagnostic blind spot, enabling broader early detection strategies and ushering in a new era of proactive risk management.

02.
arXiv (quant-ph) 2026-06-25

Finite-Shot Sensitivity for Moment Estimation in Quantum Metrology

arXiv:2606.25920v1 Announce Type: new Abstract: The quantum Cramér-Rao bound can be saturated only asymptotically and does not specify how many measurements are needed for a concrete estimator to approach it. We develop a finite-measurement theory for method-of-moments estimation, where the parameter is inferred from the sample mean of a calibrating observable rather than from the full likelihood. For general quantum statistical models, the expansion is written in terms of the calibration curve and the central moments of the measured observable. Nonlinear calibration curves make the usual moment estimator biased at finite measurement number; we construct a bias-corrected estimator with bias $O(\nu^{-3})$. This gives sensitivity corrections beyond the leading error-propagation term of the chosen moment protocol. We identify a general density-matrix condition under which the full $1/\nu^2$ correction vanishes. In unitary examples, the leading residual correction appears at order $1/\nu^3$, is governed by calibration curvature, and can be reduced or cancelled by higher-rank components of the same measured observable. The resulting thresholds quantify how many measurements are needed before the asymptotic sensitivity of a moment-estimation protocol is operationally visible.

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

Eigen-Spike Emergence and Quadratic Equivalents for Conjugate Kernels on Nonlinearly Separable Data

arXiv:2605.29669v2 Announce Type: replace-cross Abstract: Recent work in random matrix theory (RMT) has developed the notion of deterministic equivalents: typically linear surrogate models that approximate the spectral behavior of large nonlinear random matrices, such as nonlinear feature maps in neural networks (NNs). Such equivalents make theoretical predictions tractable by reducing a complex model to a simpler one with properties that fall under the umbrella of classical RMT tools. However, this leaves open the question of whether this idealized linear equivalence remains meaningful for classification of high-dimensional nonlinearly separable data. Motivated by this, we consider the conjugate kernel (CK), which is the nonlinear feature map of a one-layer feedforward NN, under a canonical nonlinearly separable dataset for the XOR problem; and we use the study of informative outlier eigenvalues in the CK and whether their corresponding eigenvectors asymptotically align with XOR labels as a proxy for nonlinear learnability. We develop a robust quadratic equivalent of the CK matrix that enables a precise analysis of emergent informative spikes, as one modifies various knobs common in ML practice: sample complexity, signal-to-noise ratio (SNR), nonlinear activation choice, and pretrained features. We identify regimes in which these knobs move the CK beyond the linear equivalent and produce BBP-type transitions to label-aligned outlier eigenspaces. Our analysis helps bring deterministic-equivalence tools from RMT to bear on problems of practical relevance in ML.

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

Integrating Multi-Label Classification and Generative AI for Scalable Analysis of User Feedback

arXiv:2601.23018v1 Announce Type: cross Abstract: In highly competitive software markets, user experience (UX) evaluation is crucial for ensuring software quality and fostering long-term product success. Such UX evaluations typically combine quantitative metrics from standardized questionnaires with qualitative feedback collected through open-ended questions. While open-ended feedback offers valuable insights for improvement and helps explain quantitative results, analyzing large volumes of user comments is challenging and time-consuming. In this paper, we present techniques developed during a long-term UX measurement project at a major software company to efficiently process and interpret extensive volumes of user comments. To provide a high-level overview of the collected comments, we employ a supervised machine learning approach that assigns meaningful, pre-defined topic labels to each comment. Additionally, we demonstrate how generative AI (GenAI) can be leveraged to create concise and informative summaries of user feedback, facilitating effective communication of findings to the organization and especially upper management. Finally, we investigate whether the sentiment expressed in user comments can serve as an indicator for overall product satisfaction. Our results show that sentiment analysis alone does not reliably reflect user satisfaction. Instead, product satisfaction needs to be assessed explicitly in surveys to measure the user's perception of the product.

