LinearCoFold and LinearCoPartition: Linear-Time Algorithms for Secondary Structure Prediction of Interacting RNA molecules

Many ncRNAs function through RNA-RNA interactions. Fast and reliable RNA structure prediction with consideration of RNA-RNA interaction is useful. Some existing tools are less accurate due to omitting the competing of intermolecular and intramolecular base pairs, or focus more on predicting the binding region rather than predicting the complete secondary structure of two interacting strands. Vienna RNAcofold, which reduces the problem into the classical single sequence folding by concatenating two strands, scales in cubic time against the combined sequence length, and is slow for long sequences. To address these issues, we present LinearCoFold, which predicts the complete minimum free energy structure of two strands in linear runtime, and LinearCoPartition, which calculates the cofolding partition function and base pairing probabilities in linear runtime. LinearCoFold and LinearCoPartition follows the concatenation strategy of RNAcofold, but are orders of magnitude faster than RNAcofold. For example, on a sequence pair with combined length of 26,190 nt, LinearCoFold is 86.8x faster than RNAcofold MFE mode (0.6 minutes vs. 52.1 minutes), and LinearCoPartition is 642.3x faster than RNAcofold partition function mode (1.8 minutes vs. 1156.2 minutes). Different from the local algorithms, LinearCoFold and LinearCoPartition are global cofolding algorithms without restriction on base pair length. Surprisingly, LinearCoFold and LinearCoPartition's predictions have higher PPV and sensitivity of intermolecular base pairs. Furthermore, we apply LinearCoFold to predict the RNA-RNA interaction between SARS-CoV-2 gRNA and human U4 snRNA, which has been experimentally studied, and observe that LinearCoFold's prediction correlates better to the wet lab results

Quantum-Inspired Support Vector Machine

Support vector machine (SVM) is a particularly powerful and flexible supervised learning model that analyzes data for both classification and regression, whose usual algorithm complexity scales polynomially with the dimension of data space and the number of data points. To tackle the big data challenge, a quantum SVM algorithm was proposed, which is claimed to achieve exponential speedup for least squares SVM (LS-SVM). Here, inspired by the quantum SVM algorithm, we present a quantum-inspired classical algorithm for LS-SVM. In our approach, a improved fast sampling technique, namely indirect sampling, is proposed for sampling the kernel matrix and classifying. We first consider the LS-SVM with a linear kernel, and then discuss the generalization of our method to non-linear kernels. Theoretical analysis shows our algorithm can make classification with arbitrary success probability in logarithmic runtime of both the dimension of data space and the number of data points for low rank, low condition number and high dimensional data matrix, matching the runtime of the quantum SVM

A Graph Isomorphism Network with Weighted Multiple Aggregators for Speech Emotion Recognition

Speech emotion recognition (SER) is an essential part of human-computer interaction. In this paper, we propose an SER network based on a Graph Isomorphism Network with Weighted Multiple Aggregators (WMA-GIN), which can effectively handle the problem of information confusion when neighbour nodes' features are aggregated together in GIN structure. Moreover, a Full-Adjacent (FA) layer is adopted for alleviating the over-squashing problem, which is existed in all Graph Neural Network (GNN) structures, including GIN. Furthermore, a multi-phase attention mechanism and multi-loss training strategy are employed to avoid missing the useful emotional information in the stacked WMA-GIN layers. We evaluated the performance of our proposed WMA-GIN on the popular IEMOCAP dataset. The experimental results show that WMA-GIN outperforms other GNN-based methods and is comparable to some advanced non-graph-based methods by achieving 72.48% of weighted accuracy (WA) and 67.72% of unweighted accuracy (UA).Comment: Accepted by Interspeech 202