The field of proteomics aims to study and understand the complex landscape of proteins present within a biological system.

PROSPECT provides value to proteomics and machine learning researchers by including several high-quality annotations and by being accessible in terms of format and structure for applying machinelearning.

The field of proteomics aims to study and understand the complex landscape of proteins present within a biological system.

White blood cell (WBC) classification plays a vital role in hematology for diagnosing various medical conditions. However, it faces significant challenges due to domain shifts caused by variations in sample sources (e.g., blood or bone marrow) and differing imaging conditions across hospitals. Traditional deep learning models often suffer from catastrophic forgetting in such dynamic environments, while foundation models, though generally robust, experience performance degradation when the distribution of inference data differs from that of the training data. To address these challenges, we propose a generative replay-based Continual Learning (CL) strategy designed to prevent forgetting in foundation models for WBC classification. Our method employs lightweight generators to mimic past data with a synthetic latent representation to enable privacy-preserving replay. To showcase the effectiveness, we carry out extensive experiments with a total of four datasets with different task ordering and four backbone models including ResNet50, RetCCL, CTransPath, and UNI. Experimental results demonstrate that conventional fine-tuning methods degrade performance on previously learned tasks and struggle with domain shifts. In contrast, our continual learning strategy effectively mitigates catastrophic forgetting, preserving model performance across varying domains. This work presents a practical solution for maintaining reliable WBC classification in real-world clinical settings, where data distributions frequently evolve.

Researchers have used the technology to predict the notes that waft off whisky and determine whether a dram was made in the US or Scotland. The work is a step towards automated systems that can predict the complex aroma of whisky from its molecular makeup. Expert panels usually assess woody, smoky, buttery or caramel aromas, which can help to ensure they don't vary substantially between batches of the same product. "The beautiful thing about the AI is that it is very consistent," said Dr Andreas Grasskamp, who led the research at the Fraunhofer Institute for Process Engineering and Packaging in Freising, Germany. "You have this subjectivity still in trained experts. We are not replacing the human nose with this, but we are really supporting it through efficiency and consistency."

Batch effects in omics data obscure true biological signals and constitute a major challenge for privacy-preserving analyses of distributed patient data. Existing batch effect correction methods either require data centralization, which may easily conflict with privacy requirements, or lack support for missing values and automated workflows. To bridge this gap, we developed fedRBE, a federated implementation of limma's removeBatchEffect method. We implemented it as an app for the FeatureCloud platform. Unlike its existing analogs, fedRBE effectively handles data with missing values and offers an automated, user-friendly online user interface ( https://featurecloud.ai/app/fedrbe). Leveraging secure multi-party computation provides enhanced security guarantees over classical federated learning approaches. We evaluated our fedRBE algorithm on simulated and real omics data, achieving performance comparable to the centralized method with negligible differences (no greater than 3.6E-13). By enabling collaborative correction without data sharing, fedRBE facilitates large-scale omics studies where batch effect correction is crucial.

Dependencies among attributes are a common aspect of tabular data. However, whether existing tabular data generation algorithms preserve these dependencies while generating synthetic data is yet to be explored. In addition to the existing notion of functional dependencies, we introduce the notion of logical dependencies among the attributes in this article. Moreover, we provide a measure to quantify logical dependencies among attributes in tabular data. Utilizing this measure, we compare several state-of-the-art synthetic data generation algorithms and test their capability to preserve logical and functional dependencies on several publicly available datasets. We demonstrate that currently available synthetic tabular data generation algorithms do not fully preserve functional dependencies when they generate synthetic datasets. In addition, we also showed that some tabular synthetic data generation models can preserve inter-attribute logical dependencies. Our review and comparison of the state-of-the-art reveal research needs and opportunities to develop task-specific synthetic tabular data generation models. Keywords: Synthetic tabular data, Logical dependencies, Functional dependencies, Generative models 1. Introduction Dependencies among attributes are a common aspect of tabular data. A well-known fact in Database Management Systems is that if one wants to remove redundancies by dividing larger tables into smaller ones (Normalization) [1], one needs tools to identify functional dependencies present among the attributes of the larger table [2]. Preserving functional dependencies in synthetic tabular data is an area that has not been explored. Dependencies exist in both tabular and image data.

Most complex diseases, including cancer and non-malignant diseases like asthma, have distinct molecular subtypes that require distinct clinical approaches. However, existing computational patient stratification methods have been benchmarked almost exclusively on cancer omics data and only perform well when mutually exclusive subtypes can be characterized by many biomarkers. Here, we contribute with a massive evaluation attempt, quantitatively exploring the power of 22 unsupervised patient stratification methods using both, simulated and real transcriptome data. From this experience, we developed UnPaSt (https://apps.cosy.bio/unpast/) optimizing unsupervised patient stratification, working even with only a limited number of subtype-predictive biomarkers. We evaluated all 23 methods on real-world breast cancer and asthma transcriptomics data. Although many methods reliably detected major breast cancer subtypes, only few identified Th2-high asthma, and UnPaSt significantly outperformed its closest competitors in both test datasets. Essentially, we showed that UnPaSt can detect many biologically insightful and reproducible patterns in omic datasets.