Accurate determination of a small molecule candidate (ligand) binding pose in its target protein pocket is important for computer-aided drug discovery. Typical rigid-body docking methods ignore the pocket flexibility of protein, while the more accurate pose generation using molecular dynamics is hindered by slow protein dynamics. We develop a tiered tensor transform (3T) algorithm to rapidly generate diverse protein-ligand complex conformations for both pose and affinity estimation in drug screening, requiring neither machine learning training nor lengthy dynamics computation, while maintaining both coarse-grain-like coordinated protein dynamics and atomistic-level details of the complex pocket. The 3T conformation structures we generate are closer to experimental co-crystal structures than those generated by docking software, and more importantly achieve significantly higher accuracy in active ligand classification than traditional ensemble docking using hundreds of experimental protein conformations. 3T structure transformation is decoupled from the system physics, making future usage in other computational scientific domains possible.

Video-language pre-training has advanced the performance of various downstream video-language tasks. However, most previous methods directly inherit or adapt typical image-language pre-training paradigms to video-language pre-training, thus not fully exploiting the unique characteristic of video, i.e., temporal. In this paper, we propose a Hierarchical Temporal-Aware video-language pre-training framework, HiTeA, with two novel pre-training tasks for modeling cross-modal alignment between moments and texts as well as the temporal relations of video-text pairs. Specifically, we propose a cross-modal moment exploration task to explore moments in videos, which results in detailed video moment representation. Besides, the inherent temporal relations are captured by aligning video-text pairs as a whole in different time resolutions with multi-modal temporal relation exploration task. Furthermore, we introduce the shuffling test to evaluate the temporal reliance of datasets and video-language pre-training models. We achieve state-of-the-art results on 15 well-established video-language understanding and generation tasks, especially on temporal-oriented datasets (e.g., SSv2-Template and SSv2-Label) with 8.6% and 11.1% improvement respectively. HiTeA also demonstrates strong generalization ability when directly transferred to downstream tasks in a zero-shot manner. Models and demo will be available on ModelScope.

The typical way for relation extraction is fine-tuning large pre-trained language models on task-specific datasets, then selecting the label with the highest probability of the output distribution as the final prediction. However, the usage of the Top-k prediction set for a given sample is commonly overlooked. In this paper, we first reveal that the Top-k prediction set of a given sample contains useful information for predicting the correct label. To effectively utilizes the Top-k prediction set, we propose Label Graph Network with Top-k Prediction Set, termed as KLG. Specifically, for a given sample, we build a label graph to review candidate labels in the Top-k prediction set and learn the connections between them. We also design a dynamic $k$-selection mechanism to learn more powerful and discriminative relation representation. Our experiments show that KLG achieves the best performances on three relation extraction datasets. Moreover, we observe that KLG is more effective in dealing with long-tailed classes.

Sequence generation demonstrates promising performance in recent information extraction efforts, by incorporating large-scale pre-trained Seq2Seq models. This paper investigates the merits of employing sequence generation in relation extraction, finding that with relation names or synonyms as generation targets, their textual semantics and the correlation (in terms of word sequence pattern) among them affect model performance. We then propose Relation Extraction with Label Augmentation (RELA), a Seq2Seq model with automatic label augmentation for RE. By saying label augmentation, we mean prod semantically synonyms for each relation name as the generation target. Besides, we present an in-depth analysis of the Seq2Seq model's behavior when dealing with RE. Experimental results show that RELA achieves competitive results compared with previous methods on four RE datasets.

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.

