Floating Anchor Diffusion Model for Multi-motif Scaffolding

Motif scaffolding seeks to design scaffold structures for constructing proteins with functions derived from the desired motif, which is crucial for the design of vaccines and enzymes. Previous works approach the problem by inpainting or conditional generation. Both of them can only scaffold motifs with fixed positions, and the conditional generation cannot guarantee the presence of motifs. However, prior knowledge of the relative motif positions in a protein is not readily available, and constructing a protein with multiple functions in one protein is more general and significant because of the synergies between functions. We propose a Floating Anchor Diffusion (FADiff) model. FADiff allows motifs to float rigidly and independently in the process of diffusion, which guarantees the presence of motifs and automates the motif position design. Our experiments demonstrate the efficacy of FADiff with high success rates and designable novel scaffolds. To the best of our knowledge, FADiff is the first work to tackle the challenge of scaffolding multiple motifs without relying on the expertise of relative motif positions in the protein. Code is available at https://github.com/aim-uofa/FADiff.

De novo protein design using geometric vector field networks

Innovations like protein diffusion have enabled significant progress in de novo protein design, which is a vital topic in life science. These methods typically depend on protein structure encoders to model residue backbone frames, where atoms do not exist. Most prior encoders rely on atom-wise features, such as angles and distances between atoms, which are not available in this context. Thus far, only several simple encoders, such as IPA, have been proposed for this scenario, exposing the frame modeling as a bottleneck. In this work, we proffer the Vector Field Network (VFN), which enables network layers to perform learnable vector computations between coordinates of frame-anchored virtual atoms, thus achieving a higher capability for modeling frames. The vector computation operates in a manner similar to a linear layer, with each input channel receiving 3D virtual atom coordinates instead of scalar values. The multiple feature vectors output by the vector computation are then used to update the residue representations and virtual atom coordinates via attention aggregation. Remarkably, VFN also excels in modeling both frames and atoms, as the real atoms can be treated as the virtual atoms for modeling, positioning VFN as a potential universal encoder. In protein diffusion (frame modeling), VFN exhibits an impressive performance advantage over IPA, excelling in terms of both designability (67.04% vs. 53.58%) and diversity (66.54% vs. 51.98%). In inverse folding (frame and atom modeling), VFN outperforms the previous SoTA model, PiFold (54.7% vs. 51.66%), on sequence recovery rate. We also propose a method of equipping VFN with the ESM model, which significantly surpasses the previous ESM-based SoTA (62.67% vs. 55.65%), LM-Design, by a substantial margin.

Stecformer: Spatio-temporal Encoding Cascaded Transformer for Multivariate Long-term Time Series Forecasting

Multivariate long-term time series forecasting is of great application across many domains, such as energy consumption and weather forecasting. With the development of transformer-based methods, the performance of multivariate long-term time series forecasting has been significantly improved, however, the study of spatial features extracting in transformer-based model is rare and the consistency of different prediction periods is unsatisfactory due to the large span. In this work, we propose a complete solution to address these problems in terms of feature extraction and target prediction. For extraction, we design an efficient spatio-temporal encoding extractor including a semi-adaptive graph to acquire sufficient spatio-temporal information. For prediction, we propose a Cascaded Decoding Predictor (CDP) to strengthen the correlation between different intervals, which can also be utilized as a generic component to improve the performance of transformer-based methods. The proposed method, termed as Spatio-temporal Encoding Cascaded Transformer (Stecformer), achieving a notable gap over the baseline model and is comparable with the state-of-the-art performance of transformer-based methods on five benchmark datasets. We hope our attempt will serve as a regular configuration in multivariate long-term time series forecasting in the future.

Towards the Universal Defense for Query-Based Audio Adversarial Attacks

Recently, studies show that deep learning-based automatic speech recognition (ASR) systems are vulnerable to adversarial examples (AEs), which add a small amount of noise to the original audio examples. These AE attacks pose new challenges to deep learning security and have raised significant concerns about deploying ASR systems and devices. The existing defense methods are either limited in application or only defend on results, but not on process. In this work, we propose a novel method to infer the adversary intent and discover audio adversarial examples based on the AEs generation process. The insight of this method is based on the observation: many existing audio AE attacks utilize query-based methods, which means the adversary must send continuous and similar queries to target ASR models during the audio AE generation process. Inspired by this observation, We propose a memory mechanism by adopting audio fingerprint technology to analyze the similarity of the current query with a certain length of memory query. Thus, we can identify when a sequence of queries appears to be suspectable to generate audio AEs. Through extensive evaluation on four state-of-the-art audio AE attacks, we demonstrate that on average our defense identify the adversary intent with over 90% accuracy. With careful regard for robustness evaluations, we also analyze our proposed defense and its strength to withstand two adaptive attacks. Finally, our scheme is available out-of-the-box and directly compatible with any ensemble of ASR defense models to uncover audio AE attacks effectively without model retraining.

Towards the Transferable Audio Adversarial Attack via Ensemble Methods

In recent years, deep learning (DL) models have achieved significant progress in many domains, such as autonomous driving, facial recognition, and speech recognition. However, the vulnerability of deep learning models to adversarial attacks has raised serious concerns in the community because of their insufficient robustness and generalization. Also, transferable attacks have become a prominent method for black-box attacks. In this work, we explore the potential factors that impact adversarial examples (AEs) transferability in DL-based speech recognition. We also discuss the vulnerability of different DL systems and the irregular nature of decision boundaries. Our results show a remarkable difference in the transferability of AEs between speech and images, with the data relevance being low in images but opposite in speech recognition. Motivated by dropout-based ensemble approaches, we propose random gradient ensembles and dynamic gradient-weighted ensembles, and we evaluate the impact of ensembles on the transferability of AEs. The results show that the AEs created by both approaches are valid for transfer to the black box API.

