Few-shot genes selection: subset of PAM50 genes for breast cancer subtypes classification

Abstract Background In recent years, researchers have made significant strides in understanding the heterogeneity of breast cancer and its various subtypes. However, the wealth of genomic and proteomic data available today necessitates efficient frameworks, instruments, and computational tools for meaningful analysis. Despite its success as a prognostic tool, the PAM50 gene signature’s reliance on many genes presents challenges in terms of cost and complexity. Consequently, there is a need for more efficient methods to classify breast cancer subtypes using a reduced gene set accurately. Results This study explores the potential of achieving precise breast cancer subtype categorization using a reduced gene set derived from the PAM50 gene signature. By employing a “Few-Shot Genes Selection” method, we randomly select smaller subsets from PAM50 and evaluate their performance using metrics and a linear model, specifically the Support Vector Machine (SVM) classifier. In addition, we aim to assess whether a more compact gene set can maintain performance while simplifying the classification process. Our findings demonstrate that certain reduced gene subsets can perform comparable or superior to the full PAM50 gene signature. Conclusions The identified gene subsets, with 36 genes, have the potential to contribute to the development of more cost-effective and streamlined diagnostic tools in breast cancer research and clinical settings

Additional file 1 of Few-shot genes selection: subset of PAM50 genes for breast cancer subtypes classification

Additional file 1. Additional Clinical Variables

Recent invasion by a non-native cyprinid (common bream Abramis brama) is followed by major changes in the ecological quality of a shallow lake in southern Europe

We present an example of how an invasion by a non-native cyprinid (common bream, Abramis brama (Pisces: Cyprinidae), hereafter bream) in a natural shallow lake in southern Europe (Lake Montorfano, northern Italy) may have adversely affected the state of the lake’s ecosystem. In less than two decades, bream became the most abundant species and characterized by a stunted population with asymptotic length 33.5 cm, an estimated mean length at first maturity of 19.6 cm, a total mortality rate of 0.64 year−1 and a diet overwhelmingly dominated by microcrustaceans. Following bream establishment, nutrients and phytoplankton biomass rose, the proportion of Cyanobacteria by numbers increased markedly and water transparency decreased. Total zooplankton abundance increased with a marked increase in small cladocerans and copepods, whereas the abundance of large herbivorous cladocerans did not change. The coverage of submerged macrophytes declined, as did the abundance of native pelagic zooplanktivorous fish. The composition of the fish community shifted towards a higher proportion of zoobenthivorous species, such as bream and pumpkinseed (Lepomis gibbosus). Our results indicate that bream affected water quality through bottom-up mechanisms, while top-down effects were comparatively weak. Selective removal of bream and perhaps stocking of native piscivores might improve the ecological status of the lake