Due to the issue that existing wireless sensor network (WSN)-based anomaly detection methods only consider and analyze temporal features, in this paper, a self-supervised learning-based anomaly node detection method based on an autoencoder is designed. This method integrates temporal WSN data flow feature extraction, spatial position feature extraction and intermodal WSN correlation feature extraction into the design of the autoencoder to make full use of the spatial and temporal information of the WSN for anomaly detection. First, a fully connected network is used to extract the temporal features of nodes by considering a single mode from a local spatial perspective. Second, a graph neural network (GNN) is used to introduce the WSN topology from a global spatial perspective for anomaly detection and extract the spatial and temporal features of the data flows of nodes and their neighbors by considering a single mode. Then, the adaptive fusion method involving weighted summation is used to extract the relevant features between different models. In addition, this paper introduces a gated recurrent unit (GRU) to solve the long-term dependence problem of the time dimension. Eventually, the reconstructed output of the decoder and the hidden layer representation of the autoencoder are fed into a fully connected network to calculate the anomaly probability of the current system. Since the spatial feature extraction operation is advanced, the designed method can be applied to the task of large-scale network anomaly detection by adding a clustering operation. Experiments show that the designed method outperforms the baselines, and the F1 score reaches 90.6%, which is 5.2% higher than those of the existing anomaly detection methods based on unsupervised reconstruction and prediction. Code and model are available at https://github.com/GuetYe/anomaly_detection/GLSL

Multilingual BERT (mBERT) has demonstrated considerable cross-lingual syntactic ability, whereby it enables effective zero-shot cross-lingual transfer of syntactic knowledge. The transfer is more successful between some languages, but it is not well understood what leads to this variation and whether it fairly reflects difference between languages. In this work, we investigate the distributions of grammatical relations induced from mBERT in the context of 24 typologically different languages. We demonstrate that the distance between the distributions of different languages is highly consistent with the syntactic difference in terms of linguistic formalisms. Such difference learnt via self-supervision plays a crucial role in the zero-shot transfer performance and can be predicted by variation in morphosyntactic properties between languages. These results suggest that mBERT properly encodes languages in a way consistent with linguistic diversity and provide insights into the mechanism of cross-lingual transfer.

In recent years, vision-centric perception has flourished in various autonomous driving tasks, including 3D detection, semantic map construction, motion forecasting, and depth estimation. Nevertheless, the latency of vision-centric approaches is too high for practical deployment (e.g., most camera-based 3D detectors have a runtime greater than 300ms). To bridge the gap between ideal research and real-world applications, it is necessary to quantify the trade-off between performance and efficiency. Traditionally, autonomous-driving perception benchmarks perform the offline evaluation, neglecting the inference time delay. To mitigate the problem, we propose the Autonomous-driving StreAming Perception (ASAP) benchmark, which is the first benchmark to evaluate the online performance of vision-centric perception in autonomous driving. On the basis of the 2Hz annotated nuScenes dataset, we first propose an annotation-extending pipeline to generate high-frame-rate labels for the 12Hz raw images. Referring to the practical deployment, the Streaming Perception Under constRained-computation (SPUR) evaluation protocol is further constructed, where the 12Hz inputs are utilized for streaming evaluation under the constraints of different computational resources. In the ASAP benchmark, comprehensive experiment results reveal that the model rank alters under different constraints, suggesting that the model latency and computation budget should be considered as design choices to optimize the practical deployment. To facilitate further research, we establish baselines for camera-based streaming 3D detection, which consistently enhance the streaming performance across various hardware. ASAP project page: https://github.com/JeffWang987/ASAP.

Dense retrievers have made significant strides in obtaining state-of-the-art results on text retrieval and open-domain question answering (ODQA). Yet most of these achievements were made possible with the help of large annotated datasets, unsupervised learning for dense retrieval models remains an open problem. In this work, we explore two categories of methods for creating pseudo query-document pairs, named query extraction (QExt) and transferred query generation (TQGen), to augment the retriever training in an annotation-free and scalable manner. Specifically, QExt extracts pseudo queries by document structures or selecting salient random spans, and TQGen utilizes generation models trained for other NLP tasks (e.g., summarization) to produce pseudo queries. Extensive experiments show that dense retrievers trained with individual augmentation methods can perform comparably well with multiple strong baselines, and combining them leads to further improvements, achieving state-of-the-art performance of unsupervised dense retrieval on both BEIR and ODQA datasets.

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.