Mass spectrometry is the dominant technology in the field of proteomics, enabling high-throughput analysis of the protein content of complex biological samples. Due to the complexity of the instrumentation and resulting data, sophisticated computational methods are required for the processing and interpretation of acquired mass spectra. Machine learning has shown great promise to improve the analysis of mass spectrometry data, with numerous purpose-built methods for improving specific steps in the data acquisition and analysis pipeline reaching widespread adoption. Here, we propose unifying various spectrum prediction tasks under a single foundation model for mass spectra. To this end, we pre-train a spectrum encoder using de novo sequencing as a pre-training task. We then show that using these pre-trained spectrum representations improves our performance on the four downstream tasks of spectrum quality prediction, chimericity prediction, phosphorylation prediction, and glycosylation status prediction. Finally, we perform multi-task fine-tuning and find that this approach improves the performance on each task individually. Overall, our work demonstrates that a foundation model for tandem mass spectrometry proteomics trained on de novo sequencing learns generalizable representations of spectra, improves performance on downstream tasks where training data is limited, and can ultimately enhance data acquisition and analysis in proteomics experiments.

Psychiatric disorders affect millions globally, yet their diagnosis faces significant challenges in clinical practice due to subjective assessments and accessibility concerns, leading to potential delays in treatment. To help address this issue, we present Heart2Mind, a human-centered contestable psychiatric disorder diagnosis system using wearable electrocardiogram (ECG) monitors. Our approach leverages cardiac biomarkers, particularly heart rate variability (HRV) and R-R intervals (RRI) time series, as objective indicators of autonomic dysfunction in psychiatric conditions. The system comprises three key components: (1) a Cardiac Monitoring Interface (CMI) for real-time data acquisition from Polar H9/H10 devices; (2) a Multi-Scale Temporal-Frequency Transformer (MSTFT) that processes RRI time series through integrated time-frequency domain analysis; (3) a Contestable Diagnosis Interface (CDI) combining Self-Adversarial Explanations (SAEs) with contestable Large Language Models (LLMs). Our MSTFT achieves 91.7% accuracy on the HRV-ACC dataset using leave-one-out cross-validation, outperforming state-of-the-art methods. SAEs successfully detect inconsistencies in model predictions by comparing attention-based and gradient-based explanations, while LLMs enable clinicians to validate correct predictions and contest erroneous ones. This work demonstrates the feasibility of combining wearable technology with Explainable Artificial Intelligence (XAI) and contestable LLMs to create a transparent, contestable system for psychiatric diagnosis that maintains clinical oversight while leveraging advanced AI capabilities. Our implementation is publicly available at: https://github.com/Analytics-Everywhere-Lab/heart2mind.

Simulation of high-order nonlinear system requires extensive computational resources, especially in modern VLSI backend design where bifurcation-induced instability and chaos-like transient behaviors pose challenges. We present S-Crescendo - a nested transformer weaving framework that synergizes S-domain with neural operators for scalable time-domain prediction in high-order nonlinear networks, alleviating the computational bottlenecks of conventional solvers via Newton-Raphson method. By leveraging the partial-fraction decomposition of an n-th order transfer function into first-order modal terms with repeated poles and residues, our method bypasses the conventional Jacobian matrix-based iterations and efficiently reduces computational complexity from cubic $O(n^3)$ to linear $O(n)$.The proposed architecture seamlessly integrates an S-domain encoder with an attention-based correction operator to simultaneously isolate dominant response and adaptively capture higher-order non-linearities. Validated on order-1 to order-10 networks, our method achieves up to 0.99 test-set ($R^2$) accuracy against HSPICE golden waveforms and accelerates simulation by up to 18(X), providing a scalable, physics-aware framework for high-dimensional nonlinear modeling.

Graph structure learning is a core problem in graph-based machine learning, essential for uncovering latent relationships and ensuring model interpretability. However, most existing approaches are ill-suited for large-scale and dynamically evolving graphs, as they often require complete re-learning of the structure upon the arrival of new nodes and incur substantial computational and memory costs. In this work, we propose GraphFLEx: a unified and scalable framework for Graph Structure Learning in Large and Expanding Graphs. GraphFLEx mitigates the scalability bottlenecks by restricting edge formation to structurally relevant subsets of nodes identified through a combination of clustering and coarsening techniques. This dramatically reduces the search space and enables efficient, incremental graph updates. The framework supports 48 flexible configurations by integrating diverse choices of learning paradigms, coarsening strategies, and clustering methods, making it adaptable to a wide range of graph settings and learning objectives. Extensive experiments across 26 diverse datasets and Graph Neural Network architectures demonstrate that GraphFLEx achieves state-of-the-art performance with significantly improved scalability.

Advanced healthcare predictions offer significant improvements in patient outcomes by leveraging predictive analytics. Existing works primarily utilize various views of Electronic Health Record (EHR) data, such as diagnoses, lab tests, or clinical notes, for model training. These methods typically assume the availability of complete EHR views and that the designed model could fully leverage the potential of each view. However, in practice, random missing views and view laziness present two significant challenges that hinder further improvements in multi-view utilization. To address these challenges, we introduce Diffmv, an innovative diffusion-based generative framework designed to advance the exploitation of multiple views of EHR data. Specifically, to address random missing views, we integrate various views of EHR data into a unified diffusion-denoising framework, enriched with diverse contextual conditions to facilitate progressive alignment and view transformation. To mitigate view laziness, we propose a novel reweighting strategy that assesses the relative advantages of each view, promoting a balanced utilization of various data views within the model. Our proposed strategy achieves superior performance across multiple health prediction tasks derived from three popular datasets, including multi-view and multi-modality scenarios.

