MOTIVATION: Metagenomic binning methods to reconstruct metagenome-assembled genomes (MAGs) from environmental samples have been widely used in large-scale metagenomic studies. The recently proposed semi-supervised binning method, SemiBin, achieved state-of-the-art binning results in several environments. However, this required annotating contigs, a computationally costly and potentially biased process. RESULTS: We propose SemiBin2, which uses self-supervised learning to learn feature embeddings from the contigs. In simulated and real datasets, we show that self-supervised learning achieves better results than the semi-supervised learning used in SemiBin1 and that SemiBin2 outperforms other state-of-the-art binners. Compared to SemiBin1, SemiBin2 can reconstruct 8.3-21.5% more high-quality bins and requires only 25% of the running time and 11% of peak memory usage in real short-read sequencing samples. To extend SemiBin2 to long-read data, we also propose ensemble-based DBSCAN clustering algorithm, resulting in 13.1-26.3% more high-quality genomes than the second best binner for long-read data. AVAILABILITY AND IMPLEMENTATION: SemiBin2 is available as open source software at https://github.com/BigDataBiology/SemiBin/ and the analysis scripts used in the study can be found at https://github.com/BigDataBiology/SemiBin2_benchmark.

Positive and Unlabeled learning (PU learning) aims to train a binary classifier based on only positive and unlabeled examples, where the unlabeled examples could be either positive or negative. The state-of-the-art algorithms usually cast PU learning as a cost-sensitive learning problem and impose distinct weights to different training examples via a manual or automatic way. However, such weight adjustment or estimation can be inaccurate and thus often lead to unsatisfactory performance. Therefore, this paper regards all unlabeled examples as negative, which means that some of the original positive data are mistakenly labeled as negative. By doing so, we convert PU learning into the risk minimization problem in the presence of false negative label noise, and propose a novel PU learning algorithm termed ?Loss Decomposition and Centroid Estimation? (LDCE). By decomposing the hinge loss function into two parts, we show that only the second part is influenced by label noise, of which the adverse effect can be reduced by estimating the centroid of negative examples. We intensively validate our approach on synthetic dataset, UCI benchmark datasets and real-world datasets, and the experimental results firmly demonstrate the effectiveness of our approach when compared with other state-of-the-art PU learning methodologies.