Benefiting from its single-photon sensitivity, single-photon avalanche diode (SPAD) array has been widely applied in various fields such as fluorescence lifetime imaging and quantum computing. However, large-scale high-fidelity single-photon imaging remains a big challenge, due to the complex hardware manufacture craft and heavy noise disturbance of SPAD arrays. In this work, we introduce deep learning into SPAD, enabling super-resolution single-photon imaging over an order of magnitude, with significant enhancement of bit depth and imaging quality. We first studied the complex photon flow model of SPAD electronics to accurately characterize multiple physical noise sources, and collected a real SPAD image dataset (64 $\times$ 32 pixels, 90 scenes, 10 different bit depth, 3 different illumination flux, 2790 images in total) to calibrate noise model parameters. With this real-world physical noise model, we for the first time synthesized a large-scale realistic single-photon image dataset (image pairs of 5 different resolutions with maximum megapixels, 17250 scenes, 10 different bit depth, 3 different illumination flux, 2.6 million images in total) for subsequent network training. To tackle the severe super-resolution challenge of SPAD inputs with low bit depth, low resolution, and heavy noise, we further built a deep transformer network with a content-adaptive self-attention mechanism and gated fusion modules, which can dig global contextual features to remove multi-source noise and extract full-frequency details. We applied the technique on a series of experiments including macroscopic and microscopic imaging, microfluidic inspection, and Fourier ptychography. The experiments validate the technique's state-of-the-art super-resolution SPAD imaging performance, with more than 5 dB superiority on PSNR compared to the existing methods.

Recently, there has been increasing interest in synthesizing data to improve downstream text-to-SQL tasks. In this paper, we first examined the existing synthesized datasets and discovered that state-of-the-art text-to-SQL algorithms did not further improve on popular benchmarks when trained with augmented synthetic data. We observed two shortcomings: illogical synthetic SQL queries from independent column sampling and arbitrary table joins. To address these issues, we propose a novel synthesis framework that incorporates key relationships from schema, imposes strong typing, and conducts schema-distance-weighted column sampling. We also adopt an intermediate representation (IR) for the SQL-to-text task to further improve the quality of the generated natural language questions. When existing powerful semantic parsers are pre-finetuned on our high-quality synthesized data, our experiments show that these models have significant accuracy boosts on popular benchmarks, including new state-of-the-art performance on Spider.

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.

In this paper, we study a novel and widely existing problem in graph matching (GM), namely, Bi-level Noisy Correspondence (BNC), which refers to node-level noisy correspondence (NNC) and edge-level noisy correspondence (ENC). In brief, on the one hand, due to the poor recognizability and viewpoint differences between images, it is inevitable to inaccurately annotate some keypoints with offset and confusion, leading to the mismatch between two associated nodes, i.e., NNC. On the other hand, the noisy node-to-node correspondence will further contaminate the edge-to-edge correspondence, thus leading to ENC. For the BNC challenge, we propose a novel method termed Contrastive Matching with Momentum Distillation. Specifically, the proposed method is with a robust quadratic contrastive loss which enjoys the following merits: i) better exploring the node-to-node and edge-to-edge correlations through a GM customized quadratic contrastive learning paradigm; ii) adaptively penalizing the noisy assignments based on the confidence estimated by the momentum teacher. Extensive experiments on three real-world datasets show the robustness of our model compared with 12 competitive baselines.

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.

Monocular 3D human pose estimation is quite challenging due to the inherent ambiguity and occlusion, which often lead to high uncertainty and indeterminacy. On the other hand, diffusion models have recently emerged as an effective tool for generating high-quality images from noise. Inspired by their capability, we explore a novel pose estimation framework (DiffPose) that formulates 3D pose estimation as a reverse diffusion process. We incorporate novel designs into our DiffPose that facilitate the diffusion process for 3D pose estimation: a pose-specific initialization of pose uncertainty distributions, a Gaussian Mixture Model-based forward diffusion process, and a context-conditioned reverse diffusion process. Our proposed DiffPose significantly outperforms existing methods on the widely used pose estimation benchmarks Human3.6M and MPI-INF-3DHP.

With the development of deep learning and Transformer-based pre-trained models like BERT, the accuracy of many NLP tasks has been dramatically improved. However, the large number of parameters and computations also pose challenges for their deployment. For instance, using BERT can improve the predictions in the financial sentiment analysis (FSA) task but slow it down, where speed and accuracy are equally important in terms of profits. To address these issues, we first propose an efficient and lightweight BERT (ELBERT) along with a novel confidence-window-based (CWB) early exit mechanism. Based on ELBERT, an innovative method to accelerate text processing on the GPU platform is developed, solving the difficult problem of making the early exit mechanism work more effectively with a large input batch size. Afterward, a fast and high-accuracy FSA system is built. Experimental results show that the proposed CWB early exit mechanism achieves significantly higher accuracy than existing early exit methods on BERT under the same computation cost. By using this acceleration method, our FSA system can boost the processing speed by nearly 40 times to over 1000 texts per second with sufficient accuracy, which is nearly twice as fast as FastBERT, thus providing a more powerful text processing capability for modern trading systems.

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.

视频和文本之间的跨模式检索因网络上的视频迅速出现而越来越多。通常，视频包含丰富的实例和事件信息，查询文本仅描述了信息的一部分。因此，视频可以对应于多个不同的文本说明和查询。我们将此现象称为``视频文本对应歧义''问题。当前技术主要集中于挖掘视频和文本内容之间的本地或多级对齐（\ textit {e.g。}，对实体和动词的动作对象）。这些方法很难通过仅使用一个单个功能来描述视频来减轻视频文本的歧义，这需要同时与多个不同的文本功能匹配。为了解决这个问题，我们提出了一个文本自适应多个视觉原型匹配模型，该模型会自动捕获多个原型，以通过自适应聚合视频令牌功能来描述视频。给定查询文本，相似性由最相似的原型确定，以在视频中找到对应关系，该视频称为文本自适应匹配。为了学习代表视频中丰富信息的多种原型，我们提出了差异损失，以鼓励不同的原型参与视频的不同内容。我们的方法在四个公共视频检索数据集上优于最先进的方法。

细粒度识别的目的是成功区分具有微妙差异的动作类别。为了解决这个问题，我们从人类视觉系统中获得灵感，该系统包含大脑中专门用于处理特定任务的专业区域。我们设计了一个新型的动态时空专业化（DSTS）模块，该模块由专门的神经元组成，这些神经元仅针对高度相似的样品子集激活。在训练过程中，损失迫使专门的神经元学习判别性细粒差异，以区分这些相似的样品，从而改善细粒度的识别。此外，一种时空专业化方法进一步优化了专业神经元的架构，以捕获更多的空间或时间细粒信息，以更好地解决视频中各种时空变化的范围。最后，我们设计了上游下游学习算法，以优化训练过程中模型的动态决策，从而提高DSTS模块的性能。我们在两个广泛使用的细粒度识别数据集上获得了最先进的性能。