Proteins are fundamental biological entities that play a key role in life activities. The amino acid sequences of proteins can be folded into stable 3D structures in the real physicochemical world, forming a special kind of sequence-structure data. With the development of Artificial Intelligence (AI) techniques, Protein Representation Learning (PRL) has recently emerged as a promising research topic for extracting informative knowledge from massive protein sequences or structures. To pave the way for AI researchers with little bioinformatics background, we present a timely and comprehensive review of PRL formulations and existing PRL methods from the perspective of model architectures, pretext tasks, and downstream applications. We first briefly introduce the motivations for protein representation learning and formulate it in a general and unified framework. Next, we divide existing PRL methods into three main categories: sequence-based, structure-based, and sequence-structure co-modeling. Finally, we discuss some technical challenges and potential directions for improving protein representation learning. The latest advances in PRL methods are summarized in a GitHub repository https://github.com/LirongWu/awesome-protein-representation-learning.

Time-series anomaly detection is an important task and has been widely applied in the industry. Since manual data annotation is expensive and inefficient, most applications adopt unsupervised anomaly detection methods, but the results are usually sub-optimal and unsatisfactory to end customers. Weak supervision is a promising paradigm for obtaining considerable labels in a low-cost way, which enables the customers to label data by writing heuristic rules rather than annotating each instance individually. However, in the time-series domain, it is hard for people to write reasonable labeling functions as the time-series data is numerically continuous and difficult to be understood. In this paper, we propose a Label-Efficient Interactive Time-Series Anomaly Detection (LEIAD) system, which enables a user to improve the results of unsupervised anomaly detection by performing only a small amount of interactions with the system. To achieve this goal, the system integrates weak supervision and active learning collaboratively while generating labeling functions automatically using only a few labeled data. All of these techniques are complementary and can promote each other in a reinforced manner. We conduct experiments on three time-series anomaly detection datasets, demonstrating that the proposed system is superior to existing solutions in both weak supervision and active learning areas. Also, the system has been tested in a real scenario in industry to show its practicality.

Video representation learning has been successful in video-text pre-training for zero-shot transfer, where each sentence is trained to be close to the paired video clips in a common feature space. For long videos, given a paragraph of description where the sentences describe different segments of the video, by matching all sentence-clip pairs, the paragraph and the full video are aligned implicitly. However, such unit-level similarity measure may ignore the global temporal context over a long time span, which inevitably limits the generalization ability. In this paper, we propose a contrastive learning framework TempCLR to compare the full video and the paragraph explicitly. As the video/paragraph is formulated as a sequence of clips/sentences, under the constraint of their temporal order, we use dynamic time warping to compute the minimum cumulative cost over sentence-clip pairs as the sequence-level distance. To explore the temporal dynamics, we break the consistency of temporal order by shuffling the video clips or sentences according to the temporal granularity. In this way, we obtain the representations for clips/sentences, which perceive the temporal information and thus facilitate the sequence alignment. In addition to pre-training on the video and paragraph, our approach can also generalize on the matching between different video instances. We evaluate our approach on video retrieval, action step localization, and few-shot action recognition, and achieve consistent performance gain over all three tasks. Detailed ablation studies are provided to justify the approach design.

Deep neural networks are incredibly vulnerable to crafted, human-imperceptible adversarial perturbations. Although adversarial training (AT) has proven to be an effective defense approach, we find that the AT-trained models heavily rely on the input low-frequency content for judgment, accounting for the low standard accuracy. To close the large gap between the standard and robust accuracies during AT, we investigate the frequency difference between clean and adversarial inputs, and propose a frequency regularization (FR) to align the output difference in the spectral domain. Besides, we find Stochastic Weight Averaging (SWA), by smoothing the kernels over epochs, further improves the robustness. Among various defense schemes, our method achieves the strongest robustness against attacks by PGD-20, C\&W and Autoattack, on a WideResNet trained on CIFAR-10 without any extra data.

Medical image quality assessment (MIQA) is a vital prerequisite in various medical image analysis applications. Most existing MIQA algorithms are fully supervised that request a large amount of annotated data. However, annotating medical images is time-consuming and labor-intensive. In this paper, we propose an unsupervised anomaly-aware framework with test-time clustering for optical coherence tomography angiography (OCTA) image quality assessment in a setting wherein only a set of high-quality samples are accessible in the training phase. Specifically, a feature-embedding-based low-quality representation module is proposed to quantify the quality of OCTA images and then to discriminate between outstanding quality and non-outstanding quality. Within the non-outstanding quality class, to further distinguish gradable images from ungradable ones, we perform dimension reduction and clustering of multi-scale image features extracted by the trained OCTA quality representation network. Extensive experiments are conducted on one publicly accessible dataset sOCTA-3*3-10k, with superiority of our proposed framework being successfully established.

