13 papers · ranked by Valyu relevance
Helen L. Smith, Patrick J. Biggs, Nigel P. French, Adam N. H. Smith + 1 more
To date, there remains no satisfactory solution for absent levels in random forest models. Absent levels are levels of a predictor variable encountered during prediction for which no explicit rule exists. Imposing an order on nominal predictors allows absent levels to be integrated and used for prediction. The ordering…
Ivan Croydon Veleslavov, Michael P.H. Stumpf
Single cell transcriptomics has laid bare the heterogeneity of apparently identical cells at the level of gene expression. For many cell-types we now know that there is variability in the abundance of many transcripts, and that average transcript abun-dance or average gene expression can be a unhelpful concept. A range…
Thomas A. Lake, Brit B. Laginhas, Brennen T. Farrell, Ross K. Meentemeyer + 1 more
Accurate and up-to-date catalogs of urban tree populations are crucial for quantifying ecosystem services and enhancing the quality of life in cities. However, identifying and mapping tree species cost-effectively remains a significant challenge. Remote sensing is an active area of research where scientists are…
Björn-Hergen Laabs von Holt, Ana Westenberger, Inke R. König
In life sciences random forests are often used to train predictive models. However, gaining any explanatory insight into the mechanics leading to a specific outcome is rather complex, which impedes the implementation of random forests into clinical practice. By simplifying a complex ensemble of decision trees to a…
Silvana C. S. Cardoso, Douglas S. Domingues, Alexandre R. Paschoal, Carlos N. Fischer + 1 more
Transposable Elements (TEs) are genetic sequences that can relocate within the genome, thus promoting genetic diversity. Classifying TEs in eukaryotes involves a hierarchy formed by classes, subclasses, orders, superfamilies, families, and subfamilies. According to this taxonomy, LTR retrotransposons (LTR-RT)…
Nadia Tahiri
Each gene has its own evolutionary history which can substantially differ from the evolutionary histories of other genes. For example, some individual genes or operons can be affected by specific horizontal gene transfer or hybridization events. Thus, the evolutionary history of each gene should be represented by its…
James G C Ball, Sadiq Jaffer, Anthony Laybros, Colin Prieur + 5 more
To understand how tropical rainforests will adapt to climate change and the extent to which their diversity imparts resilience, precise, taxonomically informed monitoring of individual trees is required. However, the density, diversity and complexity of tropical rainforests present considerable challenges to remote…
Gihad N. Sohsah, Ali Reza Ibrahimzada, Huzeyfe Ayaz, Ali Cakmak
Taxonomy of living organisms gains major importance in making the study of vastly heterogeneous living things easier. In addition, various fields of applied biology (e.g., agriculture) depend on classification of living creatures. Specific fragments of the DNA sequence of a living organism have been defined as DNA…
János Podani, David A. Morrison
This study is an attempt to expand a previous survey by Fisler and Lecointre (FL) for systematizing ideas on the use of the tree metaphor in classification, as expressed by various historically important figures in their writings. FL used a cladistic approach to analyze their data, as employed in biological…
Valentin Rineau, René Zaragüeta, Jérémie Bardin
The three-taxon statement (also called triplet) is the fundamental unit of rooted trees in phylogenetic systematics. Various supertree and phylogenetic methods use three-taxon statements that are minimal rooted statements of degree of kinship relationships. Because of their fundamental role in phylogenetics…
Stephen R. Piccolo, Terry J. Lee, Erica Suh, Kimball Hill
Classification algorithms assign observations to groups based on patterns in data. The machine-learning community have developed myriad classification algorithms, which are employed in diverse life-science research domains. When applying such algorithms, researchers face the challenge of deciding which algorithm(s) to…
Qingxuan Song, Sofia D Merajver, Jun Z. Li
Classification is an everyday instinct as well as a full-fledged scientific discipline. Throughout the history of medicine, disease classification is central to how we develop knowledge, make diagnosis, and assign treatment. Here we discuss the classification of cancer, the process of categorizing cancer subtypes based…
Andrew Francis, Mike Steel
Phylogenetic networks are mathematical representations of evolutionary history that are able to capture both tree-like evolutionary processes (speciations), and non-tree-like “reticulate” processes such as hybridization or horizontal gene transfer. The additional complexity that comes with this capacity, however, makes…