Contrastive learning (CL), which can extract the information shared between different contrastive views, has become a popular paradigm for vision representation learning. Inspired by the success in computer vision, recent work introduces CL into graph modeling, dubbed as graph contrastive learning (GCL). However, generating contrastive views in graphs is more challenging than that in images, since we have little prior knowledge on how to significantly augment a graph without changing its labels. We argue that typical data augmentation techniques (e.g., edge dropping) in GCL cannot generate diverse enough contrastive views to filter out noises. Moreover, previous GCL methods employ two view encoders with exactly the same neural architecture and tied parameters, which further harms the diversity of augmented views. To address this limitation, we propose a novel paradigm named model augmented GCL (MA-GCL), which will focus on manipulating the architectures of view encoders instead of perturbing graph inputs. Specifically, we present three easy-to-implement model augmentation tricks for GCL, namely asymmetric, random and shuffling, which can respectively help alleviate high- frequency noises, enrich training instances and bring safer augmentations. All three tricks are compatible with typical data augmentations. Experimental results show that MA-GCL can achieve state-of-the-art performance on node classification benchmarks by applying the three tricks on a simple base model. Extensive studies also validate our motivation and the effectiveness of each trick. (Code, data and appendix are available at https://github.com/GXM1141/MA-GCL. )

In the field of antibody engineering, an essential task is to design a novel antibody whose paratopes bind to a specific antigen with correct epitopes. Understanding antibody structure and its paratope can facilitate a mechanistic understanding of its function. Therefore, antibody structure prediction from its sequence alone has always been a highly valuable problem for de novo antibody design. AlphaFold2, a breakthrough in the field of structural biology, provides a solution to predict protein structure based on protein sequences and computationally expensive coevolutionary multiple sequence alignments (MSAs). However, the computational efficiency and undesirable prediction accuracy of antibodies, especially on the complementarity-determining regions (CDRs) of antibodies limit their applications in the industrially high-throughput drug design. To learn an informative representation of antibodies, we employed a deep antibody language model (ALM) on curated sequences from the observed antibody space database via a transformer model. We also developed a novel model named xTrimoABFold to predict antibody structure from antibody sequence based on the pretrained ALM as well as efficient evoformers and structural modules. The model was trained end-to-end on the antibody structures in PDB by minimizing the ensemble loss of domain-specific focal loss on CDR and the frame-aligned point loss. xTrimoABFold outperforms AlphaFold2 and other protein language model based SOTAs, e.g., OmegaFold, HelixFold-Single, and IgFold with a large significant margin (30+\% improvement on RMSD) while performing 151 times faster than AlphaFold2. To the best of our knowledge, xTrimoABFold achieved state-of-the-art antibody structure prediction. Its improvement in both accuracy and efficiency makes it a valuable tool for de novo antibody design and could make further improvements in immuno-theory.

Brain midline shift (MLS) is one of the most critical factors to be considered for clinical diagnosis and treatment decision-making for intracranial hemorrhage. Existing computational methods on MLS quantification not only require intensive labeling in millimeter-level measurement but also suffer from poor performance due to their dependence on specific landmarks or simplified anatomical assumptions. In this paper, we propose a novel semi-supervised framework to accurately measure the scale of MLS from head CT scans. We formulate the MLS measurement task as a deformation estimation problem and solve it using a few MLS slices with sparse labels. Meanwhile, with the help of diffusion models, we are able to use a great number of unlabeled MLS data and 2793 non-MLS cases for representation learning and regularization. The extracted representation reflects how the image is different from a non-MLS image and regularization serves an important role in the sparse-to-dense refinement of the deformation field. Our experiment on a real clinical brain hemorrhage dataset has achieved state-of-the-art performance and can generate interpretable deformation fields.

Current mainstream object detection methods for large aerial images usually divide large images into patches and then exhaustively detect the objects of interest on all patches, no matter whether there exist objects or not. This paradigm, although effective, is inefficient because the detectors have to go through all patches, severely hindering the inference speed. This paper presents an Objectness Activation Network (OAN) to help detectors focus on fewer patches but achieve more efficient inference and more accurate results, enabling a simple and effective solution to object detection in large images. In brief, OAN is a light fully-convolutional network for judging whether each patch contains objects or not, which can be easily integrated into many object detectors and jointly trained with them end-to-end. We extensively evaluate our OAN with five advanced detectors. Using OAN, all five detectors acquire more than 30.0% speed-up on three large-scale aerial image datasets, meanwhile with consistent accuracy improvements. On extremely large Gaofen-2 images (29200$\times$27620 pixels), our OAN improves the detection speed by 70.5%. Moreover, we extend our OAN to driving-scene object detection and 4K video object detection, boosting the detection speed by 112.1% and 75.0%, respectively, without sacrificing the accuracy. Code is available at https://github.com/Ranchosky/OAN.

