Fold2Seq: A Joint Sequence(1D)-Fold(3D) Embedding-based Generative Model for Protein Design

Designing novel protein sequences for a desired 3D topological fold is a fundamental yet non-trivial task in protein engineering. Challenges exist due to the complex sequence--fold relationship, as well as the difficulties to capture the diversity of the sequences (therefore structures and functions) within a fold. To overcome these challenges, we propose Fold2Seq, a novel transformer-based generative framework for designing protein sequences conditioned on a specific target fold. To model the complex sequence--structure relationship, Fold2Seq jointly learns a sequence embedding using a transformer and a fold embedding from the density of secondary structural elements in 3D voxels. On test sets with single, high-resolution and complete structure inputs for individual folds, our experiments demonstrate improved or comparable performance of Fold2Seq in terms of speed, coverage, and reliability for sequence design, when compared to existing state-of-the-art methods that include data-driven deep generative models and physics-based RosettaDesign. The unique advantages of fold-based Fold2Seq, in comparison to a structure-based deep model and RosettaDesign, become more evident on three additional real-world challenges originating from low-quality, incomplete, or ambiguous input structures. Source code and data are available at https://github.com/IBM/fold2seq.

Breaking Shortcut: Exploring Fully Convolutional Cycle-Consistency for Video Correspondence Learning

Previous cycle-consistency correspondence learning methods usually leverage image patches for training. In this paper, we present a fully convolutional method, which is simpler and more coherent to the inference process. While directly applying fully convolutional training results in model collapse, we study the underline reason behind this collapse phenomenon, indicating that the absolute positions of pixels provide a shortcut to easily accomplish cycle-consistence, which hinders the learning of meaningful visual representations. To break this absolute position shortcut, we propose to apply different crops for forward and backward frames, and adopt feature warping to establish correspondence between two crops of a same frame. The former technique enforces the corresponding pixels at forward and back tracks to have different absolute positions, and the latter effectively blocks the shortcuts going between forward and back tracks. In three label propagation benchmarks for pose tracking, face landmark tracking and video object segmentation, our method largely improves the results of vanilla fully convolutional cycle-consistency method, achieving very competitive performance compared with the self-supervised state-of-the-art approaches.

Self-Supervised Learning with Swin Transformers

We are witnessing a modeling shift from CNN to Transformers in computer vision. In this work, we present a self-supervised learning approach called MoBY, with Vision Transformers as its backbone architecture. The approach basically has no new inventions, which is combined from MoCo v2 and BYOL and tuned to achieve reasonably high accuracy on ImageNet-1K linear evaluation: 72.8% and 75.0% top-1 accuracy using DeiT-S and Swin-T, respectively, by 300-epoch training. The performance is slightly better than recent works of MoCo v3 and DINO which adopt DeiT as the backbone, but with much lighter tricks. More importantly, the general-purpose Swin Transformer backbone enables us to also evaluate the learnt representations on downstream tasks such as object detection and semantic segmentation, in contrast to a few recent approaches built on ViT/DeiT which only report linear evaluation results on ImageNet-1K due to ViT/DeiT not tamed for these dense prediction tasks. We hope our results can facilitate more comprehensive evaluation of self-supervised learning methods designed for Transformer architectures. Our code and models are available at https://github.com/SwinTransformer/Transformer-SSL, which will be continually enriched.

Group-Free 3D Object Detection via Transformers

Recently, directly detecting 3D objects from 3D point clouds has received increasing attention. To extract object representation from an irregular point cloud, existing methods usually take a point grouping step to assign the points to an object candidate so that a PointNet-like network could be used to derive object features from the grouped points. However, the inaccurate point assignments caused by the hand-crafted grouping scheme decrease the performance of 3D object detection. In this paper, we present a simple yet effective method for directly detecting 3D objects from the 3D point cloud. Instead of grouping local points to each object candidate, our method computes the feature of an object from all the points in the point cloud with the help of an attention mechanism in the Transformers \cite{vaswani2017attention}, where the contribution of each point is automatically learned in the network training. With an improved attention stacking scheme, our method fuses object features in different stages and generates more accurate object detection results. With few bells and whistles, the proposed method achieves state-of-the-art 3D object detection performance on two widely used benchmarks, ScanNet V2 and SUN RGB-D. The code and models are publicly available at \url{https://github.com/zeliu98/Group-Free-3D}

Swin Transformer: Hierarchical Vision Transformer using Shifted Windows

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{https://github.com/microsoft/Swin-Transformer}.

Pseudo-ISP: Learning Pseudo In-camera Signal Processing Pipeline from A Color Image Denoiser

The success of deep denoisers on real-world color photographs usually relies on the modeling of sensor noise and in-camera signal processing (ISP) pipeline. Performance drop will inevitably happen when the sensor and ISP pipeline of test images are different from those for training the deep denoisers (i.e., noise discrepancy). In this paper, we present an unpaired learning scheme to adapt a color image denoiser for handling test images with noise discrepancy. We consider a practical training setting, i.e., a pre-trained denoiser, a set of test noisy images, and an unpaired set of clean images. To begin with, the pre-trained denoiser is used to generate the pseudo clean images for the test images. Pseudo-ISP is then suggested to jointly learn the pseudo ISP pipeline and signal-dependent rawRGB noise model using the pairs of test and pseudo clean images. We further apply the learned pseudo ISP and rawRGB noise model to clean color images to synthesize realistic noisy images for denoiser adaption. Pseudo-ISP is effective in synthesizing realistic noisy sRGB images, and improved denoising performance can be achieved by alternating between Pseudo-ISP training and denoiser adaption. Experiments show that our Pseudo-ISP not only can boost simple Gaussian blurring-based denoiser to achieve competitive performance against CBDNet, but also is effective in improving state-of-the-art deep denoisers, e.g., CBDNet and RIDNet.

ParaSCI: A Large Scientific Paraphrase Dataset for Longer Paraphrase Generation

We propose ParaSCI, the first large-scale paraphrase dataset in the scientific field, including 33,981 paraphrase pairs from ACL (ParaSCI-ACL) and 316,063 pairs from arXiv (ParaSCI-arXiv). Digging into characteristics and common patterns of scientific papers, we construct this dataset though intra-paper and inter-paper methods, such as collecting citations to the same paper or aggregating definitions by scientific terms. To take advantage of sentences paraphrased partially, we put up PDBERT as a general paraphrase discovering method. The major advantages of paraphrases in ParaSCI lie in the prominent length and textual diversity, which is complementary to existing paraphrase datasets. ParaSCI obtains satisfactory results on human evaluation and downstream tasks, especially long paraphrase generation.

Global Context Networks

The Non-Local Network (NLNet) presents a pioneering approach for capturing long-range dependencies within an image, via aggregating query-specific global context to each query position. However, through a rigorous empirical analysis, we have found that the global contexts modeled by the non-local network are almost the same for different query positions. In this paper, we take advantage of this finding to create a simplified network based on a query-independent formulation, which maintains the accuracy of NLNet but with significantly less computation. We further replace the one-layer transformation function of the non-local block by a two-layer bottleneck, which further reduces the parameter number considerably. The resulting network element, called the global context (GC) block, effectively models global context in a lightweight manner, allowing it to be applied at multiple layers of a backbone network to form a global context network (GCNet). Experiments show that GCNet generally outperforms NLNet on major benchmarks for various recognition tasks. The code and network configurations are available at https://github.com/xvjiarui/GCNet.