Gene Ontology (GO) is the primary gene function knowledge base that enables computational tasks in biomedicine. The basic element of GO is a term, which includes a set of genes with the same function. Existing research efforts of GO mainly focus on predicting gene term associations. Other tasks, such as generating descriptions of new terms, are rarely pursued. In this paper, we propose a novel task: GO term description generation. This task aims to automatically generate a sentence that describes the function of a GO term belonging to one of the three categories, i.e., molecular function, biological process, and cellular component. To address this task, we propose a Graph-in-Graph network that can efficiently leverage the structural information of GO. The proposed network introduces a two-layer graph: the first layer is a graph of GO terms where each node is also a graph (gene graph). Such a Graph-in-Graph network can derive the biological functions of GO terms and generate proper descriptions. To validate the effectiveness of the proposed network, we build three large-scale benchmark datasets. By incorporating the proposed Graph-in-Graph network, the performances of seven different sequence-to-sequence models can be substantially boosted across all evaluation metrics, with up to 34.7%, 14.5%, and 39.1% relative improvements in BLEU, ROUGE-L, and METEOR, respectively.
We consider a joint information extraction (IE) model, solving named entity recognition, coreference resolution and relation extraction jointly over the whole document. In particular, we study how to inject information from a knowledge base (KB) in such IE model, based on unsupervised entity linking. The used KB entity representations are learned from either (i) hyperlinked text documents (Wikipedia), or (ii) a knowledge graph (Wikidata), and appear complementary in raising IE performance. Representations of corresponding entity linking (EL) candidates are added to text span representations of the input document, and we experiment with (i) taking a weighted average of the EL candidate representations based on their prior (in Wikipedia), and (ii) using an attention scheme over the EL candidate list. Results demonstrate an increase of up to 5% F1-score for the evaluated IE tasks on two datasets. Despite a strong performance of the prior-based model, our quantitative and qualitative analysis reveals the advantage of using the attention-based approach.
Coronavirus disease (COVID-19) is an infectious disease, which is caused by the SARS-CoV-2 virus. Due to the growing literature on COVID-19, it is hard to get precise, up-to-date information about the virus. Practitioners, front-line workers, and researchers require expert-specific methods to stay current on scientific knowledge and research findings. However, there are a lot of research papers being written on the subject, which makes it hard to keep up with the most recent research. This problem motivates us to propose the design of the COVID-19 Search Engine (CO-SE), which is an algorithmic system that finds relevant documents for each query (asked by a user) and answers complex questions by searching a large corpus of publications. The CO-SE has a retriever component trained on the TF-IDF vectorizer that retrieves the relevant documents from the system. It also consists of a reader component that consists of a Transformer-based model, which is used to read the paragraphs and find the answers related to the query from the retrieved documents. The proposed model has outperformed previous models, obtaining an exact match ratio score of 71.45% and a semantic answer similarity score of 78.55%. It also outperforms other benchmark datasets, demonstrating the generalizability of the proposed approach.
In this paper, we investigated a speech augmentation based unsupervised learning approach for keyword spotting (KWS) task. KWS is a useful speech application, yet also heavily depends on the labeled data. We designed a CNN-Attention architecture to conduct the KWS task. CNN layers focus on the local acoustic features, and attention layers model the long-time dependency. To improve the robustness of KWS model, we also proposed an unsupervised learning method. The unsupervised loss is based on the similarity between the original and augmented speech features, as well as the audio reconstructing information. Two speech augmentation methods are explored in the unsupervised learning: speed and intensity. The experiments on Google Speech Commands V2 Dataset demonstrated that our CNN-Attention model has competitive results. Moreover, the augmentation based unsupervised learning could further improve the classification accuracy of KWS task. In our experiments, with augmentation based unsupervised learning, our KWS model achieves better performance than other unsupervised methods, such as CPC, APC, and MPC.
Recently, Transformers were shown to enhance the performance of multi-view stereo by enabling long-range feature interaction. In this work, we propose Window-based Transformers (WT) for local feature matching and global feature aggregation in multi-view stereo. We introduce a Window-based Epipolar Transformer (WET) which reduces matching redundancy by using epipolar constraints. Since point-to-line matching is sensitive to erroneous camera pose and calibration, we match windows near the epipolar lines. A second Shifted WT is employed for aggregating global information within cost volume. We present a novel Cost Transformer (CT) to replace 3D convolutions for cost volume regularization. In order to better constrain the estimated depth maps from multiple views, we further design a novel geometric consistency loss (Geo Loss) which punishes unreliable areas where multi-view consistency is not satisfied. Our WT multi-view stereo method (WT-MVSNet) achieves state-of-the-art performance across multiple datasets and ranks $1^{st}$ on Tanks and Temples benchmark.