Robust Table Structure Recognition with Dynamic Queries Enhanced Detection Transformer

We present a new table structure recognition (TSR) approach, called TSRFormer, to robustly recognizing the structures of complex tables with geometrical distortions from various table images. Unlike previous methods, we formulate table separation line prediction as a line regression problem instead of an image segmentation problem and propose a new two-stage dynamic queries enhanced DETR based separation line regression approach, named DQ-DETR, to predict separation lines from table images directly. Compared to Vallina DETR, we propose three improvements in DQ-DETR to make the two-stage DETR framework work efficiently and effectively for the separation line prediction task: 1) A new query design, named Dynamic Query, to decouple single line query into separable point queries which could intuitively improve the localization accuracy for regression tasks; 2) A dynamic queries based progressive line regression approach to progressively regressing points on the line which further enhances localization accuracy for distorted tables; 3) A prior-enhanced matching strategy to solve the slow convergence issue of DETR. After separation line prediction, a simple relation network based cell merging module is used to recover spanning cells. With these new techniques, our TSRFormer achieves state-of-the-art performance on several benchmark datasets, including SciTSR, PubTabNet, WTW and FinTabNet. Furthermore, we have validated the robustness and high localization accuracy of our approach to tables with complex structures, borderless cells, large blank spaces, empty or spanning cells as well as distorted or even curved shapes on a more challenging real-world in-house dataset.

Mixline: A Hybrid Reinforcement Learning Framework for Long-horizon Bimanual Coffee Stirring Task

Bimanual activities like coffee stirring, which require coordination of dual arms, are common in daily life and intractable to learn by robots. Adopting reinforcement learning to learn these tasks is a promising topic since it enables the robot to explore how dual arms coordinate together to accomplish the same task. However, this field has two main challenges: coordination mechanism and long-horizon task decomposition. Therefore, we propose the Mixline method to learn sub-tasks separately via the online algorithm and then compose them together based on the generated data through the offline algorithm. We constructed a learning environment based on the GPU-accelerated Isaac Gym. In our work, the bimanual robot successfully learned to grasp, hold and lift the spoon and cup, insert them together and stir the coffee. The proposed method has the potential to be extended to other long-horizon bimanual tasks.

TSRFormer: Table Structure Recognition with Transformers

We present a new table structure recognition (TSR) approach, called TSRFormer, to robustly recognizing the structures of complex tables with geometrical distortions from various table images. Unlike previous methods, we formulate table separation line prediction as a line regression problem instead of an image segmentation problem and propose a new two-stage DETR based separator prediction approach, dubbed \textbf{Sep}arator \textbf{RE}gression \textbf{TR}ansformer (SepRETR), to predict separation lines from table images directly. To make the two-stage DETR framework work efficiently and effectively for the separation line prediction task, we propose two improvements: 1) A prior-enhanced matching strategy to solve the slow convergence issue of DETR; 2) A new cross attention module to sample features from a high-resolution convolutional feature map directly so that high localization accuracy is achieved with low computational cost. After separation line prediction, a simple relation network based cell merging module is used to recover spanning cells. With these new techniques, our TSRFormer achieves state-of-the-art performance on several benchmark datasets, including SciTSR, PubTabNet and WTW. Furthermore, we have validated the robustness of our approach to tables with complex structures, borderless cells, large blank spaces, empty or spanning cells as well as distorted or even curved shapes on a more challenging real-world in-house dataset.

Real-time Localized Photorealistic Video Style Transfer

We present a novel algorithm for transferring artistic styles of semantically meaningful local regions of an image onto local regions of a target video while preserving its photorealism. Local regions may be selected either fully automatically from an image, through using video segmentation algorithms, or from casual user guidance such as scribbles. Our method, based on a deep neural network architecture inspired by recent work in photorealistic style transfer, is real-time and works on arbitrary inputs without runtime optimization once trained on a diverse dataset of artistic styles. By augmenting our video dataset with noisy semantic labels and jointly optimizing over style, content, mask, and temporal losses, our method can cope with a variety of imperfections in the input and produce temporally coherent videos without visual artifacts. We demonstrate our method on a variety of style images and target videos, including the ability to transfer different styles onto multiple objects simultaneously, and smoothly transition between styles in time.

Joint Bilateral Learning for Real-time Universal Photorealistic Style Transfer

Photorealistic style transfer is the task of transferring the artistic style of an image onto a content target, producing a result that is plausibly taken with a camera. Recent approaches, based on deep neural networks, produce impressive results but are either too slow to run at practical resolutions, or still contain objectionable artifacts. We propose a new end-to-end model for photorealistic style transfer that is both fast and inherently generates photorealistic results. The core of our approach is a feed-forward neural network that learns local edge-aware affine transforms that automatically obey the photorealism constraint. When trained on a diverse set of images and a variety of styles, our model can robustly apply style transfer to an arbitrary pair of input images. Compared to the state of the art, our method produces visually superior results and is three orders of magnitude faster, enabling real-time performance at 4K on a mobile phone. We validate our method with ablation and user studies.