Weakly-supervised object localization aims to indicate the category as well as the scope of an object in an image given only the image-level labels. Most of the existing works are based on Class Activation Mapping (CAM) and endeavor to enlarge the discriminative area inside the activation map to perceive the whole object, yet ignore the co-occurrence confounder of the object and context (e.g., fish and water), which makes the model inspection hard to distinguish object boundaries. Besides, the use of CAM also brings a dilemma problem that the classification and localization always suffer from a performance gap and can not reach their highest accuracy simultaneously. In this paper, we propose a casual knowledge distillation method, dubbed KD-CI-CAM, to address these two under-explored issues in one go. More specifically, we tackle the co-occurrence context confounder problem via causal intervention (CI), which explores the causalities among image features, contexts, and categories to eliminate the biased object-context entanglement in the class activation maps. Based on the de-biased object feature, we additionally propose a multi-teacher causal distillation framework to balance the absorption of classification knowledge and localization knowledge during model training. Extensive experiments on several benchmarks demonstrate the effectiveness of KD-CI-CAM in learning clear object boundaries from confounding contexts and addressing the dilemma problem between classification and localization performance.

Diagram object detection is the key basis of practical applications such as textbook question answering. Because the diagram mainly consists of simple lines and color blocks, its visual features are sparser than those of natural images. In addition, diagrams usually express diverse knowledge, in which there are many low-frequency object categories in diagrams. These lead to the fact that traditional data-driven detection model is not suitable for diagrams. In this work, we propose a gestalt-perception transformer model for diagram object detection, which is based on an encoder-decoder architecture. Gestalt perception contains a series of laws to explain human perception, that the human visual system tends to perceive patches in an image that are similar, close or connected without abrupt directional changes as a perceptual whole object. Inspired by these thoughts, we build a gestalt-perception graph in transformer encoder, which is composed of diagram patches as nodes and the relationships between patches as edges. This graph aims to group these patches into objects via laws of similarity, proximity, and smoothness implied in these edges, so that the meaningful objects can be effectively detected. The experimental results demonstrate that the proposed GPTR achieves the best results in the diagram object detection task. Our model also obtains comparable results over the competitors in natural image object detection.

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.

Transfer learning refers to the transfer of knowledge or information from a relevant source domain to a target domain. However, most existing transfer learning theories and algorithms focus on IID tasks, where the source/target samples are assumed to be independent and identically distributed. Very little effort is devoted to theoretically studying the knowledge transferability on non-IID tasks, e.g., cross-network mining. To bridge the gap, in this paper, we propose rigorous generalization bounds and algorithms for cross-network transfer learning from a source graph to a target graph. The crucial idea is to characterize the cross-network knowledge transferability from the perspective of the Weisfeiler-Lehman graph isomorphism test. To this end, we propose a novel Graph Subtree Discrepancy to measure the graph distribution shift between source and target graphs. Then the generalization error bounds on cross-network transfer learning, including both cross-network node classification and link prediction tasks, can be derived in terms of the source knowledge and the Graph Subtree Discrepancy across domains. This thereby motivates us to propose a generic graph adaptive network (GRADE) to minimize the distribution shift between source and target graphs for cross-network transfer learning. Experimental results verify the effectiveness and efficiency of our GRADE framework on both cross-network node classification and cross-domain recommendation tasks.

Table of contents (ToC) extraction aims to extract headings of different levels in documents to better understand the outline of the contents, which can be widely used for document understanding and information retrieval. Existing works often use hand-crafted features and predefined rule-based functions to detect headings and resolve the hierarchical relationship between headings. Both the benchmark and research based on deep learning are still limited. Accordingly, in this paper, we first introduce a standard dataset, HierDoc, including image samples from 650 documents of scientific papers with their content labels. Then we propose a novel end-to-end model by using the multimodal tree decoder (MTD) for ToC as a benchmark for HierDoc. The MTD model is mainly composed of three parts, namely encoder, classifier, and decoder. The encoder fuses the multimodality features of vision, text, and layout information for each entity of the document. Then the classifier recognizes and selects the heading entities. Next, to parse the hierarchical relationship between the heading entities, a tree-structured decoder is designed. To evaluate the performance, both the metric of tree-edit-distance similarity (TEDS) and F1-Measure are adopted. Finally, our MTD approach achieves an average TEDS of 87.2% and an average F1-Measure of 88.1% on the test set of HierDoc. The code and dataset will be released at: https://github.com/Pengfei-Hu/MTD.

