Deep learning-based antimicrobial peptide (AMP) discovery faces critical challenges such as limited controllability, lack of representations that efficiently model antimicrobial properties, and low experimental hit rates. To address these challenges, we introduce OmegAMP, a framework designed for reliable AMP generation with increased controllability. Its diffusion-based generative model leverages a novel conditioning mechanism to achieve fine-grained control over desired physicochemical properties and to direct generation towards specific activity profiles, including species-specific effectiveness. This is further enhanced by a biologically informed encoding space that significantly improves overall generative performance. Complementing these generative capabilities, OmegAMP leverages a novel synthetic data augmentation strategy to train classifiers for AMP filtering, drastically reducing false positive rates and thereby increasing the likelihood of experimental success. Our in silico experiments demonstrate that OmegAMP delivers state-of-the-art performance across key stages of the AMP discovery pipeline, enabling us to achieve an unprecedented success rate in wet lab experiments. We tested 25 candidate peptides, 24 of them (96%) demonstrated antimicrobial activity, proving effective even against multi-drug resistant strains. Our findings underscore OmegAMP's potential to significantly advance computational frameworks in the fight against antimicrobial resistance.

We consider the problem of federated learning (FL) with graph-structured data distributed across multiple clients. In particular, we address the prevalent scenario of interconnected subgraphs, where interconnections between clients significantly influence the learning process. Existing approaches suffer from critical limitations, either requiring the exchange of sensitive node embeddings, thereby posing privacy risks, or relying on computationally-intensive steps, which hinders scalability. To tackle these challenges, we propose FedLap, a novel framework that leverages global structure information via Laplacian smoothing in the spectral domain to effectively capture inter-node dependencies while ensuring privacy and scalability. We provide a formal analysis of the privacy of FedLap, demonstrating that it preserves privacy. Notably, FedLap is the first subgraph FL scheme with strong privacy guarantees. Extensive experiments on benchmark datasets demonstrate that FedLap achieves competitive or superior utility compared to existing techniques.

Positive--Unlabeled (PU) learning considers settings in which only positive and unlabeled data are available, while negatives are missing or left unlabeled. This situation is common in real applications where annotating reliable negatives is difficult or costly. Despite substantial progress in PU learning, the multi-class case (MPU) remains challenging: many existing approaches do not ensure \emph{unbiased risk estimation}, which limits performance and stability. We propose a cost-sensitive multi-class PU method based on \emph{adaptive loss weighting}. Within the empirical risk minimization framework, we assign distinct, data-dependent weights to the positive and \emph{inferred-negative} (from the unlabeled mixture) loss components so that the resulting empirical objective is an unbiased estimator of the target risk. We formalize the MPU data-generating process and establish a generalization error bound for the proposed estimator. Extensive experiments on \textbf{eight} public datasets, spanning varying class priors and numbers of classes, show consistent gains over strong baselines in both accuracy and stability.

Discrete audio representations are gaining traction in speech modeling due to their interpretability and compatibility with large language models, but are not always optimized for noisy or real-world environments. Building on existing works that quantize Whisper embeddings for speech-to-unit modeling, we propose disentangling semantic speech content from background noise in the latent space. Our end-to-end model separates clean speech in the form of codebook tokens, while extracting interpretable noise vectors as quantization residue which are supervised via a lightweight classifier. We show that our approach improves alignment between clean/noisy speech and text, producing speech tokens that display a high degree of noiseinvariance, and improves ASR performance. Keeping Whisper frozen, we show an 82% reduction in error rate compared to Whisper, and 35% improvement over baseline methods on the VBDemand test set. Further analyses show that the learned token space generalizes well to both seen and unseen acoustic conditions.

Graph neural networks (GNNs) excel on relational data by passing messages over node features and structure, but they can amplify training data biases, propagating discriminatory attributes and structural imbalances into unfair outcomes. Many fairness methods treat bias as a single source, ignoring distinct attribute and structure effects and leading to suboptimal fairness and utility trade-offs. To overcome this challenge, we propose FairMIB, a multi-view information bottleneck framework designed to decompose graphs into feature, structural, and diffusion views for mitigating complexity biases in GNNs. Especially, the proposed FairMIB employs contrastive learning to maximize cross-view mutual information for bias-free representation learning. It further integrates multi-perspective conditional information bottleneck objectives to balance task utility and fairness by minimizing mutual information with sensitive attributes. Additionally, FairMIB introduces an inverse probability-weighted (IPW) adjacency correction in the diffusion view, which reduces the spread of bias propagation during message passing. Experiments on five real-world benchmark datasets demonstrate that FairMIB achieves state-of-the-art performance across both utility and fairness metrics. Graph Neural Networks (GNNs) represent a pivotal advancement in machine learning, offering a powerful paradigm for modeling complex relational data Wu et al. (2020b). Through a message-passing mechanism, GNNs iteratively aggregate information from a node and its neighbors, effectively capturing both node attributes and the graph's structural dependencies Mo et al. (2025). This capability to learn from intricate patterns has established GNNs as indispensable tools in various high-stakes domains, such as recommendation systems Amara et al. (2025), drug discovery Wang et al. (2025), and social network analysis Feng & Qian (2025).

