Yi Wu

Yingying Wu, Shusheng Xu, Shing-Tung Yau et al.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused an ongoing pandemic infecting 219 million people as of 10/19/21, with a 3.6% mortality rate. Natural selection can generate favorable mutations with improved fitness advantages; however, the identified coronaviruses may be the tip of the iceberg, and potentially more fatal variants of concern (VOCs) may emerge over time. Understanding the patterns of emerging VOCs and forecasting mutations that may lead to gain of function or immune escape is urgently required. Here we developed PhyloTransformer, a Transformer-based discriminative model that engages a multi-head self-attention mechanism to model genetic mutations that may lead to viral reproductive advantage. In order to identify complex dependencies between the elements of each input sequence, PhyloTransformer utilizes advanced modeling techniques, including a novel Fast Attention Via positive Orthogonal Random features approach (FAVOR+) from Performer, and the Masked Language Model (MLM) from Bidirectional Encoder Representations from Transformers (BERT). PhyloTransformer was trained with 1,765,297 genetic sequences retrieved from the Global Initiative for Sharing All Influenza Data (GISAID) database. Firstly, we compared the prediction accuracy of novel mutations and novel combinations using extensive baseline models; we found that PhyloTransformer outperformed every baseline method with statistical significance. Secondly, we examined predictions of mutations in each nucleotide of the receptor binding motif (RBM), and we found our predictions were precise and accurate. Thirdly, we predicted modifications of N-glycosylation sites to identify mutations associated with altered glycosylation that may be favored during viral evolution. We anticipate that PhyloTransformer may guide proactive vaccine design for effective targeting of future SARS-CoV-2 variants.

Guoqing Zhang, Yuhao Chen, Yang Dai et al.

Recently, video-based person re-identification (re-ID) has drawn increasing attention in compute vision community because of its practical application prospects. Due to the inaccurate person detections and pose changes, pedestrian misalignment significantly increases the difficulty of feature extraction and matching. To address this problem, in this paper, we propose a \textbf{R}eference-\textbf{A}ided \textbf{P}art-\textbf{A}ligned (\textbf{RAPA}) framework to disentangle robust features of different parts. Firstly, in order to obtain better references between different videos, a pose-based reference feature learning module is introduced. Secondly, an effective relation-based part feature disentangling module is explored to align frames within each video. By means of using both modules, the informative parts of pedestrian in videos are well aligned and more discriminative feature representation is generated. Comprehensive experiments on three widely-used benchmarks, i.e. iLIDS-VID, PRID-2011 and MARS datasets verify the effectiveness of the proposed framework. Our code will be made publicly available.

Yi Wang, Yang Yang, Weiguo Zhu et al.

Industrial AI systems are mostly end-to-end machine learning (ML) workflows. A typical recommendation or business intelligence system includes many online micro-services and offline jobs. We describe SQLFlow for developing such workflows efficiently in SQL. SQL enables developers to write short programs focusing on the purpose (what) and ignoring the procedure (how). Previous database systems extended their SQL dialect to support ML. SQLFlow (https://sqlflow.org/sqlflow ) takes another strategy to work as a bridge over various database systems, including MySQL, Apache Hive, and Alibaba MaxCompute, and ML engines like TensorFlow, XGBoost, and scikit-learn. We extended SQL syntax carefully to make the extension working with various SQL dialects. We implement the extension by inventing a collaborative parsing algorithm. SQLFlow is efficient and expressive to a wide variety of ML techniques -- supervised and unsupervised learning; deep networks and tree models; visual model explanation in addition to training and prediction; data processing and feature extraction in addition to ML. SQLFlow compiles a SQL program into a Kubernetes-native workflow for fault-tolerable execution and on-cloud deployment. Current industrial users include Ant Financial, DiDi, and Alibaba Group.