Background: Nonnegative matrix factorization (NMF) is a feature extraction method that has the property of intuitive part-based representation of the original features. This uniqu...
Motivation Protein remote homology prediction and fold recognition are central problems in computational biology. Supervised learning algorithms based on support vector machines a...
Background: Profile hidden Markov models (profile-HMMs) are sensitive tools for remote protein homology detection, but the main scoring algorithms, Viterbi or Forward, require con...
Background: The identification and study of proteins from metagenomic datasets can shed light on the roles and interactions of the source organisms in their communities. However, ...
Recent studies in protein sequence analysis have leveraged the power of unlabeled data. For example, the profile and mismatch neighborhood kernels have shown significant improveme...