Connected Component Level Research Articles

Effect of de novo transcriptome assembly on transcript quantification

Correct quantification of transcript expression is essential to understand the functional elements in different physiological conditions. For the organisms without the reference transcriptome, de novo transcriptome assembly must be carried out prior to quantification. However, a large number of erroneous contigs produced by the assemblers might result in unreliable estimation. In this regard, this study investigates how assembly quality affects the performance of quantification based on de novo transcriptome assembly. We examined the over-extended and incomplete contigs, and demonstrated that assembly completeness has a strong impact on the estimation of contig abundance. Then we investigated the behavior of the quantifiers with respect to sequence ambiguity which might be originally presented in the transcriptome or accidentally produced by assemblers. The results suggested that the quantifiers often over-estimate the expression of family-collapse contigs and under-estimate the expression of duplicated contigs. For organisms without reference transcriptome, it remains challenging to detect the inaccurate estimation on family-collapse contigs. On the contrary, we observed that the situation of under-estimation on duplicated contigs can be warned through analyzing the read proportion of estimated abundance (RPEA) of contigs in the connected component inferenced by the quantifiers. In addition, we suggest that the estimated quantification results on the connected component level have better accuracy over sequence level quantification. The analytic results conducted in this study provides valuable insights for future development of transcriptome assembly and quantification.

A combined approach for the binarization of handwritten document images

There are many challenges addressed in handwritten document image binarization, such as faint characters, bleed-through and large background ink stains. Usually, binarization methods cannot deal with all the degradation types effectively. Motivated by the low detection rate of faint characters in binarization of handwritten document images, a combination of a global and a local adaptive binarization method at connected component level is proposed that aims in an improved overall performance. Initially, background estimation is applied along with image normalization based on background compensation. Afterwards, global binarization is performed on the normalized image. In the binarized image very small components are discarded and representative characteristics of a document image such as the stroke width and the contrast are computed. Furthermore, local adaptive binarization is performed on the normalized image taking into account the aforementioned characteristics. Finally, the two binarization outputs are combined at connected component level. Our method achieves top performance after extensive testing on the DIBCO (Document Image Binarization Contest) series datasets which include a variety of degraded handwritten document images.