05.
arXiv (CS.AI) 2026-06-15

CSPO: Constraint-Sensitive Policy Optimization for Safe Reinforcement Learning

arXiv:2606.14415v1 Announce Type: new Abstract: Safe reinforcement learning (Safe RL) aims to maximize expected return while satisfying safety constraints, typically modeled as Constrained Markov Decision Processes (CMDPs). While primal-dual methods scale well to deep RL, they often suffer from delayed constraint correction, leading to oscillatory behavior and prolonged safety violations. In this paper, we propose Constraint-Sensitive Policy Optimization (CSPO), a first-order primal-dual method that incorporates local constraint sensitivity into policy updates. CSPO augments the primal objective with a constraint-sensitive correction derived from the shortest signed distance to the safety boundary, enabling smarter recovery steps back to safety, compensating for delayed Lagrange multiplier updates, reducing oscillations near the boundary, and preserving the KKT solutions of the original constrained problem. Experiments on navigation and locomotion benchmarks demonstrate that CSPO achieves faster safety recovery and high reward preservation, resulting in higher constrained returns compared to state-of-the-art primal-dual and penalty-based methods

06.
arXiv (quant-ph) 2026-06-24

Entanglement in the Dicke subspace

arXiv:2602.15800v2 Announce Type: replace Abstract: We provide a complete mathematical theory for the entanglement of mixtures of Dicke states. These quantum states form an important subclass of bosonic states arising in the study of indistinguishable particles. We introduce a tensor-based parametrization where the diagonal entries of these states are encoded as a symmetric tensor, enabling a direct translation between entanglement properties and well-studied convex cones of tensors. Our results bridge multipartite entanglement theory with semialgebraic geometry and the theory of completely positive and copositive tensors. This dictionary maps separability to completely positive tensors, the PPT property to moment tensors, entanglement witnesses to copositive tensors, and decomposable witnesses to sum of squares tensors. Using this framework, we construct explicit PPT entangled states in three or more qutrits, disproving a recent conjecture. We establish that PPT entanglement exists for all multipartite systems with local dimension d >= 3 and n >= 3 parties. We also show that, for mixtures of Dicke states, the PPT condition with respect to the most balanced bipartition implies all other PPT conditions. We further connect bosonic extendibility of mixtures of Dicke states to the duals of known hierarchies for non-negative polynomials, such as the ones by Reznick and Polya. We thus provide semidefinite programming relaxations for separability and entanglement testing in the Dicke subspace.

07.
arXiv (CS.AI) 2026-06-11

Towards Data-free and Training-free Compression for Speech Foundation Models Using Parameter Clustering

arXiv:2606.11836v1 Announce Type: cross Abstract: This paper presents a novel data-free and training-free compression approach for speech foundation models using channelwise clustering via k-means. More fine-grained, mixed sparsity pruning by layer-level varying number of parameter clusters is also explored. Experiments conducted on the LibriSpeech dataset suggest that when operating with pruning sparsity of 50% on HuBERT-large, consistent WER reductions of 27.73%/18.61% absolute (34.37%/21.91% relative) over the magnitude-based pruning were obtained on the test-clean and test-other subsets before fine-tuning and 0.19%/0.79% absolute (3.36%/4.62% relative) after fine-tuning with only 3 epochs. Similar WER reductions of 2.86%/5.02% absolute (59.21%/55.29% relative) were observed against magnitudebased pruning on Whisper-large-v3 at 10% sparsity, all with no significant WER increase relative to the uncompressed baseline.

