• Genomics & Informatics
• /
• v.21 no.3
• /
• pp.40.1-40.11
• /
• 2023

Microbial community profiling using 16S rRNA amplicon sequencing allows for taxonomic characterization of diverse microorganisms. While amplicon sequence variant (ASV) methods are increasingly favored for their fine-grained resolution of sequence variants, they often discard substantial portions of sequencing reads during quality control, particularly in datasets with large number samples. We present a streamlined pipeline that integrates FastP for read trimming, HmmUFOtu for operational taxonomic units (OTU) clustering, Vsearch for chimera checking, and Kraken2 for taxonomic assignment. To assess the pipeline's performance, we reprocessed two published stool datasets of normal Korean populations: one with 890 and the other with 1,462 independent samples. In the first dataset, HmmUFOtu retained 93.2% of over 104 million read pairs after quality trimming, discarding chimeric or unclassifiable reads, while DADA2, a commonly used ASV method, retained only 44.6% of the reads. Nonetheless, both methods yielded qualitatively similar β-diversity plots. For the second dataset, HmmUFOtu retained 89.2% of read pairs, while DADA2 retained a mere 18.4% of the reads. HmmUFOtu, being a closed-reference clustering method, facilitates merging separately processed datasets, with shared OTUs between the two datasets exhibiting a correlation coefficient of 0.92 in total abundance (log scale). While the first two dimensions of the β-diversity plot exhibited a cohesive mixture of the two datasets, the third dimension revealed the presence of a batch effect. Our comparative evaluation of ASV and OTU methods within this streamlined pipeline provides valuable insights into their performance when processing large-scale microbial 16S rRNA amplicon sequencing data. The strengths of HmmUFOtu and its potential for dataset merging are highlighted.

• Journal of the Microelectronics and Packaging Society
• /
• v.12 no.4 s.37
• /
• pp.275-280
• /
• 2005

We propose a new approach to greatly simplify the fabrication of conventional nanoimprint lithography (NIL) by combined nanoimprint and photolithography (CNP). We introduce a hybrid mask mold (HMM) made from UV transparent material with a UV-blocking Cr metal layer placed on top of the mold protrusions. We used a negative tone photo resist (PR) with higher selectivity to substrate the CNP process instead of the UV curable monomer and thermal plastic polymer that has been commonly used in NIL. Self-assembled monolayer (SAM) on HMM plays a reliable role for pattern transfer when the HMM is separated from the transfer layer. Hydrophilic $SiO_2$ thin film was deposited on all parts of the HMM, which improved the formation of SAM. This $SiO_2$ film made a sub-10nm formation without any pattern damage. In the CNP technique with HMM, the 'residual layer' of the PR was chemically removed by the conventional developing process. Thus, it was possible to simplify the process by eliminating the dry etching process, which was essential in the conventional NIL method.

• The Journal of the Acoustical Society of Korea
• /
• v.25 no.5
• /
• pp.213-221
• /
• 2006

Phone segmentation of speech waveform is especially important for concatenative text to speech synthesis which uses segmented corpora for the construction of synthetic units. because the quality of synthesized speech depends critically on the accuracy of the segmentation. In the beginning. the phone segmentation was manually performed. but it brings the huge effort and the large time delay. HMM-based approaches adopted from automatic speech recognition are most widely used for automatic segmentation in speech synthesis, providing a consistent and accurate phone labeling scheme. Even the HMM-based approach has been successful, it may locate a phone boundary at a different position than expected. In this paper. we categorized adjacent phoneme pairs and analyzed the mismatches between hand-labeled transcriptions and HMM-based labels. Then we described the dominant error patterns that must be improved for the speech synthesis. For the experiment. hand labeled standard Korean speech DB from ETRI was used as a reference DB. Time difference larger than 20ms between hand-labeled phoneme boundary and auto-aligned boundary is treated as an automatic segmentation error. Our experimental results from female speaker revealed that plosive-vowel, affricate-vowel and vowel-liquid pairs showed high accuracies, 99%, 99.5% and 99% respectively. But stop-nasal, stop-liquid and nasal-liquid pairs showed very low accuracies, 45%, 50% and 55%. And these from male speaker revealed similar tendency.