Graph Neural Networks (GNNs) have shown great power in learning node representations on graphs. However, they may inherit historical prejudices from training data, leading to discriminatory bias in predictions. Although some work has developed fair GNNs, most of them directly borrow fair representation learning techniques from non-graph domains without considering the potential problem of sensitive attribute leakage caused by feature propagation in GNNs. However, we empirically observe that feature propagation could vary the correlation of previously innocuous non-sensitive features to the sensitive ones. This can be viewed as a leakage of sensitive information which could further exacerbate discrimination in predictions. Thus, we design two feature masking strategies according to feature correlations to highlight the importance of considering feature propagation and correlation variation in alleviating discrimination. Motivated by our analysis, we propose Fair View Graph Neural Network (FairVGNN) to generate fair views of features by automatically identifying and masking sensitive-correlated features considering correlation variation after feature propagation. Given the learned fair views, we adaptively clamp weights of the encoder to avoid using sensitive-related features. Experiments on real-world datasets demonstrate that FairVGNN enjoys a better trade-off between model utility and fairness. Our code is publicly available at \href{https://github.com/YuWVandy/FairVGNN}{\textcolor{blue}{https://github.com/YuWVandy/FairVGNN}}.
Modern GANs excel at generating high quality and diverse images. However, when transferring the pretrained GANs on small target data (e.g., 10-shot), the generator tends to replicate the training samples. Several methods have been proposed to address this few-shot image generation task, but there is a lack of effort to analyze them under a unified framework. As our first contribution, we propose a framework to analyze existing methods during the adaptation. Our analysis discovers that while some methods have disproportionate focus on diversity preserving which impede quality improvement, all methods achieve similar quality after convergence. Therefore, the better methods are those that can slow down diversity degradation. Furthermore, our analysis reveals that there is still plenty of room to further slow down diversity degradation. Informed by our analysis and to slow down the diversity degradation of the target generator during adaptation, our second contribution proposes to apply mutual information (MI) maximization to retain the source domain's rich multi-level diversity information in the target domain generator. We propose to perform MI maximization by contrastive loss (CL), leverage the generator and discriminator as two feature encoders to extract different multi-level features for computing CL. We refer to our method as Dual Contrastive Learning (DCL). Extensive experiments on several public datasets show that, while leading to a slower diversity-degrading generator during adaptation, our proposed DCL brings visually pleasant quality and state-of-the-art quantitative performance.
Few-shot relational learning for static knowledge graphs (KGs) has drawn greater interest in recent years, while few-shot learning for temporal knowledge graphs (TKGs) has hardly been studied. Compared to KGs, TKGs contain rich temporal information, thus requiring temporal reasoning techniques for modeling. This poses a greater challenge in learning few-shot relations in the temporal context. In this paper, we revisit the previous work related to few-shot relational learning in KGs and extend two existing TKG reasoning tasks, i.e., interpolated and extrapolated link prediction, to the one-shot setting. We propose four new large-scale benchmark datasets and develop a TKG reasoning model for learning one-shot relations in TKGs. Experimental results show that our model can achieve superior performance on all datasets in both interpolation and extrapolation tasks.
Sentence semantic understanding is a key topic in the field of natural language processing. Recently, contextualized word representations derived from pre-trained language models such as ELMO and BERT have shown significant improvements for a wide range of semantic tasks, e.g. question answering, text classification and sentiment analysis. However, how to add external knowledge to further improve the semantic modeling capability of model is worth probing. In this paper, we propose a novel approach to combining syntax information with a pre-trained language model. In order to evaluate the effect of the pre-training model, first, we introduce RNN-based and Transformer-based pre-trained language models; secondly, to better integrate external knowledge, such as syntactic information integrate with the pre-training model, we propose a dependency syntax expansion (DSE) model. For evaluation, we have selected two subtasks: sentence completion task and biological relation extraction task. The experimental results show that our model achieves 91.2\% accuracy, outperforming the baseline model by 37.8\% on sentence completion task. And it also gets competitive performance by 75.1\% $F_{1}$ score on relation extraction task.
Machine Learning for Software Engineering (ML4SE) is an actively growing research area that focuses on methods that help programmers in their work. In order to apply the developed methods in practice, they need to achieve reasonable quality in order to help rather than distract developers. While the development of new approaches to code representation and data collection improves the overall quality of the models, it does not take into account the information that we can get from the project at hand. In this work, we investigate how the model's quality can be improved if we target a specific project. We develop a framework to assess quality improvements that models can get after fine-tuning for the method name prediction task on a particular project. We evaluate three models of different complexity and compare their quality in three settings: trained on a large dataset of Java projects, further fine-tuned on the data from a particular project, and trained from scratch on this data. We show that per-project fine-tuning can greatly improve the models' quality as they capture the project's domain and naming conventions. We open-source the tool we used for data collection, as well as the code to run the experiments: https://zenodo.org/record/6040745.