Task transfer learning is a popular technique in image processing applications that uses pre-trained models to reduce the supervision cost of related tasks. An important question is to determine task transferability, i.e. given a common input domain, estimating to what extent representations learned from a source task can help in learning a target task. Typically, transferability is either measured experimentally or inferred through task relatedness, which is often defined without a clear operational meaning. In this paper, we present a novel metric, H-score, an easily-computable evaluation function that estimates the performance of transferred representations from one task to another in classification problems using statistical and information theoretic principles. Experiments on real image data show that our metric is not only consistent with the empirical transferability measurement, but also useful to practitioners in applications such as source model selection and task transfer curriculum learning.

Compared to typical multi-sensor systems, monocular 3D object detection has attracted much attention due to its simple configuration. However, there is still a significant gap between LiDAR-based and monocular-based methods. In this paper, we find that the ill-posed nature of monocular imagery can lead to depth ambiguity. Specifically, objects with different depths can appear with the same bounding boxes and similar visual features in the 2D image. Unfortunately, the network cannot accurately distinguish different depths from such non-discriminative visual features, resulting in unstable depth training. To facilitate depth learning, we propose a simple yet effective plug-and-play module, One Bounding Box Multiple Objects (OBMO). Concretely, we add a set of suitable pseudo labels by shifting the 3D bounding box along the viewing frustum. To constrain the pseudo-3D labels to be reasonable, we carefully design two label scoring strategies to represent their quality. In contrast to the original hard depth labels, such soft pseudo labels with quality scores allow the network to learn a reasonable depth range, boosting training stability and thus improving final performance. Extensive experiments on KITTI and Waymo benchmarks show that our method significantly improves state-of-the-art monocular 3D detectors by a significant margin (The improvements under the moderate setting on KITTI validation set are $\mathbf{1.82\sim 10.91\%}$ mAP in BEV and $\mathbf{1.18\sim 9.36\%}$ mAP in 3D}. Codes have been released at https://github.com/mrsempress/OBMO.

The number of international benchmarking competitions is steadily increasing in various fields of machine learning (ML) research and practice. So far, however, little is known about the common practice as well as bottlenecks faced by the community in tackling the research questions posed. To shed light on the status quo of algorithm development in the specific field of biomedical imaging analysis, we designed an international survey that was issued to all participants of challenges conducted in conjunction with the IEEE ISBI 2021 and MICCAI 2021 conferences (80 competitions in total). The survey covered participants' expertise and working environments, their chosen strategies, as well as algorithm characteristics. A median of 72% challenge participants took part in the survey. According to our results, knowledge exchange was the primary incentive (70%) for participation, while the reception of prize money played only a minor role (16%). While a median of 80 working hours was spent on method development, a large portion of participants stated that they did not have enough time for method development (32%). 25% perceived the infrastructure to be a bottleneck. Overall, 94% of all solutions were deep learning-based. Of these, 84% were based on standard architectures. 43% of the respondents reported that the data samples (e.g., images) were too large to be processed at once. This was most commonly addressed by patch-based training (69%), downsampling (37%), and solving 3D analysis tasks as a series of 2D tasks. K-fold cross-validation on the training set was performed by only 37% of the participants and only 50% of the participants performed ensembling based on multiple identical models (61%) or heterogeneous models (39%). 48% of the respondents applied postprocessing steps.

Solving partial differential equations is difficult. Recently proposed neural resolution-invariant models, despite their effectiveness and efficiency, usually require equispaced spatial points of data. However, sampling in spatial domain is sometimes inevitably non-equispaced in real-world systems, limiting their applicability. In this paper, we propose a Non-equispaced Fourier PDE Solver (\textsc{NFS}) with adaptive interpolation on resampled equispaced points and a variant of Fourier Neural Operators as its components. Experimental results on complex PDEs demonstrate its advantages in accuracy and efficiency. Compared with the spatially-equispaced benchmark methods, it achieves superior performance with $42.85\%$ improvements on MAE, and is able to handle non-equispaced data with a tiny loss of accuracy. Besides, to our best knowledge, \textsc{NFS} is the first ML-based method with mesh invariant inference ability to successfully model turbulent flows in non-equispaced scenarios, with a minor deviation of the error on unseen spatial points.

Over the years, Machine Learning models have been successfully employed on neuroimaging data for accurately predicting brain age. Deviations from the healthy brain aging pattern are associated to the accelerated brain aging and brain abnormalities. Hence, efficient and accurate diagnosis techniques are required for eliciting accurate brain age estimations. Several contributions have been reported in the past for this purpose, resorting to different data-driven modeling methods. Recently, deep neural networks (also referred to as deep learning) have become prevalent in manifold neuroimaging studies, including brain age estimation. In this review, we offer a comprehensive analysis of the literature related to the adoption of deep learning for brain age estimation with neuroimaging data. We detail and analyze different deep learning architectures used for this application, pausing at research works published to date quantitatively exploring their application. We also examine different brain age estimation frameworks, comparatively exposing their advantages and weaknesses. Finally, the review concludes with an outlook towards future directions that should be followed by prospective studies. The ultimate goal of this paper is to establish a common and informed reference for newcomers and experienced researchers willing to approach brain age estimation by using deep learning models