08.
arXiv (CS.CV) 2026-06-12

ViPER: Vision-based Packing-Aware Encoder for Robust Malware Detection

Visualization-based malware detection maps raw binary bytes to grayscale images and applies learned visual classifiers, providing an evasion-resistant and disassembly-free alternative to conventional analysis pipelines. However, executable packing remains a critical failure mode: packed binaries produce high-entropy images that obscure the structural patterns these models rely on. Because packing is also prevalent in benign software (e.g., for compression or copy protection), packing state alone is not a reliable indicator of maliciousness, and existing approaches do not address this challenge within a unified supervised framework. We present ViPER, a Vision-based Packing-Aware Encoder for Robust malware detection. ViPER builds on a LoRA-adapted ViT-B/14 backbone with a dual-head architecture that jointly learns malware classification and packing detection. A packing-aware gating mechanism conditions malware predictions on the inferred packing state, enabling distinct decision boundaries for packed and unpacked inputs. To address packing label skew during training, we employ frequency-weighted losses with stratified sampling over joint class-packing strata. Evaluated on 200,000 Windows PE byteplot images, ViPER achieves a balanced accuracy of 0.8521, ROC-AUC of 0.9260, and AUPR of 0.9279, outperforming representative state-of-the-art baselines across all primary metrics, while attaining a packing detection AUC of 0.9949.

09.
arXiv (CS.AI) 2026-06-17

Discrete Autoregressive Transformer for Generative Mechanism Synthesis

arXiv:2606.17409v1 Announce Type: cross Abstract: Planar path synthesis requires mechanisms whose coupler curves match a prescribed trajectory; the mapping from curve to linkage is inherently one-to-many across four-, six-, and eight-bar topologies. We address this design problem with simulation-grounded evaluation on a curated corpus of over one million mechanisms, reporting Chamfer distance and dynamic time warping after forward kinematics and geometric alignment. We formulate synthesis as conditional autoregressive sequence modeling: joint coordinates are uniformly quantized to tokens and generated by a decoder-only transformer with a variational-autoencoder (VAE) latent of the target curve and an explicit mechanism-type token. Training combines token cross-entropy with a Gaussian-smoothed bin auxiliary loss that respects ordinal structure among bins. At inference, a bounded latent-noise schedule decodes all mechanism types at each noise level; we retain the top five candidates by geometric error, yielding diverse accurate families without dataset lookup. On held-out tests, aggregate mean Chamfer distance is $0.0132$ and mean dynamic time warping is $0.153$; a latent $k$-nearest-neighbor baseline that conditions on training-set neighbor latents in VAE space achieves matched-topology mean Chamfer distance $0.0071$ and mean dynamic time warping $0.117$ using the same decoder.

10.
arXiv (CS.LG) 2026-06-15

Free Heavy-Tailed Lunch for Muon: A Theoretical Justification of Empirical Success

arXiv:2606.14560v1 Announce Type: cross Abstract: Non-Euclidean optimisation methods with matrix-valued updates, such as Muon and Scion, have recently shown strong empirical performance for training Transformer models, yet their theoretical advantages over Euclidean methods remain poorly understood. We address this gap in the heavy-tailed non-convex regime, where stochastic gradients have bounded $p$-th central moments, $p \in (1,2]$. We show that certain non-Euclidean methods achieve optimal sample complexity under stronger stationarity measures, while Euclidean methods incur additional dimension-dependent costs. As a consequence, for $m \times n$ matrices, Muon finds an $\varepsilon$-stationary point in nuclear norm within $\mathcal{O}\left(\min\{m, n\} \frac{\Delta_1 L}{\varepsilon^2} \left(\frac \sigma \varepsilon \right)^{\frac p {p-1}}\right)$ samples, absorbing heavy-tailed noise without extra dimension dependence, unlike Euclidean methods. We further prove this sample complexity, including its dimension dependence, is optimal for all first-order methods under nuclear-norm stationarity. Experiments on large language models support our theory. Surprisingly, our results suggest that other Schatten geometries beyond the spectral geometry of Muon can perform competitively in certain settings.

12.
arXiv (CS.AI) 2026-06-24

FISHER: A Foundation Model for Multi-Modal Industrial Signal Comprehensive Representation

