An Xiao

Bio: An Xiao is an academic researcher from Tsinghua University. The author has contributed to research in topics: Transformer (machine learning model) & Biological network. The author has an hindex of 10, co-authored 21 publications receiving 418 citations. Previous affiliations of An Xiao include Huawei.

NeoDTI: neural integration of neighbor information from a heterogeneous network for discovering new drug-target interactions.

Abstract: Motivation Accurately predicting drug-target interactions (DTIs) in silico can guide the drug discovery process and thus facilitate drug development. Computational approaches for DTI prediction that adopt the systems biology perspective generally exploit the rationale that the properties of drugs and targets can be characterized by their functional roles in biological networks. Results Inspired by recent advance of information passing and aggregation techniques that generalize the convolution neural networks to mine large-scale graph data and greatly improve the performance of many network-related prediction tasks, we develop a new nonlinear end-to-end learning model, called NeoDTI, that integrates diverse information from heterogeneous network data and automatically learns topology-preserving representations of drugs and targets to facilitate DTI prediction. The substantial prediction performance improvement over other state-of-the-art DTI prediction methods as well as several novel predicted DTIs with evidence supports from previous studies have demonstrated the superior predictive power of NeoDTI. In addition, NeoDTI is robust against a wide range of choices of hyperparameters and is ready to integrate more drug and target related information (e.g. compound-protein binding affinity data). All these results suggest that NeoDTI can offer a powerful and robust tool for drug development and drug repositioning. Availability and implementation The source code and data used in NeoDTI are available at: https://github.com/FangpingWan/NeoDTI. Supplementary information Supplementary data are available at Bioinformatics online.

Transformer in Transformer

Abstract: Transformer is a new kind of neural architecture which encodes the input data as powerful features via the attention mechanism. Basically, the visual transformers first divide the input images into several local patches and then calculate both representations and their relationship. Since natural images are of high complexity with abundant detail and color information, the granularity of the patch dividing is not fine enough for excavating features of objects in different scales and locations. In this paper, we point out that the attention inside these local patches are also essential for building visual transformers with high performance and we explore a new architecture, namely, Transformer iN Transformer (TNT). Specifically, we regard the local patches (e.g., 16$\times$16) as "visual sentences" and present to further divide them into smaller patches (e.g., 4$\times$4) as "visual words". The attention of each word will be calculated with other words in the given visual sentence with negligible computational costs. Features of both words and sentences will be aggregated to enhance the representation ability. Experiments on several benchmarks demonstrate the effectiveness of the proposed TNT architecture, e.g., we achieve an $81.5%$ top-1 accuracy on the ImageNet, which is about $1.7%$ higher than that of the state-of-the-art visual transformer with similar computational cost. The PyTorch code is available at this https URL, and the MindSpore code is at this https URL.

Weight-Sharing Neural Architecture Search: A Battle to Shrink the Optimization Gap

Abstract: Neural architecture search (NAS) has attracted increasing attentions in both academia and industry. In the early age, researchers mostly applied individual search methods which sample and evaluate the candidate architectures separately and thus incur heavy computational overheads. To alleviate the burden, weight-sharing methods were proposed in which exponentially many architectures share weights in the same super-network, and the costly training procedure is performed only once. These methods, though being much faster, often suffer the issue of instability. This paper provides a literature review on NAS, in particular the weight-sharing methods, and points out that the major challenge comes from the optimization gap between the super-network and the sub-architectures. From this perspective, we summarize existing approaches into several categories according to their efforts in bridging the gap, and analyze both advantages and disadvantages of these methodologies. Finally, we share our opinions on the future directions of NAS and AutoML. Due to the expertise of the authors, this paper mainly focuses on the application of NAS to computer vision problems and may bias towards the work in our group.

A Survey on Visual Transformer

Abstract: Transformer, first applied to the field of natural language processing, is a type of deep neural network mainly based on the self-attention mechanism. Thanks to its strong representation capabilities, researchers are looking at ways to apply transformer to computer vision tasks. In a variety of visual benchmarks, transformer-based models perform similar to or better than other types of networks such as convolutional and recurrent networks. Given its high performance and no need for human-defined inductive bias, transformer is receiving more and more attention from the computer vision community. In this paper, we review these visual transformer models by categorizing them in different tasks and analyzing their advantages and disadvantages. The main categories we explore include the backbone network, high/mid-level vision, low-level vision, and video processing. We also take a brief look at the self-attention mechanism in computer vision, as it is the base component in transformer. Furthermore, we include efficient transformer methods for pushing transformer into real device-based applications. Toward the end of this paper, we discuss the challenges and provide several further research directions for visual transformers.

Circumventing Outliers of AutoAugment with Knowledge Distillation

Abstract: AutoAugment has been a powerful algorithm that improves the accuracy of many vision tasks, yet it is sensitive to the operator space as well as hyper-parameters, and an improper setting may degenerate network optimization. This paper delves deep into the working mechanism, and reveals that AutoAugment may remove part of discriminative information from the training image and so insisting on the ground-truth label is no longer the best option. To relieve the inaccuracy of supervision, we make use of knowledge distillation that refers to the output of a teacher model to guide network training. Experiments are performed in standard image classification benchmarks, and demonstrate the effectiveness of our approach in suppressing noise of data augmentation and stabilizing training. Upon the cooperation of knowledge distillation and AutoAugment, we claim the new state-of-the-art on ImageNet classification with a top-1 accuracy of \(\mathbf {85.8\%}\).

