Automated speaker identification (SID) is a crucial step for the personalization of a wide range of speech-enabled services. Typical SID systems use a symmetric enrollment-verification framework with a single model to derive embeddings both offline for voice profiles extracted from enrollment utterances, and online from runtime utterances. Due to the distinct circumstances of enrollment and runtime, such as different computation and latency constraints, several applications would benefit from an asymmetric enrollment-verification framework that uses different models for enrollment and runtime embedding generation. To support this asymmetric SID where each of the two models can be updated independently, we propose using a lightweight neural network to map the embeddings from the two independent models to a shared speaker embedding space. Our results show that this approach significantly outperforms cosine scoring in a shared speaker logit space for models that were trained with a contrastive loss on large datasets with many speaker identities. This proposed Neural Embedding Speaker Space Alignment (NESSA) combined with an asymmetric update of only one of the models delivers at least 60% of the performance gain achieved by updating both models in the standard symmetric SID approach.

We address performance fairness for speaker verification using the adversarial reweighting (ARW) method.ARW is reformulated for speaker verification with metric learning, and shown to improve results across different subgroups of gender and nationality, without requiring annotation of subgroups in the training data.An adversarial network learns a weight for each training sample in the batch so that the main learner is forced to focus on poorly performing instances.Using a min-max optimization algorithm, this method improves overall speaker verification fairness.We present three different ARW formulations: accumulated pairwise similarity, pseudo-labeling, and pairwise weighting, and measure their performance in terms of equal error rate (EER) on the VoxCeleb corpus.Results show that the pairwise weighting method can achieve 1.08% overall EER, 1.25% for male and 0.67% for female speakers, with relative EER reductions of 7.7%, 10.1% and 3.0%, respectively.For nationality subgroups, the proposed algorithm showed 1.04% EER for US speakers, 0.76% for UK speakers, and 1.22% for all others.The absolute EER gap between gender groups was reduced from 0.70% to 0.58%, while the standard deviation over nationality groups decreased from 0.21 to 0.19.

By implicitly recognizing a user based on his/her speech input, speaker identification enables many downstream applications, such as personalized system behavior and expedited shopping checkouts.Based on whether the speech content is constrained or not, both text-dependent (TD) and text-independent (TI) speaker recognition models may be used.We wish to combine the advantages of both types of models through an ensemble system to make more reliable predictions.However, any such combined approach has to be robust to incomplete inputs, i.e., when either TD or TI input is missing.As a solution we propose a fusion of embeddings network (FOEnet) architecture, combining joint learning with neural attention.We compare FOEnet with four competitive baseline methods on a dataset of voice assistant inputs, and show that it achieves higher accuracy than the baseline and score fusion methods, especially in the presence of incomplete inputs.

MOTIVATION: Circular RNA (circRNA) is a novel class of long non-coding RNAs that have been broadly discovered in the eukaryotic transcriptome. The circular structure arises from a non-canonical splicing process, where the donor site backspliced to an upstream acceptor site. These circRNA sequences are conserved across species. More importantly, rising evidence suggests their vital roles in gene regulation and association with diseases. As the fundamental effort toward elucidating their functions and mechanisms, several computational methods have been proposed to predict the circular structure from the primary sequence. Recently, advanced computational methods leverage deep learning to capture the relevant patterns from RNA sequences and model their interactions to facilitate the prediction. However, these methods fail to fully explore positional information of splice junctions and their deep interaction. RESULTS: We present a robust end-to-end framework, Junction Encoder with Deep Interaction (JEDI), for circRNA prediction using only nucleotide sequences. JEDI first leverages the attention mechanism to encode each junction site based on deep bidirectional recurrent neural networks and then presents the novel cross-attention layer to model deep interaction among these sites for backsplicing. Finally, JEDI can not only predict circRNAs but also interpret relationships among splice sites to discover backsplicing hotspots within a gene region. Experiments demonstrate JEDI significantly outperforms state-of-the-art approaches in circRNA prediction on both isoform level and gene level. Moreover, JEDI also shows promising results on zero-shot backsplicing discovery, where none of the existing approaches can achieve. AVAILABILITY AND IMPLEMENTATION: The implementation of our framework is available at https://github.com/hallogameboy/JEDI. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Information networks, such as social and citation networks, are ubiquitous in the real world so that network analysis plays an important role in data mining and knowledge discovery. To alleviate the sparsity problem of network analysis, it is common to capture the network semantics by projecting nodes onto a vector space as network embeddings. Moreover, random walks are usually exploited to efficiently learn node embeddings and preserve network proximity. In addition to proximity structure, heterogeneous networks have more knowledge about the types of nodes. However, to profit from heterogeneous knowledge, most of the existing approaches guide the random walks through predefined meta-paths or specific strategies, which can distort the understanding of network structures. Furthermore, traditional random walk-based approaches much favor the nodes with higher degrees while other nodes are equivalently important for the downstream applications. In this paper, we propose Meta-context Aware Random Walks (MARU) to overcome these challenges, thereby learning richer and more unbiased representations for heterogeneous networks. To reduce the bias in classical random walks, the algorithm of bidirectional extended random walks is introduced to improve the fairness of representation learning. Based on the enhanced random walks, the meta-context aware skip-gram model is then presented to learn robust network embeddings with dynamic meta-contexts. Therefore, MARU can not only fairly understand the overall network structures but also leverage the sophisticated heterogeneous knowledge in the networks. Extensive experiments have been conducted on three real-world large-scale publicly available datasets. The experimental results demonstrate that MARU significantly outperforms state-of-the-art heterogeneous network embedding methods across three general machine learning tasks, including multi-label node classification, node clustering, and link prediction.