arXiv:2507.16696v3 Announce Type: replace-cross Abstract: Industrial signal analysis is hindered by severe data heterogeneity, which we characterize as the M5 problem. Existing solutions rely on specialized models that lack robustness and scalability, while large-scale pre-training has rarely been investigated in this area. In this work, we derive a prioritized roadmap for the M5 problem and propose FISHER, a Foundation model for multi-modal Industrial Signal compreHEnsive Representation. To address the foremost multi-sampling-rate problem, FISHER utilizes a novel sub-band modeling approach that treats sampling rate increments as concatenated sub-band information, enabling the adaptive usage of full signal bandwidth without resampling. FISHER is pre-trained by teacher-student self-distillation over external audio and music data. We also establish the RMIS benchmark, comprising 19 datasets across four modalities. In the experiment, FISHER outperforms 24 state-of-the-art series encoders (up to 2B) with much smaller sizes (up to 16x), showcasing groundbreaking diagnostic accuracy and remarkable versatility. We further demonstrate that 1) seamless adaptation to variable sampling rates is the key to generalization 2) audio and music data provide better temporal variability, which is essential for pre-training. Both FISHER and RMIS are open-sourced.

13.
bioRxiv (Bioinfo) 2026-06-19

ContinuumCellAgent: A Framework-Guided Agent for Long-Horizon Scientific Research

AI-scientist systems are beginning to automate parts of scientific research. We present ContinuumCellAgent, an autonomous agent that executes literature review, hypothesis formation, computational experimentation, manuscript drafting, and adversarial peer review as a single unattended run. Existing AI scientist systems remain difficult to diagnose because they lack modularity, systematic prompt grounding, and observability into long-running behavior. ContinuumCellAgent addresses these gaps with a modular supernode architecture for stage-wise backend swapping, protocols grounded in curated research-method checklists that also define reviewer rubrics, and a diagnostics layer that records file-based artifacts, message traces, and state transitions. We evaluate the system on open-domain QA benchmarks and biomedical/longevity case studies, showing that it can produce checkable research artifacts while exposing pipeline dynamics for rigorous AI co-scientist research.

14.
arXiv (quant-ph) 2026-06-24

A Quantum Non-Gaussianity Criterion Based on Photon Correlations $g^{(2)}$ and $g^{(3)}$

arXiv:2511.08488v2 Announce Type: replace Abstract: Quantum non-Gaussian states, which cannot be written as mixtures of Gaussian states, are necessary to achieve a quantum advantage in continuous variable systems. They represent an important benchmark for the realization of an advanced quantum light source, as they cannot be made by simple means such as displacement and squeezing. We introduce an attenuation-resistant sufficient criterion for quantum non-Gaussian states based on the second- and third-order correlation functions, $g^{(2)}$ and $g^{(3)}$. The general non-linear bound for classical mixtures of Gaussian states is $\sqrt{g^{(3)}} + 3 \sqrt{g^{(2)}} \geq 2$. Any mixture of Gaussian states must fulfill this inequality, thus, the violation of it represents a direct confirmation of quantum non-Gaussianity. We experimentally show the non-Gaussianity of the state produced by a quantum dot single-photon source, where we obtain $\sqrt{g^{(3)}} + 3 \sqrt{g^{(2)}} = 0.174 (13)$, which represents a statistical significance of more than $100$ standard deviations.

15.
Nature Biotechnology 2026-06-23

Efficient generation of epitope-targeted antibodies with Germinal

Obtaining antibodies to specific protein targets is a widely important yet experimentally laborious process. Meanwhile, computational methods for antibody design have been limited by low success rates that require resource-intensive screening. Here we introduce Germinal, a broadly enabling generative pipeline that designs antibodies against specific epitopes with nanomolar binding affinities while requiring only low-n experimental testing. Our method co-optimizes antibody structure and sequence by integrating a structure predictor with an antibody-specific protein language model to perform de novo design of functional complementarity-determining regions onto a user-specified structural framework. When tested against four diverse protein targets, Germinal designed functional antibodies across all targets and binder formats, testing only 43–101 designs for each antigen. Validated designs also exhibited robust expression in mammalian cells and high sequence and structural novelty. We provide open-source code and full computational and experimental protocols to facilitate wide adoption. Germinal achieves epitope-targeted, de novo complementarity-determining region design with high experimental success rates.

