Shan He

Rui He, Zeyu Dai, Shan He et al.

In multi-domain learning (MDL) scenarios, high labeling effort is required due to the complexity of collecting data from various domains. Active Learning (AL) presents an encouraging solution to this issue by annotating a smaller number of highly informative instances, thereby reducing the labeling effort. Previous research has relied on conventional AL strategies for MDL scenarios, which underutilize the domain-shared information of each instance during the selection procedure. To mitigate this issue, we propose a novel perturbation-based two-stage multi-domain active learning (P2S-MDAL) method incorporated into the well-regarded ASP-MTL model. Specifically, P2S-MDAL involves allocating budgets for domains and establishing regions for diversity selection, which are further used to select the most cross-domain influential samples in each region. A perturbation metric has been introduced to evaluate the robustness of the shared feature extractor of the model, facilitating the identification of potentially cross-domain influential samples. Experiments are conducted on three real-world datasets, encompassing both texts and images. The superior performance over conventional AL strategies shows the effectiveness of the proposed strategy. Additionally, an ablation study has been carried out to demonstrate the validity of each component. Finally, we outline several intriguing potential directions for future MDAL research, thus catalyzing the field's advancement.

Shan He, Yalong Ma, Tao Song et al.

Planning a safe and feasible trajectory for autonomous vehicles in real-time by fully utilizing perceptual information in complex urban environments is challenging. In this paper, we propose a spatio-temporal trajectory planning method based on graph optimization. It efficiently extracts the multi-modal information of the perception module by constructing a semantic spatio-temporal map through separation processing of static and dynamic obstacles, and then quickly generates feasible trajectories via sparse graph optimization based on a semantic spatio-temporal hypergraph. Extensive experiments have proven that the proposed method can effectively handle complex urban public road scenarios and perform in real time. We will also release our codes to accommodate benchmarking for the research community

Zhangfan Yang, Junkai Ji, Shan He et al.

Molecular docking is a crucial step in drug development, which enables the virtual screening of compound libraries to identify potential ligands that target proteins of interest. However, the computational complexity of traditional docking models increases as the size of the compound library increases. Recently, deep learning algorithms can provide data-driven research and development models to increase the speed of the docking process. Unfortunately, few models can achieve superior screening performance compared to that of traditional models. Therefore, a novel deep learning-based docking approach named Dockformer is introduced in this study. Dockformer leverages multimodal information to capture the geometric topology and structural knowledge of molecules and can directly generate binding conformations with the corresponding confidence measures in an end-to-end manner. The experimental results show that Dockformer achieves success rates of 90.53% and 82.71% on the PDBbind core set and PoseBusters benchmarks, respectively, and more than a 100-fold increase in the inference process speed, outperforming almost all state-of-the-art docking methods. In addition, the ability of Dockformer to identify the main protease inhibitors of coronaviruses is demonstrated in a real-world virtual screening scenario. Considering its high docking accuracy and screening efficiency, Dockformer can be regarded as a powerful and robust tool in the field of drug design.

Rui He, Shengcai Liu, Jiahao Wu et al.

Multi-domain learning (MDL) refers to simultaneously constructing a model or a set of models on datasets collected from different domains. Conventional approaches emphasize domain-shared information extraction and domain-private information preservation, following the shared-private framework (SP models), which offers significant advantages over single-domain learning. However, the limited availability of annotated data in each domain considerably hinders the effectiveness of conventional supervised MDL approaches in real-world applications. In this paper, we introduce a novel method called multi-domain contrastive learning (MDCL) to alleviate the impact of insufficient annotations by capturing both semantic and structural information from both labeled and unlabeled data.Specifically, MDCL comprises two modules: inter-domain semantic alignment and intra-domain contrast. The former aims to align annotated instances of the same semantic category from distinct domains within a shared hidden space, while the latter focuses on learning a cluster structure of unlabeled instances in a private hidden space for each domain. MDCL is readily compatible with many SP models, requiring no additional model parameters and allowing for end-to-end training. Experimental results across five textual and image multi-domain datasets demonstrate that MDCL brings noticeable improvement over various SP models.Furthermore, MDCL can further be employed in multi-domain active learning (MDAL) to achieve a superior initialization, eventually leading to better overall performance.

Gourab Ghosh Roy, Nicholas Geard, Karin Verspoor et al.

Survival risk prediction using gene expression data is important in making treatment decisions in cancer. Standard neural network (NN) survival analysis models are black boxes with lack of interpretability. More interpretable visible neural network (VNN) architectures are designed using biological pathway knowledge. But they do not model how pathway structures can change for particular cancer types. We propose a novel Mutated Pathway VNN or MPVNN architecture, designed using prior signaling pathway knowledge and gene mutation data-based edge randomization simulating signal flow disruption. As a case study, we use the PI3K-Akt pathway and demonstrate overall improved cancer-specific survival risk prediction results of MPVNN over standard non-NN and other similar sized NN survival analysis methods. We show that trained MPVNN architecture interpretation, which points to smaller sets of genes connected by signal flow within the PI3K-Akt pathway that are important in risk prediction for particular cancer types, is reliable.

Yingying Wang, Cunliang Kong, Liner Yang et al.

Learner corpus collects language data produced by L2 learners, that is second or foreign-language learners. This resource is of great relevance for second language acquisition research, foreign-language teaching, and automatic grammatical error correction. However, there is little focus on learner corpus for Chinese as Foreign Language (CFL) learners. Therefore, we propose to construct a large-scale, multidimensional annotated Chinese learner corpus. To construct the corpus, we first obtain a large number of topic-rich texts generated by CFL learners. Then we design an annotation scheme including a sentence acceptability score as well as grammatical error and fluency-based corrections. We build a crowdsourcing platform to perform the annotation effectively (https://yaclc.wenmind.net). We name the corpus YACLC (Yet Another Chinese Learner Corpus) and release it as part of the CUGE benchmark (http://cuge.baai.ac.cn). By analyzing the original sentences and annotations in the corpus, we found that YACLC has a considerable size and very high annotation quality. We hope this corpus can further enhance the studies on Chinese International Education and Chinese automatic grammatical error correction.

Rui He, Shengcai Liu, Shan He et al.

Multi-domain learning (MDL) refers to learning a set of models simultaneously, where each model is specialized to perform a task in a particular domain. Generally, a high labeling effort is required in MDL, as data needs to be labeled by human experts for every domain. Active learning (AL) can be utilized in MDL to reduce the labeling effort by only using the most informative data. The resultant paradigm is termed multi-domain active learning (MDAL). In this work, we provide an exhaustive literature review for MDAL on the relevant fields, including AL, cross-domain information sharing schemes, and cross-domain instance evaluation approaches. It is found that the few studies which have been directly conducted on MDAL cannot serve as off-the-shelf solutions on more general MDAL tasks. To fill this gap, we construct a pipeline of MDAL and present a comprehensive comparative study of thirty different algorithms, which are established by combining six representative MDL models and five commonly used AL strategies. We evaluate the algorithms on six datasets involving textual and visual classification tasks. In most cases, AL brings notable improvements to MDL, and the naive BvSB (best vs. second best) Uncertainty strategy can perform competitively with the state-of-the-art AL strategies. Besides, BvSB with the MAN (multinomial adversarial networks) model can consistently achieve top or above-average performance on all the datasets. Furthermore, we qualitatively analyze the behaviors of the well-performed strategies and models, shedding light on their superior performance in the comparison. Finally, we recommend using BvSB with the MAN model in the application of MDAL due to their good performance in the experiments.