Speaker embeddings carry valuable emotion-related information, which makes them a promising resource for enhancing speech emotion recognition (SER), especially with limited labeled data. Traditionally, it has been assumed that emotion information is indirectly embedded within speaker embeddings, leading to their under-utilization. Our study reveals a direct and useful link between emotion and state-of-the-art speaker embeddings in the form of intra-speaker clusters. By conducting a thorough clustering analysis, we demonstrate that emotion information can be readily extracted from speaker embeddings. In order to leverage this information, we introduce a novel contrastive pretraining approach applied to emotion-unlabeled data for speech emotion recognition. The proposed approach involves the sampling of positive and the negative examples based on the intra-speaker clusters of speaker embeddings. The proposed strategy, which leverages extensive emotion-unlabeled data, leads to a significant improvement in SER performance, whether employed as a standalone pretraining task or integrated into a multi-task pretraining setting.

MOTIVATION: RNA threading aims to identify remote homologies for template-based modeling of RNA 3D structure. Existing RNA alignment methods primarily rely on secondary structure alignment. They are often time- and memory-consuming, limiting large-scale applications. In addition, the accuracy is far from satisfactory. RESULTS: Using RNA secondary structure and sequence profile, we developed a novel RNA threading algorithm, named RNAthreader. To enhance the alignment process and minimize memory usage, a novel approach has been introduced to simplify RNA secondary structures into compact diagrams. RNAthreader employs a two-step methodology. Initially, integer programming and dynamic programming are combined to create an initial alignment for the simplified diagram. Subsequently, the final alignment is obtained using dynamic programming, taking into account the initial alignment derived from the previous step. The benchmark test on 80 RNAs illustrates that RNAthreader generates more accurate alignments than other methods, especially for RNAs with pseudoknots. Another benchmark, involving 30 RNAs from the RNA-Puzzles experiments, exhibits that the models constructed using RNAthreader templates have a lower average RMSD than those created by alternative methods. Remarkably, RNAthreader takes less than two hours to complete alignments with ∼5000 RNAs, which is 3-40 times faster than other methods. These compelling results suggest that RNAthreader is a promising algorithm for RNA template detection. AVAILABILITY AND IMPLEMENTATION: https://yanglab.qd.sdu.edu.cn/RNAthreader.

Expressive voice conversion performs identity conversion for emotional speakers by jointly converting speaker identity and emotional style. Due to the hierarchical structure of speech emotion, it is challenging to disentangle the emotional style for different speakers. Inspired by the recent success of speaker disentanglement with variational autoencoder (VAE), we propose an any-to-any expressive voice conversion framework, that is called StyleVC. StyleVC is designed to disentangle linguistic content, speaker identity, pitch, and emotional style information. We study the use of style encoder to model emotional style explicitly. At run-time, StyleVC converts both speaker identity and emotional style for arbitrary speakers. Experiments validate the effectiveness of our proposed framework in both objective and subjective evaluations.

MOTIVATION: Significant progress has been achieved in distance-based protein folding, due to improved prediction of inter-residue distance by deep learning. Many efforts are thus made to improve distance prediction in recent years. However, it remains unknown what is the best way of objectively assessing the accuracy of predicted distance. RESULTS: A total of 19 metrics were proposed to measure the accuracy of predicted distance. These metrics were discussed and compared quantitatively on three benchmark datasets, with distance and structure models predicted by the trRosetta pipeline. The experiments show that a few metrics, such as distance precision, have a high correlation with the model accuracy measure TM-score (Pearson's correlation coefficient >0.7). In addition, the metrics are applied to rank the distance prediction groups in CASP14. The ranking by our metrics coincides largely with the official version. These data suggest that the proposed metrics are effective for measuring distance prediction. We anticipate that this study paves the way for objectively monitoring the progress of inter-residue distance prediction. A web server and a standalone package are provided to implement the proposed metrics. AVAILABILITY AND IMPLEMENTATION: http://yanglab.nankai.edu.cn/APD. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Traditional voice conversion (VC) has been focused on speaker identity conversion for speech with a neutral expression. We note that emotional expression plays an essential role in daily communication, and the emotional style of speech can be speaker-dependent. In this paper, we study a technique to jointly convert the speaker identity and speaker-dependent emotional style, that is called expressive voice conversion. We propose a StarGAN-based framework to learn a many-to-many mapping across different speakers, that takes into account speaker-dependent emotional style without the need for parallel data. To this end, we condition the generator on emotional style encoding derived from a pre-trained speech emotion recognition (SER) model. The experiments validate the effectiveness of our proposed framework in both objective and subjective evaluations. To our best knowledge, this is the first study on expressive voice conversion.

MOTIVATION: Threading is one of the most effective methods for protein structure prediction. In recent years, the increasing accuracy in protein contact map prediction opens a new avenue to improve the performance of threading algorithms. Several preliminary studies suggest that with predicted contacts, the performance of threading algorithms can be improved greatly. There is still much room to explore to make better use of predicted contacts. RESULTS: We have developed a new contact-assisted threading algorithm named CATHER using both conventional sequential profiles and contact map predicted by a deep learning-based algorithm. Benchmark tests on an independent test set and the CASP12 targets demonstrated that CATHER made significant improvement over other methods which only use either sequential profile or predicted contact map. Our method was ranked at the Top 10 among all 39 participated server groups on the 32 free modeling targets in the blind tests of the CASP13 experiment. These data suggest that it is promising to push forward the threading algorithms by using predicted contacts. AVAILABILITY AND IMPLEMENTATION: http://yanglab.nankai.edu.cn/CATHER/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.