16.
arXiv (CS.CV) 2026-06-25

KidRisk: Benchmark Dataset for Children Dangerous Action Recognition

Children are naturally energetic, and during their spontaneous activities, they often encounter potentially dangerous situations, especially when lacking parental supervision. Identifying actions that pose risks plays a crucial role in ensuring their safety. This paper build a novel challenging dataset, namely KidRisk, including 2,500 short videos of children's actions and 10,000 images for dangerous action of children. We also introduce a benchmark on our newly constructs dataset and find that traditional deep learning models demonstrated limited effectiveness on these tasks. Therefore, we develop vision-language based baselines with exceptional context understanding of visual information. Our proposed methods achieved an accuracy of 83.53% in classifying children's actions and 96.14% in recognizing children's dangerous actions, significantly outperforming traditional approaches. These results confirm that vision-language models are not only feasible but also highly effective in detecting hazardous actions, contributing positively to safeguarding children's safety.

17.
medRxiv (Medicine) 2026-06-22

AFFORDABILITY OF INTOXICATION FROM CHEAP ETHANOL: EVIDENCE FROM RETAIL ALCOHOL MARKETS IN UGANDA

Background: Alcohol affordability is a determinant of consumption and alcohol-related harm. In many low- and middle-income countries (LMICs), informal production, variable alcohol strength, and non-standard packaging complicate conventional affordability measures, limiting evidence on the economic accessibility of alcohol and the cost of intoxication. Objective: To assess the affordability of intoxication in Uganda by estimating the cost of obtaining ethanol to reach intoxication across alcohol products, packaging types, and retail contexts. Methods: Data were collected on 824 alcoholic beverages from urban, rural, and urban-slum retail markets. Ethanol-standardized pricing (price per gram of alcohol) was calculated, and the cost of consuming 60 g of ethanol was estimated. Multivariate regression identified determinants of ethanol affordability. Results: Affordability varied by product type and packaging. Opaque beers and illicit spirits provided the cheapest pathways to intoxication, with median costs of UGX 1,200-1,500 per 60 g of ethanol. Plastic packaging was associated with lower ethanol costs than glass packaging. Ethanol prices differed across formal and informal markets (p < 0.01), while rural areas and urban informal settlements had 20-25% lower costs than urban areas. Regulatory status alone did not predict affordability. Conclusions: In Ugandas diverse alcohol market, affordability is driven by access to ethanol rather than beverage price alone. Low-cost, high-strength alcohol sold through informal channels enables intoxication at minimal expense, among disadvantaged populations. Implications: Alcohol policies should target ethanol content through minimum unit pricing, alcohol-content-based taxation, and regulation of informal markets and packaging practices to reduce harmful consumption and inequities.

18.
Nature (Science) 2026-06-22

Daily briefing: First-ever ‘nuclear’ clocks put atomic clocks in the shade

Authors:

Two research teams have created a new, long-awaited type of timekeeper. Plus, how backlash has saved an ocean-monitoring network targeted by Trump and how our cultural heritage is put at risk by climate change. Two research teams have created a new, long-awaited type of timekeeper. Plus, how backlash has saved an ocean-monitoring network targeted by Trump and how our cultural heritage is put at risk by climate change.

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

David vs. Goliath in Next Activity Prediction: Argmax vs. LSTM, Transformer, and LLM

arXiv:2606.15868v1 Announce Type: new Abstract: Next activity prediction (NAP) is a cornerstone of predictive process monitoring (PPM), enabling organizations to move from retrospective analysis to proactive process steering. The PPM field has progressed from classical machine learning through deep learning architectures such as LSTMs and Transformers to large language models (LLMs). Despite growing model complexity, no benchmark jointly compares LLMs, Transformers, LSTMs, and simple baselines in a direct sequence modeling setting for NAP. In this paper, we fill this gap with a systematic benchmark. We compare vocabulary-adapted LLMs, Transformers trained from scratch, LLM-distilled Transformers, and LSTMs against a simple counting-based argmax baseline across seven real-life event logs. Our results tell a David vs. Goliath story: pretraining confers no consistent improvement over training from scratch, model size shows little effect on performance, and on most datasets the argmax baseline matches or approaches the performance of billion-parameter LLMs.

