Minimalistic Unsupervised Learning with the Sparse Manifold Transform

We describe a minimalistic and interpretable method for unsupervised learning, without resorting to data augmentation, hyperparameter tuning, or other engineering designs, that achieves performance close to the SOTA SSL methods. Our approach leverages the sparse manifold transform, which unifies sparse coding, manifold learning, and slow feature analysis. With a one-layer deterministic sparse manifold transform, one can achieve 99.3% KNN top-1 accuracy on MNIST, 81.1% KNN top-1 accuracy on CIFAR-10 and 53.2% on CIFAR-100. With a simple gray-scale augmentation, the model gets 83.2% KNN top-1 accuracy on CIFAR-10 and 57% on CIFAR-100. These results significantly close the gap between simplistic ``white-box'' methods and the SOTA methods. Additionally, we provide visualization to explain how an unsupervised representation transform is formed. The proposed method is closely connected to latent-embedding self-supervised methods and can be treated as the simplest form of VICReg. Though there remains a small performance gap between our simple constructive model and SOTA methods, the evidence points to this as a promising direction for achieving a principled and white-box approach to unsupervised learning

Knowledge-Rich Approach to Automatic Grammatical Information Acquisition: Enriching Chinese Sketch Engine with a Lexical Grammar

PACLIC 20 / Wuhan, China / 1-3 November, 200

Knowledge-Rich Approach to Automatic Grammatical Information Acquisition: Enriching Chinese Sketch Engine with a Lexical Grammar

PACLIC 20 / Wuhan, China / 1-3 November, 200

Using combination of lifting wavelet and multiclass SVM based on global optimization class strategy for fault pattern identification

This paper presents a new method based on lifting wavelet for obtaining a fast multiclass SVM classification based on global optimization class strategy for fault diagnosis of roller bearing. Decision making was performed in two stages: feature extraction by computing the lifting wavelet coefficients and classification using the multiclass SVM classifiers trained on the extracted features. Experiments demonstrate that in comparison to discrete wavelet transform the lifting wavelet feature extraction can speed up the identification phase as well as achieve higher accuracy of multiclass SVM that is based on global optimization class strategy. Experimental results also reveal that the proposed multiclass SVM of global optimization is better than strategy of one against one and DAGSVM

Noninvasive prenatal diagnosis of 21-Hydroxylase deficiency using target capture sequencing of maternal plasma DNA.

Here, we aimed to validate a noninvasive method using capture sequencing for prenatal diagnosis of congenital adrenal hyperplasia due to 21-Hydroxylase deficiency (21-OHD). Noninvasive prenatal diagnosis (NIPD) of 21-OHD was based on 14 plasma samples collected from 12 families, including four plasma sample collected during the first trimester. Targeted capture sequencing was performed using genomic DNA from the parents and child trios to determine the pathogenic and wild-type alleles associated with the haplotypes. Maternal plasma DNA was also sequenced to determine the fetal inheritance of the allele using hidden Markov model-based haplotype linkage analysis. The effect of fetal DNA fraction and sequencing depth on the accuracy of NIPD was investigated. The lower limit of fetal DNA fraction was 2% and the threshold mean sequence depth was 38, suggesting potential advantage if used in early gestation. The CYP21A2 genotype of the fetus was accurately determined in all the 14 plasma samples as early as day 1 and 8 weeks of gestation. Results suggest the accuracy and feasibility of NIPD of 21-OHD using a small target capture region with a low threshold for fetal DNA fraction and sequence depth. Our method is cost-effective and suggests diagnostic applications in clinical practice

Identification of miRNAs and their target genes in developing soybean seeds by deep sequencing

<p>Abstract</p> <p>Background</p> <p>MicroRNAs (miRNAs) regulate gene expression by mediating gene silencing at transcriptional and post-transcriptional levels in higher plants. miRNAs and related target genes have been widely studied in model plants such as <it>Arabidopsis </it>and rice; however, the number of identified miRNAs in soybean (<it>Glycine max</it>) is limited, and global identification of the related miRNA targets has not been reported in previous research.</p> <p>Results</p> <p>In our study, a small RNA library and a degradome library were constructed from developing soybean seeds for deep sequencing. We identified 26 new miRNAs in soybean by bioinformatic analysis and further confirmed their expression by stem-loop RT-PCR. The miRNA star sequences of 38 known miRNAs and 8 new miRNAs were also discovered, providing additional evidence for the existence of miRNAs. Through degradome sequencing, 145 and 25 genes were identified as targets of annotated miRNAs and new miRNAs, respectively. GO analysis indicated that many of the identified miRNA targets may function in soybean seed development. Additionally, a soybean homolog of Arabidopsis SUPPRESSOR OF GENE SLIENCING 3 (<it>AtSGS3</it>) was detected as a target of the newly identified miRNA Soy_25, suggesting the presence of feedback control of miRNA biogenesis.</p> <p>Conclusions</p> <p>We have identified large numbers of miRNAs and their related target genes through deep sequencing of a small RNA library and a degradome library. Our study provides more information about the regulatory network of miRNAs in soybean and advances our understanding of miRNA functions during seed development.</p