Swin Transformer: Hierarchical Vision Transformer using Shifted Windows.

Abstract: This paper presents a new vision Transformer, called Swin Transformer, that capably serves as a general-purpose backbone for computer vision. Challenges in adapting Transformer from language to vision arise from differences between the two domains, such as large variations in the scale of visual entities and the high resolution of pixels in images compared to words in text. To address these differences, we propose a hierarchical Transformer whose representation is computed with shifted windows. The shifted windowing scheme brings greater efficiency by limiting self-attention computation to non-overlapping local windows while also allowing for cross-window connection. This hierarchical architecture has the flexibility to model at various scales and has linear computational complexity with respect to image size. These qualities of Swin Transformer make it compatible with a broad range of vision tasks, including image classification (86.4 top-1 accuracy on ImageNet-1K) and dense prediction tasks such as object detection (58.7 box AP and 51.1 mask AP on COCO test-dev) and semantic segmentation (53.5 mIoU on ADE20K val). Its performance surpasses the previous state-of-the-art by a large margin of +2.7 box AP and +2.6 mask AP on COCO, and +3.2 mIoU on ADE20K, demonstrating the potential of Transformer-based models as vision backbones. The code and models will be made publicly available at~\url{this https URL}.

Integrative Genomics Viewer

Abstract: Rapid improvements in sequencing and array-based platforms are resulting in a flood of diverse genome-wide data, including data from exome and whole-genome sequencing, epigenetic surveys, expression profiling of coding and noncoding RNAs, single nucleotide polymorphism (SNP) and copy number profiling, and functional assays. Analysis of these large, diverse data sets holds the promise of a more comprehensive understanding of the genome and its relation to human disease. Experienced and knowledgeable human review is an essential component of this process, complementing computational approaches. This calls for efficient and intuitive visualization tools able to scale to very large data sets and to flexibly integrate multiple data types, including clinical data. However, the sheer volume and scope of data pose a significant challenge to the development of such tools.

Automated Eukaryotic Gene Structure Annotation Using EVidenceModeler and the Program to Assemble Spliced Alignments

Abstract: EVidenceModeler (EVM) is presented as an automated eukaryotic gene structure annotation tool that reports eukaryotic gene structures as a weighted consensus of all available evidence. EVM, when combined with the Program to Assemble Spliced Alignments (PASA), yields a comprehensive, configurable annotation system that predicts protein-coding genes and alternatively spliced isoforms. Our experiments on both rice and human genome sequences demonstrate that EVM produces automated gene structure annotation approaching the quality of manual curation.

Pyramid Vision Transformer: A Versatile Backbone for Dense Prediction without Convolutions

Abstract: Although using convolutional neural networks (CNNs) as backbones achieves great successes in computer vision, this work investigates a simple backbone network useful for many dense prediction tasks without convolutions. Unlike the recently-proposed Transformer model (e.g., ViT) that is specially designed for image classification, we propose Pyramid Vision Transformer~(PVT), which overcomes the difficulties of porting Transformer to various dense prediction tasks. PVT has several merits compared to prior arts. (1) Different from ViT that typically has low-resolution outputs and high computational and memory cost, PVT can be not only trained on dense partitions of the image to achieve high output resolution, which is important for dense predictions but also using a progressive shrinking pyramid to reduce computations of large feature maps. (2) PVT inherits the advantages from both CNN and Transformer, making it a unified backbone in various vision tasks without convolutions by simply replacing CNN backbones. (3) We validate PVT by conducting extensive experiments, showing that it boosts the performance of many downstream tasks, e.g., object detection, semantic, and instance segmentation. For example, with a comparable number of parameters, RetinaNet+PVT achieves 40.4 AP on the COCO dataset, surpassing RetinNet+ResNet50 (36.3 AP) by 4.1 absolute AP. We hope PVT could serve as an alternative and useful backbone for pixel-level predictions and facilitate future researches. Code is available at this https URL.

Sharpness-Aware Minimization for Efficiently Improving Generalization

Abstract: In today's heavily overparameterized models, the value of the training loss provides few guarantees on model generalization ability. Indeed, optimizing only the training loss value, as is commonly done, can easily lead to suboptimal model quality. Motivated by prior work connecting the geometry of the loss landscape and generalization, we introduce a novel, effective procedure for instead simultaneously minimizing loss value and loss sharpness. In particular, our procedure, Sharpness-Aware Minimization (SAM), seeks parameters that lie in neighborhoods having uniformly low loss; this formulation results in a min-max optimization problem on which gradient descent can be performed efficiently. We present empirical results showing that SAM improves model generalization across a variety of benchmark datasets (e.g., CIFAR-10, CIFAR-100, ImageNet, finetuning tasks) and models, yielding novel state-of-the-art performance for several. Additionally, we find that SAM natively provides robustness to label noise on par with that provided by state-of-the-art procedures that specifically target learning with noisy labels. We open source our code at \url{this https URL}.