We study the problem of semantic segmentation calibration. For image classification, lots of existing solutions are proposed to alleviate model miscalibration of confidence. However, to date, confidence calibration research on semantic segmentation is still limited. We provide a systematic study on the calibration of semantic segmentation models and propose a simple yet effective approach. First, we find that model capacity, crop size, multi-scale testing, and prediction correctness have impact on calibration. Among them, prediction correctness, especially misprediction, is more important to miscalibration due to over-confidence. Next, we propose a simple, unifying, and effective approach, namely selective scaling, by separating correct/incorrect prediction for scaling and more focusing on misprediction logit smoothing. Then, we study popular existing calibration methods and compare them with selective scaling on semantic segmentation calibration. We conduct extensive experiments with a variety of benchmarks on both in-domain and domain-shift calibration, and show that selective scaling consistently outperforms other methods.

In this paper, we propose a large-scale language pre-training for text GENeration using dIffusion modEl, which is named GENIE. GENIE is a pre-training sequence-to-sequence text generation model which combines Transformer and diffusion. The diffusion model accepts the latent information from the encoder, which is used to guide the denoising of the current time step. After multiple such denoise iterations, the diffusion model can restore the Gaussian noise to the diverse output text which is controlled by the input text. Moreover, such architecture design also allows us to adopt large scale pre-training on the GENIE. We propose a novel pre-training method named continuous paragraph denoise based on the characteristics of the diffusion model. Extensive experiments on the XSum, CNN/DailyMail, and Gigaword benchmarks shows that GENIE can achieves comparable performance with various strong baselines, especially after pre-training, the generation quality of GENIE is greatly improved. We have also conduct a lot of experiments on the generation diversity and parameter impact of GENIE. The code for GENIE will be made publicly available.

Developing autonomous vehicles (AVs) helps improve the road safety and traffic efficiency of intelligent transportation systems (ITS). Accurately predicting the trajectories of traffic participants is essential to the decision-making and motion planning of AVs in interactive scenarios. Recently, learning-based trajectory predictors have shown state-of-the-art performance in highway or urban areas. However, most existing learning-based models trained with fixed datasets may perform poorly in continuously changing scenarios. Specifically, they may not perform well in learned scenarios after learning the new one. This phenomenon is called "catastrophic forgetting". Few studies investigate trajectory predictions in continuous scenarios, where catastrophic forgetting may happen. To handle this problem, first, a novel continual learning (CL) approach for vehicle trajectory prediction is proposed in this paper. Then, inspired by brain science, a dynamic memory mechanism is developed by utilizing the measurement of traffic divergence between scenarios, which balances the performance and training efficiency of the proposed CL approach. Finally, datasets collected from different locations are used to design continual training and testing methods in experiments. Experimental results show that the proposed approach achieves consistently high prediction accuracy in continuous scenarios without re-training, which mitigates catastrophic forgetting compared to non-CL approaches. The implementation of the proposed approach is publicly available at https://github.com/BIT-Jack/D-GSM

Data compression is becoming critical for storing scientific data because many scientific applications need to store large amounts of data and post process this data for scientific discovery. Unlike image and video compression algorithms that limit errors to primary data, scientists require compression techniques that accurately preserve derived quantities of interest (QoIs). This paper presents a physics-informed compression technique implemented as an end-to-end, scalable, GPU-based pipeline for data compression that addresses this requirement. Our hybrid compression technique combines machine learning techniques and standard compression methods. Specifically, we combine an autoencoder, an error-bounded lossy compressor to provide guarantees on raw data error, and a constraint satisfaction post-processing step to preserve the QoIs within a minimal error (generally less than floating point error). The effectiveness of the data compression pipeline is demonstrated by compressing nuclear fusion simulation data generated by a large-scale fusion code, XGC, which produces hundreds of terabytes of data in a single day. Our approach works within the ADIOS framework and results in compression by a factor of more than 150 while requiring only a few percent of the computational resources necessary for generating the data, making the overall approach highly effective for practical scenarios.

Inspired by the recent success of Transformers for Natural Language Processing and vision Transformer for Computer Vision, many researchers in the medical imaging community have flocked to Transformer-based networks for various main stream medical tasks such as classification, segmentation, and estimation. In this study, we analyze, two recently published Transformer-based network architectures for the task of multimodal head-and-tumor segmentation and compare their performance to the de facto standard 3D segmentation network - the nnU-Net. Our results showed that modeling long-range dependencies may be helpful in cases where large structures are present and/or large field of view is needed. However, for small structures such as head-and-neck tumor, the convolution-based U-Net architecture seemed to perform well, especially when training dataset is small and computational resource is limited.

Code completion is a valuable topic in both academia and industry. Recently, large-scale mono-programming-lingual (MonoPL) pre-training models have been proposed to boost the performance of code completion. However, the code completion on low-resource programming languages (PL) is difficult for the data-driven paradigm, while there are plenty of developers using low-resource PLs. On the other hand, there are few studies exploring the effects of multi-programming-lingual (MultiPL) pre-training for the code completion, especially the impact on low-resource programming languages. To this end, we propose the MultiCoder to enhance the low-resource code completion via MultiPL pre-training and MultiPL Mixture-of-Experts (MoE) layers. We further propose a novel PL-level MoE routing strategy (PL-MoE) for improving the code completion on all PLs. Experimental results on CodeXGLUE and MultiCC demonstrate that 1) the proposed MultiCoder significantly outperforms the MonoPL baselines on low-resource programming languages, and 2) the PL-MoE module further boosts the performance on six programming languages. In addition, we analyze the effects of the proposed method in details and explore the effectiveness of our method in a variety of scenarios.