Watermarking has been proposed as a lightweight mechanism to identify AI-generated text, with schemes typically relying on perturbations to token distributions. While prior work shows that paraphrasing can weaken such signals, these attacks remain partially detectable or degrade text quality. We demonstrate that cross-lingual summarization attacks (CLSA) -- translation to a pivot language followed by summarization and optional back-translation -- constitute a qualitatively stronger attack vector. By forcing a semantic bottleneck across languages, CLSA systematically destroys token-level statistical biases while preserving semantic fidelity. In experiments across multiple watermarking schemes (KGW, SIR, XSIR, Unigram) and five languages (Amharic, Chinese, Hindi, Spanish, Swahili), we show that CLSA reduces watermark detection accuracy more effectively than monolingual paraphrase at similar quality levels. Our results highlight an underexplored vulnerability that challenges the practicality of watermarking for provenance or regulation. We argue that robust provenance solutions must move beyond distributional watermarking and incorporate cryptographic or model-attestation approaches. On 300 held-out samples per language, CLSA consistently drives detection toward chance while preserving task utility. Concretely, for XSIR (explicitly designed for cross-lingual robustness), AUROC with paraphrasing is $0.827$, with Cross-Lingual Watermark Removal Attacks (CWRA) [He et al., 2024] using Chinese as the pivot, it is $0.823$, whereas CLSA drives it down to $0.53$ (near chance). Results highlight a practical, low-cost removal pathway that crosses languages and compresses content without visible artifacts.

Y et, despite this progress, the point clouds acquired by MLS systems operating in real-world environments inevitably contain uncertainty arising from various error sources during acquisition and processing. Although MLS systems have advanced rapidly in both data collection and post-processing, research on uncertainty evaluation has received comparatively less attention and remains underdeveloped (Xu et al., 2025b). From a user's perspective, the quality of point clouds from MLS systems is a critical concern. As the foundational input for many downstream tasks, inadequate assessment of MLS point clouds' quality can easily impact high-precision applications such as navigation and change analysis. This will not only undermine reliability but also result in substantial waste of time and resources, which is unacceptable in real-world applications. There is a clear need for automated and reliable solutions for uncertainty evaluation. In MLS systems, four main categories of error sources contribute to uncertainty: instrumental errors, atmospheric errors, object-and geometry-related errors, and trajectory estimation errors (Habib et al., 2009, Schenk, 2001). Considering the characteristics of these error sources, existing uncertainty evaluation methods can be broadly divided into two categories: forward modeling and backward modeling (Shi et al., 2021). The core idea of forward modeling is grounded in variance-covariance propagation, which involves detailed theoretical analysis of MLS system errors.

Understanding the evolution of brain functional networks over time is of great significance for the analysis of cognitive mechanisms and the diagnosis of neurological diseases. Existing methods often have difficulty in capturing the temporal evolution characteristics of connections between specific functional communities. To this end, this paper proposes a new path-level trajectory modeling framework (NeuroPathNet) to characterize the dynamic behavior of connection pathways between brain functional partitions. Based on medically supported static partitioning schemes (such as Yeo and Smith ICA), we extract the time series of connection strengths between each pair of functional partitions and model them using a temporal neural network. We validate the model performance on three public functional Magnetic Resonance Imaging (fMRI) datasets, and the results show that it outperforms existing mainstream methods in multiple indicators. This study can promote the development of dynamic graph learning methods for brain network analysis, and provide possible clinical applications for the diagnosis of neurological diseases.

Machine learning techniques offer an effective approach to modeling dynamical systems solely from observed data. However, without explicit structural priors -- built-in assumptions about the underlying dynamics -- these techniques typically struggle to generalize to aspects of the dynamics that are poorly represented in the training data. Here, we demonstrate that reservoir computing -- a simple, efficient, and versatile machine learning framework often used for data-driven modeling of dynamical systems -- can generalize to unexplored regions of state space without explicit structural priors. First, we describe a multiple-trajectory training scheme for reservoir computers that supports training across a collection of disjoint time series, enabling effective use of available training data. Then, applying this training scheme to multistable dynamical systems, we show that RCs trained on trajectories from a single basin of attraction can achieve out-of-domain generalization by capturing system behavior in entirely unobserved basins.

Finite-sum Coupled Compositional Optimization (FCCO), characterized by its coupled compositional objective structure, emerges as an important optimization paradigm for addressing a wide range of machine learning problems. In this paper, we focus on a challenging class of non-convex non-smooth FCCO, where the outer functions are non-smooth weakly convex or convex and the inner functions are smooth or weakly convex. Existing state-of-the-art result face two key limitations: (1) a high iteration complexity of $O(1/ε^6)$ under the assumption that the stochastic inner functions are Lipschitz continuous in expectation; (2) reliance on vanilla SGD-type updates, which are not suitable for deep learning applications. Our main contributions are two fold: (i) We propose stochastic momentum methods tailored for non-smooth FCCO that come with provable convergence guarantees; (ii) We establish a new state-of-the-art iteration complexity of $O(1/ε^5)$. Moreover, we apply our algorithms to multiple inequality constrained non-convex optimization problems involving smooth or weakly convex functional inequality constraints. By optimizing a smoothed hinge penalty based formulation, we achieve a new state-of-the-art complexity of $O(1/ε^5)$ for finding an (nearly) $ε$-level KKT solution. Experiments on three tasks demonstrate the effectiveness of the proposed algorithms.