Improving SDG Classification Precision Using Combinatorial Fusion.

Combinatorial fusion algorithm (CFA) is a machine learning and artificial intelligence (ML/AI) framework for combining multiple scoring systems using the rank-score characteristic (RSC) function and cognitive diversity (CD). When measuring the relevance of a publication or document with respect to the 17 Sustainable Development Goals (SDGs) of the United Nations, a classification scheme is used. However, this classification process is a challenging task due to the overlapping goals and contextual differences of those diverse SDGs. In this paper, we use CFA to combine a topic model classifier (Model A) and a semantic link classifier (Model B) to improve the precision of the classification process. We characterize and analyze each of the individual models using the RSC function and CD between Models A and B. We evaluate the classification results from combining the models using a score combination and a rank combination, when compared to the results obtained from human experts. In summary, we demonstrate that the combination of Models A and B can improve classification precision only if these individual models perform well and are diverse.

SeqEntropy: genome-wide assessment of repeats for short read sequencing.

BACKGROUND: Recent studies on genome assembly from short-read sequencing data reported the limitation of this technology to reconstruct the entire genome even at very high depth coverage. We investigated the limitation from the perspective of information theory to evaluate the effect of repeats on short-read genome assembly using idealized (error-free) reads at different lengths. METHODOLOGY/PRINCIPAL FINDINGS: We define a metric H(k) to be the entropy of sequencing reads at a read length k and use the relative loss of entropy ΔH(k) to measure the impact of repeats for the reconstruction of whole-genome from sequences of length k. In our experiments, we found that entropy loss correlates well with de-novo assembly coverage of a genome, and a score of ΔH(k)>1% indicates a severe loss in genome reconstruction fidelity. The minimal read lengths to achieve ΔH(k)<1% are different for various organisms and are independent of the genome size. For example, in order to meet the threshold of ΔH(k)<1%, a read length of 60 bp is needed for the sequencing of human genome (3.2 10(9) bp) and 320 bp for the sequencing of fruit fly (1.8×10(8) bp). We also calculated the ΔH(k) scores for 2725 prokaryotic chromosomes and plasmids at several read lengths. Our results indicate that the levels of repeats in different genomes are diverse and the entropy of sequencing reads provides a measurement for the repeat structures. CONCLUSIONS/SIGNIFICANCE: The proposed entropy-based measurement, which can be calculated in seconds to minutes in most cases, provides a rapid quantitative evaluation on the limitation of idealized short-read genome sequencing. Moreover, the calculation can be parallelized to scale up to large euakryotic genomes. This approach may be useful to tune the sequencing parameters to achieve better genome assemblies when a closely related genome is already available.