Motivation: Enhancers are important cis-regulatory elements that regulate a wide range of biological functions and enhance the transcription of target genes. Although many state-of-the-art computational methods have been proposed in order to efficiently identify enhancers, learning globally contextual features is still one of the challenges for computational methods. Regarding the similarities between biological sequences and natural language sentences, the novel BERT-based language techniques have been applied to extracting complex contextual features in various computational biology tasks such as protein function/structure prediction. To speed up the research on enhancer identification, it is urgent to construct a BERT-based enhancer language model. Results: In this paper, we propose a multi-scale enhancer identification method (iEnhancer-ELM) based on enhancer language models, which treat enhancer sequences as natural language sentences that are composed of k-mer nucleotides. iEnhancer-ELM can extract contextual information of multi-scale k-mers with positions from raw enhancer sequences. Benefiting from the complementary information of k-mers in multi-scale, we ensemble four iEnhancer-ELM models for improving enhancer identification. The benchmark comparisons show that our model outperforms state-of-the-art methods. By the interpretable attention mechanism, we finds 30 biological patterns, where 40% (12/30) are verified by a widely used motif tool (STREME) and a popular dataset (JASPAR), demonstrating our model has a potential ability to reveal the biological mechanism of enhancer. Availability: The source code are available at https://github.com/chen-bioinfo/iEnhancer-ELM Contact: junjiechen@hit.edu.cn and junjie.chen.hit@gmail.com; Supplementary information: Supplementary data are available at Bioinformatics online.

The mediocre performance of conventional federated learning (FL) over heterogeneous data has been facilitating personalized FL solutions, where, unlike conventional FL which trains a single global consensus model, different models are allowed for different clients. However, in most existing personalized FL algorithms, the collaborative knowledge across the federation was only implicitly passed to the clients in ways such as model aggregation or regularization. We observed that this implicit knowledge transfer fails to maximize the potential value of each client's empirical risk toward other clients. Based on our observation, in this work, we propose Personalized Global Federated Learning (PGFed), a novel personalized FL framework that enables each client to personalize its own global objective by explicitly and adaptively aggregating the empirical risks of itself and other clients. To avoid massive ($O(N^2)$) communication overhead and potential privacy leakage, each client's risk is estimated through a first-order approximation for other clients' adaptive risk aggregation. On top of PGFed, we develop a momentum upgrade, dubbed PGFedMo, to more efficiently utilize clients' empirical risks. Our extensive experiments under different federated settings with benchmark datasets show consistent improvements of PGFed over the compared state-of-the-art alternatives.

The main challenge for fine-grained few-shot image classification is to learn feature representations with higher inter-class and lower intra-class variations, with a mere few labelled samples. Conventional few-shot learning methods however cannot be naively adopted for this fine-grained setting -- a quick pilot study reveals that they in fact push for the opposite (i.e., lower inter-class variations and higher intra-class variations). To alleviate this problem, prior works predominately use a support set to reconstruct the query image and then utilize metric learning to determine its category. Upon careful inspection, we further reveal that such unidirectional reconstruction methods only help to increase inter-class variations and are not effective in tackling intra-class variations. In this paper, we for the first time introduce a bi-reconstruction mechanism that can simultaneously accommodate for inter-class and intra-class variations. In addition to using the support set to reconstruct the query set for increasing inter-class variations, we further use the query set to reconstruct the support set for reducing intra-class variations. This design effectively helps the model to explore more subtle and discriminative features which is key for the fine-grained problem in hand. Furthermore, we also construct a self-reconstruction module to work alongside the bi-directional module to make the features even more discriminative. Experimental results on three widely used fine-grained image classification datasets consistently show considerable improvements compared with other methods. Codes are available at: https://github.com/PRIS-CV/Bi-FRN.

Full-body reconstruction is a fundamental but challenging task. Owing to the lack of annotated data, the performances of existing methods are largely limited. In this paper, we propose a novel method named Full-body Reconstruction from Part Experts~(FuRPE) to tackle this issue. In FuRPE, the network is trained using pseudo labels and features generated from part-experts. An simple yet effective pseudo ground-truth selection scheme is proposed to extract high-quality pseudo labels. In this way, a large-scale of existing human body reconstruction datasets can be leveraged and contribute to the model training. In addition, an exponential moving average training strategy is introduced to train the network in a self-supervised manner, further boosting the performance of the model. Extensive experiments on several widely used datasets demonstrate the effectiveness of our method over the baseline. Our method achieves the state-of-the-art performance. Code will be publicly available for further research.

Recent years have witnessed great success in handling graph-related tasks with Graph Neural Networks (GNNs). Despite their great academic success, Multi-Layer Perceptrons (MLPs) remain the primary workhorse for practical industrial applications. One reason for this academic-industrial gap is the neighborhood-fetching latency incurred by data dependency in GNNs, which make it hard to deploy for latency-sensitive applications that require fast inference. Conversely, without involving any feature aggregation, MLPs have no data dependency and infer much faster than GNNs, but their performance is less competitive. Motivated by these complementary strengths and weaknesses, we propose a Graph Self-Distillation on Neighborhood (GSDN) framework to reduce the gap between GNNs and MLPs. Specifically, the GSDN framework is based purely on MLPs, where structural information is only implicitly used as prior to guide knowledge self-distillation between the neighborhood and the target, substituting the explicit neighborhood information propagation as in GNNs. As a result, GSDN enjoys the benefits of graph topology-awareness in training but has no data dependency in inference. Extensive experiments have shown that the performance of vanilla MLPs can be greatly improved with self-distillation, e.g., GSDN improves over stand-alone MLPs by 15.54\% on average and outperforms the state-of-the-art GNNs on six datasets. Regarding inference speed, GSDN infers 75X-89X faster than existing GNNs and 16X-25X faster than other inference acceleration methods.