IGPRED-MultiTask: A Deep Learning Model to Predict Protein Secondary Structure, Torsion Angles and Solvent Accessibility

Customized deep learning based Turkish automatic speech recognition system supported by language model

Background

In today's world, numerous applications integral to various facets of daily life include automatic speech recognition methods. Thus, the development of a successful automatic speech recognition system can significantly augment the convenience of people's daily routines. While many automatic speech recognition systems have been established for widely spoken languages like English, there has been insufficient progress in developing such systems for less common languages such as Turkish. Moreover, due to its agglutinative structure, designing a speech recognition system for Turkish presents greater challenges compared to other language groups. Therefore, our study focused on proposing deep learning models for automatic speech recognition in Turkish, complemented by the integration of a language model.

Methods

In our study, deep learning models were formulated by incorporating convolutional neural networks, gated recurrent units, long short-term memories, and transformer layers. The Zemberek library was employed to craft the language model to improve system performance. Furthermore, the Bayesian optimization method was applied to fine-tune the hyper-parameters of the deep learning models. To evaluate the model's performance, standard metrics widely used in automatic speech recognition systems, specifically word error rate and character error rate scores, were employed.

Results

Upon reviewing the experimental results, it becomes evident that when optimal hyper-parameters are applied to models developed with various layers, the scores are as follows: Without the use of a language model, the Turkish Microphone Speech Corpus dataset yields scores of 22.2 -word error rate and 14.05-character error rate, while the Turkish Speech Corpus dataset results in scores of 11.5 -word error rate and 4.15 character error rate. Upon incorporating the language model, notable improvements were observed. Specifically, for the Turkish Microphone Speech Corpus dataset, the word error rate score decreased to 9.85, and the character error rate score lowered to 5.35. Similarly, the word error rate score improved to 8.4, and the character error rate score decreased to 2.7 for the Turkish Speech Corpus dataset. These results demonstrate that our model outperforms the studies found in the existing literature.

Deep learning for protein secondary structure prediction: Pre and post-AlphaFold

This paper aims to provide a comprehensive review of the trends and challenges of deep neural networks for protein secondary structure prediction (PSSP). In recent years, deep neural networks have become the primary method for protein secondary structure prediction. Previous studies showed that deep neural networks had uplifted the accuracy of three-state secondary structure prediction to more than 80%. Favored deep learning methods, such as convolutional neural networks, recurrent neural networks, inception networks, and graph neural networks, have been implemented in protein secondary structure prediction. Methods adapted from natural language processing (NLP) and computer vision are also employed, including attention mechanism, ResNet, and U-shape networks. In the post-AlphaFold era, PSSP studies focus on different objectives, such as enhancing the quality of evolutionary information and exploiting protein language models as the PSSP input. The recent trend to utilize pre-trained language models as input features for secondary structure prediction provides a new direction for PSSP studies. Moreover, the state-of-the-art accuracy achieved by previous PSSP models is still below its theoretical limit. There are still rooms for improvement to be made in the field.