Inferring missing links or detecting spurious ones based on observed graphs, known as link prediction, is a long-standing challenge in graph data analysis. With the recent advances in deep learning, graph neural networks have been used for link prediction and have achieved state-of-the-art performance. Nevertheless, existing methods developed for this purpose are typically discriminative, computing features of local subgraphs around two neighboring nodes and predicting potential links between them from the perspective of subgraph classification. In this formalism, the selection of enclosing subgraphs and heuristic structural features for subgraph classification significantly affects the performance of the methods. To overcome this limitation, this paper proposes a novel and radically different link prediction algorithm based on the network reconstruction theory, called GraphLP. Instead of sampling positive and negative links and heuristically computing the features of their enclosing subgraphs, GraphLP utilizes the feature learning ability of deep-learning models to automatically extract the structural patterns of graphs for link prediction under the assumption that real-world graphs are not locally isolated. Moreover, GraphLP explores high-order connectivity patterns to utilize the hierarchical organizational structures of graphs for link prediction. Our experimental results on all common benchmark datasets from different applications demonstrate that the proposed method consistently outperforms other state-of-the-art methods. Unlike the discriminative neural network models used for link prediction, GraphLP is generative, which provides a new paradigm for neural-network-based link prediction.

Machine Translation Quality Estimation (QE) is the task of evaluating translation output in the absence of human-written references. Due to the scarcity of human-labeled QE data, previous works attempted to utilize the abundant unlabeled parallel corpora to produce additional training data with pseudo labels. In this paper, we demonstrate a significant gap between parallel data and real QE data: for QE data, it is strictly guaranteed that the source side is original texts and the target side is translated (namely translationese). However, for parallel data, it is indiscriminate and the translationese may occur on either source or target side. We compare the impact of parallel data with different translation directions in QE data augmentation, and find that using the source-original part of parallel corpus consistently outperforms its target-original counterpart. Moreover, since the WMT corpus lacks direction information for each parallel sentence, we train a classifier to distinguish source- and target-original bitext, and carry out an analysis of their difference in both style and domain. Together, these findings suggest using source-original parallel data for QE data augmentation, which brings a relative improvement of up to 4.0% and 6.4% compared to undifferentiated data on sentence- and word-level QE tasks respectively.

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.

Recently, the success of pre-training in text domain has been fully extended to vision, audio, and cross-modal scenarios. The proposed pre-training models of different modalities are showing a rising trend of homogeneity in their model structures, which brings the opportunity to implement different pre-training models within a uniform framework. In this paper, we present TencentPretrain, a toolkit supporting pre-training models of different modalities. The core feature of TencentPretrain is the modular design. The toolkit uniformly divides pre-training models into 5 components: embedding, encoder, target embedding, decoder, and target. As almost all of common modules are provided in each component, users can choose the desired modules from different components to build a complete pre-training model. The modular design enables users to efficiently reproduce existing pre-training models or build brand-new one. We test the toolkit on text, vision, and audio benchmarks and show that it can match the performance of the original implementations.

This work explores an efficient approach to establish a foundational video-text model for tasks including open-vocabulary video classification, text-to-video retrieval, video captioning and video question-answering. We present VideoCoCa that reuses a pretrained image-text contrastive captioner (CoCa) model and adapt it to video-text tasks with minimal extra training. While previous works adapt image-text models with various cross-frame fusion modules (for example, cross-frame attention layer or perceiver resampler) and finetune the modified architecture on video-text data, we surprisingly find that the generative attentional pooling and contrastive attentional pooling layers in the image-text CoCa design are instantly adaptable to ``flattened frame embeddings'', yielding a strong zero-shot transfer baseline for many video-text tasks. Specifically, the frozen image encoder of a pretrained image-text CoCa takes each video frame as inputs and generates \(N\) token embeddings per frame for totally \(T\) video frames. We flatten \(N \times T\) token embeddings as a long sequence of frozen video representation and apply CoCa's generative attentional pooling and contrastive attentional pooling on top. All model weights including pooling layers are directly loaded from an image-text CoCa pretrained model. Without any video or video-text data, VideoCoCa's zero-shot transfer baseline already achieves state-of-the-art results on zero-shot video classification on Kinetics 400/600/700, UCF101, HMDB51, and Charades, as well as zero-shot text-to-video retrieval on MSR-VTT and ActivityNet Captions. We also explore lightweight finetuning on top of VideoCoCa, and achieve strong results on video question-answering (iVQA, MSRVTT-QA, MSVD-QA) and video captioning (MSR-VTT, ActivityNet, Youcook2). Our approach establishes a simple and effective video-text baseline for future research.