20.
arXiv (CS.CV) 2026-06-25

HaineiFRDM: Structure-Preserving Diffusion for Film Restoration under Fast Motion and Diverse Defects

Existing film-restoration methods frequently fail under fast motion, producing limb disappearance and structural distortion due to inaccurate motion modeling. Moreover, high-resolution restoration under spatially-persistent and mixed defects remains insufficiently studied. We propose HaineiFRDM, a Film Restoration Diffusion Model that leverages the content modeling capability of diffusion models for content-aware restoration, removing defects while preserving scene structure.To enable scalable high-resolution restoration, we adopt a patch-wise strategy with position-aware global fusion modules to maintain cross-patch coherence. We further introduce a frequency-based module to enhance texture consistency and a patch-consistent inference framework to alleviate blocking artifacts introduced by patch-based processing.We also construct a film restoration dataset comprising categorized defect templates, professionally restored films, and realistic synthetic degradations.Extensive experiments demonstrate our superior restoration quality with strong structural consistency. Our design also reduces memory requirements, enabling high-resolution restoration on a single 24GB-VRAM GPU.Code and the dataset will be released at https://anonymous.4open.science/r/HaineiFRDM.

21.
arXiv (quant-ph) 2026-06-19

Near-Optimal Learning of Local Lindbladians

arXiv:2606.20535v1 Announce Type: new Abstract: We study the problem of learning local Lindbladians from black-box access to the physical evolution, and the goal is to estimate all Hamiltonian and dissipative coefficients. We give an algorithm built directly from finite-time channel probes, which runs the unknown evolution for short times, estimates the corresponding Pauli transfer matrices from classical shadows, and converts these estimates into Lindbladian coefficients by stable local Fourier inversions. For fixed locality and bounded dissipative site degree, the uses of the dynamical evolution and total evolution time scale as $\widetilde{O}(\Lambda^2/\varepsilon^2)$ and $\widetilde{O}(\Lambda/\varepsilon^2)$ respectively, in the local dynamical strength bound $\Lambda$ and target accuracy $\varepsilon$, with only logarithmic dependence on the number of qubits. The algorithm is non-adaptive, uses no ancillas, and uses only random product states as inputs followed by random Pauli measurements. The method does not require knowing the support of the Lindbladian in advance. We complement the algorithm with matching lower bounds, showing that the learning algorithm is near-optimal both in physical dynamics accesses and in total evolution time. We construct a single-qubit dephasing Lindbladian family that already requires $\Omega(\Lambda^2/\varepsilon^2)$ channel uses and $\Omega(\Lambda/\varepsilon^2)$ total evolution time, even for adaptive algorithms with arbitrary ancillas and measurements. In particular, the lower bounds imply that the Heisenberg-limited scaling achievable for Hamiltonian learning is information-theoretically impossible once dissipative coefficients must be estimated.

22.
arXiv (quant-ph) 2026-06-17

Acceleration-induced spectral blind spots in stimulated atomic transitions

arXiv:2606.17396v1 Announce Type: cross Abstract: Stimulated transitions are among the most fundamental processes in light-matter interaction, underlying resonant absorption and emission in atomic systems. Here we show that uniform acceleration can convert this familiar response into a frequency-selective absence of response. Specifically, when an incident photon has a nonzero momentum component transverse to the acceleration, the stimulated transition probability vanishes at a discrete set of frequencies fixed by the acceleration, the atomic transition frequency, and the photon propagation angle. At these spectral blind spots, both ordinary stimulated absorption and acceleration-induced excitation are simultaneously suppressed, rendering the atom effectively unresponsive to the incident radiation. The effect arises from the nontrivial response of accelerated atoms to quantum vacuum fluctuations and provides a distinctive signature of the Unruh effect through the absence, rather than the enhancement, of stimulated transitions. We further provide an order-of-magnitude estimate showing that an electron-based implementation with spin splitting in combined electric and magnetic fields could access the required parameter regime. These results reveal an unexplored form of acceleration-modified light-matter interaction and identify spectral blind spots as a new manifestation of the Unruh effect.