Identifying and recommending potential new customers for local businesses are crucial to the survival and success of local businesses. A key component to identifying the right customers is to understand the decision-making process of choosing a business over the others. However, modeling this process is an extremely challenging task as a decision is influenced by multiple factors. These factors include but are not limited to an individual's taste or preference, the location accessibility of a business, and the reputation of a business from social media. Most of the recommender systems lack the power to integrate multiple factors together and are hardly extensible to accommodate new incoming factors. In this paper, we introduce a unified framework, CORALS, which considers the personal preferences of different customers, the geographical influence, and the reputation of local businesses in the customer recommendation task. To evaluate the proposed model, we conduct a series of experiments to extensively compare with 12 state-of-the-art methods using two real-world datasets. The results demonstrate that CORALS outperforms all these baselines by a significant margin in most scenarios. In addition to identifying potential new customers, we also break down the analysis for different types of businesses to evaluate the impact of various factors that may affect customers' decisions. This information, in return, provides a great resource for local businesses to adjust their advertising strategies and business services to attract more prospective customers.

MOTIVATION: Sequence-based protein-protein interaction (PPI) prediction represents a fundamental computational biology problem. To address this problem, extensive research efforts have been made to extract predefined features from the sequences. Based on these features, statistical algorithms are learned to classify the PPIs. However, such explicit features are usually costly to extract, and typically have limited coverage on the PPI information. RESULTS: We present an end-to-end framework, PIPR (Protein-Protein Interaction Prediction Based on Siamese Residual RCNN), for PPI predictions using only the protein sequences. PIPR incorporates a deep residual recurrent convolutional neural network in the Siamese architecture, which leverages both robust local features and contextualized information, which are significant for capturing the mutual influence of proteins sequences. PIPR relieves the data pre-processing efforts that are required by other systems, and generalizes well to different application scenarios. Experimental evaluations show that PIPR outperforms various state-of-the-art systems on the binary PPI prediction problem. Moreover, it shows a promising performance on more challenging problems of interaction type prediction and binding affinity estimation, where existing approaches fall short. AVAILABILITY AND IMPLEMENTATION: The implementation is available at https://github.com/muhaochen/seq_ppi.git. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Omics phenotyping has become increasingly recognizedin our path to Precision Medicine. A major computationalchallenge of our investigator community is to identify the necessarydata analytical tools to process multi-omics data. To aidnavigation of the analytical tools fragmented across the web, wehave created a novel computational resource platform, AZTEC,that empowers users to simultaneously search a diverse arrayof digital resources including databases, standalone software,web services, publications, and large libraries composed ofmany interrelated functions. AZTEC fosters an environment ofsustainable resource support and discovery, enabling researchersto overcome the challenges of information science. An online videoof the demonstration can be viewed at https://www.youtube.com/watch?v=FIxvlof6Kbg.

RNA-Sequencing has been the leading technology to quantify expression of thousands of genes simultaneously. The data analysis of an RNA-Seq experiment starts from aligning short reads to the reference genome/transcriptome or reconstructed transcriptome. However, current aligners lack the sensitivity to distinguish reads that come from homologous regions of an genome. One group of these homologies is the paralog pseudogenes. Pseudogenes arise from duplication of a set of protein coding genes, and have been considered as degraded paralogs in the genome due to their lost of functionality. Recent studies have provided evidence to support their novel regulatory roles in biological processes. With the growing interests in quantifying the expression level of pseudogenes at different tissues or cell lines, it is critical to have a sensitive method that can correctly align ambiguous reads and accurately estimate the expression level among homologous genes. Previously in PseudoLasso, we proposed a linear regression approach to learn read alignment behaviors, and to leverage this knowledge for abundance estimation and alignment correction. In this paper, we extend the work of PseudoLasso by grouping the homologous genomic regions into different communities using a community detection algorithm, followed by building a linear regression model separately for each community. The results show that this approach is able to retain the same accuracy as PseudoLasso. By breaking the genome into smaller homologous communities, the running time is improved from quadratic growth to linear with respect to the number of genes.