Geometric deep learning has recently achieved great success in non-Euclidean domains, and learning on 3D structures of large biomolecules is emerging as a distinct research area. However, its efficacy is largely constrained due to the limited quantity of structural data. Meanwhile, protein language models trained on substantial 1D sequences have shown burgeoning capabilities with scale in a broad range of applications. Nevertheless, no preceding studies consider combining these different protein modalities to promote the representation power of geometric neural networks. To address this gap, we make the foremost step to integrate the knowledge learned by well-trained protein language models into several state-of-the-art geometric networks. Experiments are evaluated on a variety of protein representation learning benchmarks, including protein-protein interface prediction, model quality assessment, protein-protein rigid-body docking, and binding affinity prediction, leading to an overall improvement of 20% over baselines and the new state-of-the-art performance. Strong evidence indicates that the incorporation of protein language models' knowledge enhances geometric networks' capacity by a significant margin and can be generalized to complex tasks.

As an effective method to deliver external materials into biological cells, microinjection has been widely applied in the biomedical field. However, the cognition of cell mechanical property is still inadequate, which greatly limits the efficiency and success rate of injection. Thus, a new rate-dependent mechanical model based on membrane theory is proposed for the first time. In this model, an analytical equilibrium equation between the injection force and cell deformation is established by considering the speed effect of microinjection. Different from the traditional membrane-theory-based model, the elastic coefficient of the constitutive material in the proposed model is modified as a function of the injection velocity and acceleration, effectively simulating the influence of speeds on the mechanical responses and providing a more generalized and practical model. Using this model, other mechanical responses at different speeds can be also accurately predicted, including the distribution of membrane tension and stress and the deformed shape. To verify the validity of the model, numerical simulations and experiments are carried out. The results show that the proposed model can match the real mechanical responses well at different injection speeds.

Online forms are widely used to collect data from human and have a multi-billion market. Many software products provide online services for creating semi-structured forms where questions and descriptions are organized by pre-defined structures. However, the design and creation process of forms is still tedious and requires expert knowledge. To assist form designers, in this work we present FormLM to model online forms (by enhancing pre-trained language model with form structural information) and recommend form creation ideas (including question / options recommendations and block type suggestion). For model training and evaluation, we collect the first public online form dataset with 62K online forms. Experiment results show that FormLM significantly outperforms general-purpose language models on all tasks, with an improvement by 4.71 on Question Recommendation and 10.6 on Block Type Suggestion in terms of ROUGE-1 and Macro-F1, respectively.

Recent works on Lottery Ticket Hypothesis have shown that pre-trained language models (PLMs) contain smaller matching subnetworks(winning tickets) which are capable of reaching accuracy comparable to the original models. However, these tickets are proved to be notrobust to adversarial examples, and even worse than their PLM counterparts. To address this problem, we propose a novel method based on learning binary weight masks to identify robust tickets hidden in the original PLMs. Since the loss is not differentiable for the binary mask, we assign the hard concrete distribution to the masks and encourage their sparsity using a smoothing approximation of L0 regularization.Furthermore, we design an adversarial loss objective to guide the search for robust tickets and ensure that the tickets perform well bothin accuracy and robustness. Experimental results show the significant improvement of the proposed method over previous work on adversarial robustness evaluation.

实例级图像检索（IIR）或简单的实例检索，涉及在数据集中查找包含查询实例（例如对象）的数据集中所有图像的问题。本文首次尝试使用基于实例歧视的对比学习（CL）解决此问题。尽管CL在许多计算机视觉任务中表现出令人印象深刻的性能，但在IIR领域也从未找到过类似的成功。在这项工作中，我们通过探索从预先训练和微调的CL模型中得出判别表示的能力来解决此问题。首先，我们通过比较预先训练的深度神经网络（DNN）分类器与CL模型学到的功能相比，研究了IIR转移学习的功效。这些发现启发了我们提出了一种新的培训策略，该策略通过使用平均精度（AP）损失以及微调方法来学习针对IIR量身定制的对比功能表示形式，从而优化CL以学习为导向IIR的功能。我们的经验评估表明，从挑战性的牛津和巴黎数据集中的预先培训的DNN分类器中学到的现成的特征上的表现显着提高。