23.
bioRxiv (Bioinfo) 2026-06-19

FeatureMSEA: Metabolic Feature-based Metabolite Set Enrichment Analysis

Liquid chromatography-mass spectrometry (LC-MS) untargeted metabolomics detects thousands of metabolic features, but converting these chemical signals into metabolite set-level biological knowledge remains challenging. This is because most features lack unambiguous metabolite identities. Conventional metabolite set enrichment analysis (MSEA) generally requires identified metabolites and metabolite-level ranked inputs, leaving much of the untargeted feature space unused. Here, we present FeatureMSEA, a feature rank-based framework for metabolite set enrichment directly from metabolic features with ambiguous annotations. FeatureMSEA integrates multi-evidence feature-to-metabolite annotation, feature rank-based enrichment scoring, permutation-based inference, and iterative leading-edge-guided annotation refinement, with an optional LLM-assisted module for post-enrichment interpretation. In null comparisons of randomly split healthy samples, FeatureMSEA detected no significant metabolite sets, whereas metabolite-set spike-in simulations showed recovery of implanted signals. In a cerebrospinal fluid metabolomics study of Huntington's disease, FeatureMSEA identified dysregulated metabolite sets related to amino acid metabolism, mitochondrial energy metabolism, and neuroactive signaling. MS/MS-based annotation analysis further showed that FeatureMSEA refinement reduced annotation ambiguity and prioritized chemically consistent candidate metabolites. In summary, FeatureMSEA provides a general framework for extracting metabolite set-level biological insights from LC-MS untargeted metabolomics in which confident metabolite identification remains incomplete.

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

Fast and Slow Variational Continual Learning

arXiv:2606.24007v1 Announce Type: cross Abstract: Continual learning remains a major challenge for modern deep networks, partly because commonly used optimizers lack inherent mechanisms for continual adaptation. One such natural mechanism is fast and slow adaptation to balance stability and plasticity. This mechanism has deep roots in neuroscience and biology, but there is no consensus on how to best incorporate it in commonly used optimizers. Here, we show that this can be easily done via the VCL framework, where past posteriors are used as priors in the future. Our key idea is to incorporate slow adaptation via merging of past posteriors to slow down the drift in the knowledge as learning progresses. The merged posterior is then used as the prior in the VCL update to implement the fast-weight updates. These steps can be seamlessly implemented in the IVON optimizer, whose form and costs are nearly identical to that of Adam. We call this new optimizer the Continual IVON (CoVON) optimizer and show that it not only consistently improves over existing VCL optimizers, but also performs better than other weight-regularization strategies across domain-incremental learning, continual pre-training, and fine-tuning of large language models.

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

Skill-MAS: Evolving Meta-Skill for Automatic Multi-Agent Systems

arXiv:2606.18837v1 Announce Type: cross Abstract: Large Language Model (LLM)-based automatic Multi-Agent Systems (MAS) generation has become a crucial frontier for tackling complex tasks. However, existing methods face a dilemma between model capability and experience retention. Inference-time MAS leverages frozen frontier LLMs but repeats identical searches without learning from past experience. Conversely, Training-time MAS internalizes experience via gradient updates but is constrained by the low capability ceiling of smaller models, and is hard to scale to large frontier LLMs. To bridge this gap, we propose Skill-MAS, a novel third path that decouples experience retention from parametric updates by conceptualizing the high-level orchestration capability as an evolvable Meta-Skill. Skill-MAS refines this architectural knowledge through a closed optimization loop: (1) Multi-Trajectory Rollout samples a behavioral distribution for each task under the current Meta-Skill; and (2) Selective Reflection adaptively selects priority tasks and applies hierarchical contrastive analysis to distill systemic experience into generalizable, strategy-level principles. Extensive experiments across four complex benchmarks and four distinct LLMs demonstrate that Skill-MAS not only achieves remarkable performance gains but also maintains a favorable cost-performance trade-off. Further analysis reveals that the evolved Meta-Skills are highly robust and exhibit strong transferability across unseen tasks and different LLMs.