Port berthing sites are regions of high interest for monitoring and optimizing port operations. Data sourced from the Automatic Identification System (AIS) can be superimposed on berths enabling their real-time monitoring and revealing long-term utilization patterns. Ultimately, insights from multiple berths can uncover bottlenecks, and lead to the optimization of the underlying supply chain of the port and beyond. However, publicly available documentation of port berths, even when available, is frequently incomplete - e.g. there may be missing berths or inaccuracies such as incorrect boundary boxes - necessitating a more robust, data-driven approach to port berth localization. In this context, we propose an unsupervised spatial modeling method that leverages AIS data clustering and hyperparameter optimization to identify berthing sites. Trained on one month of freely available AIS data and evaluated across ports of varying sizes, our models significantly outperform competing methods, achieving a mean Bhattacharyya distance of 0.85 when comparing Gaussian Mixture Models (GMMs) trained on separate data splits, compared to 13.56 for the best existing method. Qualitative comparison with satellite images and existing berth labels further supports the superiority of our method, revealing more precise berth boundaries and improved spatial resolution across diverse port environments.

Discovering symbolic differential equations from data uncovers fundamental dynamical laws underlying complex systems. However, existing methods often struggle with the vast search space of equations and may produce equations that violate known physical laws. In this work, we address these problems by introducing the concept of \textit{symmetry invariants} in equation discovery. We leverage the fact that differential equations admitting a symmetry group can be expressed in terms of differential invariants of symmetry transformations. Thus, we propose to use these invariants as atomic entities in equation discovery, ensuring the discovered equations satisfy the specified symmetry. Our approach integrates seamlessly with existing equation discovery methods such as sparse regression and genetic programming, improving their accuracy and efficiency. We validate the proposed method through applications to various physical systems, such as fluid and reaction-diffusion, demonstrating its ability to recover parsimonious and interpretable equations that respect the laws of physics.

Keyword spotting (KWS) offers a vital mechanism to identify spoken commands in voice-enabled systems, where user demands often shift, requiring models to learn new keywords continually over time. However, a major problem is catastrophic forgetting, where models lose their ability to recognize earlier keywords. Although several continual learning methods have proven their usefulness for reducing forgetting, most existing approaches depend on storing and revisiting old data to combat catastrophic forgetting. Though effective, these methods face two practical challenges: 1) privacy risks from keeping user data and 2) large memory and time consumption that limit deployment on small devices. To address these issues, we propose an exemplar-free Analytic Continual Learning (AnalyticKWS) method that updates model parameters without revisiting earlier data. Inspired by efficient learning principles, AnalyticKWS computes a closed-form analytical solution for model updates and requires only a single epoch of adaptation for incoming keywords. AnalyticKWS demands fewer computational resources by avoiding gradient-based updates and does not store old data. By eliminating the need for back-propagation during incremental learning, the model remains lightweight and efficient. As a result, AnalyticKWS meets the challenges mentioned earlier and suits resource-limited settings well. Extensive experiments on various datasets and settings show that AnalyticKWS consistently outperforms existing continual learning methods.

Parkinson's disease (PD) poses a growing global health challenge, with Bangladesh experiencing a notable rise in PD-related mortality. Early detection of PD remains particularly challenging in resource-constrained settings, where voice-based analysis has emerged as a promising non-invasive and cost-effective alternative. However, existing studies predominantly focus on English or other major languages; notably, no voice dataset for PD exists for Bengali - posing a significant barrier to culturally inclusive and accessible healthcare solutions. Moreover, most prior studies employed only a narrow set of acoustic features, with limited or no hyperparameter tuning and feature selection strategies, and little attention to model explainability. This restricts the development of a robust and generalizable machine learning model. To address this gap, we present BenSparX, the first Bengali conversational speech dataset for PD detection, along with a robust and explainable machine learning framework tailored for early diagnosis. The proposed framework incorporates diverse acoustic feature categories, systematic feature selection methods, and state-of-the-art machine learning algorithms with extensive hyperparameter optimization. Furthermore, to enhance interpretability and trust in model predictions, the framework incorporates SHAP (SHapley Additive exPlanations) analysis to quantify the contribution of individual acoustic features toward PD detection. Our framework achieves state-of-the-art performance, yielding an accuracy of 95.77%, F1 score of 95.57%, and AUC-ROC of 0.982. We further externally validated our approach by applying the framework to existing PD datasets in other languages, where it consistently outperforms state-of-the-art approaches. To facilitate further research and reproducibility, the dataset has been made publicly available at https://github.com/Riad071/BenSParX.

While gradient-based optimizers that incorporate randomization often showcase superior performance on complex optimization, the theoretical foundations underlying this superiority remain insufficiently understood. A particularly pressing question has emerged: What is the role of randomization in dimension-free nonsmooth nonconvex optimization? To address this gap, we investigate the theoretical and empirical impact of permutation randomization within gradient-based optimization frameworks, using it as a representative case to explore broader implications. From a theoretical perspective, our analyses reveal that permutation randomization disrupts the shrinkage behavior of gradient-based optimizers, facilitating continuous convergence toward the global optimum given a sufficiently large number of iterations. Additionally, we prove that permutation randomization can preserve the convergence rate of the underlying optimizer. On the empirical side, we conduct extensive numerical experiments comparing permutation-randomized optimizer against three baseline methods. These experiments span tasks such as training deep neural networks with stacked architectures and optimizing noisy objective functions. The results not only corroborate our theoretical insights but also highlight the practical benefits of permutation randomization. In summary, this work delivers both rigorous theoretical justification and compelling empirical evidence for the effectiveness of permutation randomization. Our findings and evidence lay a foundation for extending analytics to encompass a wide array of randomization.