• The Journal of the Acoustical Society of Korea
• /
• v.17 no.2E
• /
• pp.26-30
• /
• 1998

In this paper, we compose neural network predictive HMM(NNPHMM) to provide the dynamic feature of the speech pattern for the HMM. The NNPHMM is the hybrid network of neura network and the HMM. The NNPHMM trained to predict the future vector, varies each time. It is used instead of the mean vector in the HMM. In the experiment, we compared the recognition abilities of the one hundred Korean syllables according to the variation of hidden layer, state number and prediction orders of the NNPHMM. The hidden layer of NNPHMM increased from 10 dimensions to 30 dimensions, the state number increased from 4 to 6 and the prediction orders increased from 10 dimensions to 30 dimension, the state number increased from 4 to 6 and the prediction orders increased from the second oder to the fourth order. The NNPHMM in the experiment is composed of multi-layer perceptron with one hidden layer and CMHMM. As a result of the experiment, the case of prediction order is the second, the average recognition rate increased 3.5% when the state number is changed from 4 to 5. The case of prediction order is the third, the recognition rate increased 4.0%, and the case of prediction order is fourth, the recognition rate increased 3.2%. But the recognition rate decreased when the state number is changed from 5 to 6.

• Journal of the Korea Society of Computer and Information
• /
• v.9 no.3
• /
• pp.121-125
• /
• 2004

In the most of recognizing systems of hand-written numbers. extraction of feature shape by using character elements shapes and a method of morphological analysis by using then extraction of feature shapes were usually used. In this paper, however, peculiar chain-code is used, and differential code which gets minimal value by differentiating the chain-code which is generated by the peculiar chain-code is made. We found this differential code is very successful in discriminating hand-written numbers according to the result of applying to most of the hand-written numbers. Testing recognition of hand-written numbers by HMM network. From the results, we can recognize of 96.1 percentage hand-written numbers but can not recognize extremely distorted hand-written numbers.

• Journal of KIISE:Software and Applications
• /
• v.30 no.5_6
• /
• pp.430-443
• /
• 2003

The objective of this paper is to evaluate most useful feature vector space using the angle, velocity and location features from gesture trajectory which extracted hand regions from consecutive input images and track them by connecting their positions. For this purpose, the gesture tracking algorithm using color and motion information is developed. The recognition module is a HMM model to adaptive time various data. The proposed algorithm was applied to a database containing 4,800 alphabetical handwriting gestures of 20 persons who was asked to draw his/her handwriting gestures five times for each of the 48 characters.

• The Journal of the Acoustical Society of Korea
• /
• v.13 no.3
• /
• pp.63-70
• /
• 1994

In this Paper, we propose a new codeword tying algorithm based on a tree structured classfier. The proposed algorithm which can be viewed as a kind of soft decision using statistical properties between codewords and states has an advantage of fast construction, and guarantees a unique optimal solution. Also, it can easily be applied to any speech recognition system based on discrete hidden Markov model (HMM). Experimental results on speaker-independent isolated word recognition show error reduction of $6\%$ for the codebook of size 256 and $9\%$ for 512 size and also HMM parameter reduction of about $20\%$.

• Journal of KIISE:Software and Applications
• /
• v.36 no.9
• /
• pp.683-690
• /
• 2009

One of the major problems that prevent us from building a good recognition system for large-scale on-line Chinese character recognition using HMMs is increasing recognition time. In this paper, we propose a clustering method to solve recognition speed problem and an efficient distance measure between HMMs. From the experiments, we got about twice the recognition speed and 95.37% 10-candidate recognition accuracy, which is only 0.9% decrease, for 20,902 Chinese characters defined in Unicode CJK unified ideographs.

• The Journal of the Acoustical Society of Korea
• /
• v.14 no.1
• /
• pp.81-89
• /
• 1995

In this paper, we report the continuous speech recognition system using the continuous HMM with discrete duration control and the regression coefficients. Also, we do recognition experiment using One Pass DP method(for 25 sentences of robot control commands) with finite state automata context control. In the experiment for 4 connected spoken digits, the recognition rates are $93.8\%$ when the discrete duration control and the regression coefficients are included, and $80.7\%$ when they are not included. In the experiment for 25 sentences of the robot control commands, the recognition rate are $90.9\%$ when FSN is not included and $98.4\%$ when FSN is included.

• Journal of the Korea Society of Computer and Information
• /
• v.19 no.4
• /
• pp.81-90
• /
• 2014

As mobile devices have become widely used and developed, PC based malwares can be moving towards mobile-based units. In particular, mobile Botnet reuses powerful malicious behavior of PC-based Botnet or add new malicious techniques. Different from existing PC-based Botnet detection schemes, mobile Botnet detection schemes are generally host-based. It is because mobile Botnet has various attack vectors and it is difficult to inspect all the attack vector at the same time. In this paper, to overcome limitations of host-based scheme, we compare two network-based schemes which detect mobile Botnet by applying HMM and SVM techniques. Through the verification analysis under real Botnet attacks, we present detection rates and detection properties of two schemes.