With the rapid growth of open-source ecosystems (e.g., Linux) and domain-specific software projects (e.g., aerospace), efficient management of reusable artifacts is becoming increasingly crucial for software reuse. The multi-level feature tree enables semantic management based on functionality and supports requirements-driven artifact selection. However, constructing such a tree heavily relies on domain expertise, which is time-consuming and labor-intensive.To address this issue, this paper proposes an automatic multilevel feature tree construction framework named FTBUILDER, which consists of three stages. ❶ It automatically crawls domain-specific software repositories and merges their metadata to construct a structured artifact library. ❷ It employs clustering algorithms to identify a set of artifacts with common features. ❸ It constructs a prompt and uses LLMs to summarize their common features. FTBUILDER recursively applies the identification and summarization stages to construct a multi-level feature tree from the bottom up. To validate FTBUILDER, we conduct experiments from multiple aspects (e.g., tree quality and time cost) using the Linux distribution ecosystem. Specifically, we first simultaneously develop and evaluate 24 alternative solutions in the FTBUILDER. Then we construct a three-level feature tree using the best solution among them. Compared to the official feature tree, our tree exhibits higher quality, with a 9% improvement in the silhouette coefficient and an 11% increase in GValue. Furthermore, it can save developers more time in selecting artifacts by 26% and improve the accuracy of artifact recommendations with GPT-4 by 235%. FTBUILDER can be extended to other open-source software communities and domain-specific industrial enterprises.1

Reusing third-party software packages is a common practice in software development. As the scale and complexity of open-source software (OSS) projects continue to grow (e.g., Linux distributions), the number of reused third-party packages has significantly increased. Therefore, effective package management is essential for the development and evolution of the OSS project. To achieve this, a package-to-group mechanism (P2G) is used to enable the unified installation, uninstallation, and updates of multiple packages at once. To better understand the mechanism, this paper takes Linux distributions as a case study and presents an empirical study focusing on its application trends, evolution patterns, group quality, and group tendency. By analyzing 11,746 groups and 193,548 packages from 89 versions of 5 popular Linux distributions and conducting questionnaire surveys with Linux practitioners and researchers, we derive several key insights. Our findings show that P2G is increasingly being adopted, particularly in popular Linux distributions. P2G follows six evolutionary patterns (e.g., splitting and merging groups). Interestingly, packages no longer managed through P2G are more likely to remain in Linux distributions rather than being directly removed. In addition, we propose a metric called GValue to evaluate the quality of groups and identify issues such as inadequate group descriptions and insufficient group sizes. We also summarize five types of packages that tend to adopt P2G, including graphical desktops and networks. To our knowledge, this is the first study to focus on P2G mechanisms. We hope that our study can assist in the efficient management of packages and reduce the burden on practitioners in the rapidly growing Linux distributions and other open-source software projects.

While recent developments of deep learning models have led to record-breaking achievements in many areas, the lack of sufficient interpretation remains a problem for many specific applications, such as the diagnosis prediction task in healthcare. The previous knowledge graph(KG) enhanced approaches mainly focus on learning clinically meaningful representations, the importance of medical concepts, and even the knowledge paths from inputs to labels. However, it is infeasible to interpret the diagnosis prediction, which needs to consider different medical concepts, various medical relationships, and the time-effectiveness of knowledge triples in different patient contexts. More importantly, the retrospective and prospective interpretations of disease processes are valuable to clinicians for the patients' confounding diseases. We propose KerPrint, a novel KG enhanced approach for retrospective and prospective interpretations to tackle these problems. Specifically, we propose a time-aware KG attention method to solve the problem of knowledge decay over time for trustworthy retrospective interpretation. We also propose a novel element-wise attention method to select candidate global knowledge using comprehensive representations from the local KG for prospective interpretation. We validate the effectiveness of our KerPrint through an extensive experimental study on a real-world dataset and a public dataset. The results show that our proposed approach not only achieves significant improvement over knowledge-enhanced methods but also gives the interpretability of diagnosis prediction in both retrospective and prospective views.

Due to the insufficiency of electronic health records (EHR) data utilized in practical diagnosis prediction scenarios, most works are devoted to learning powerful patient representations either from structured EHR data (e.g., temporal medical events, lab test results, etc.) or unstructured data (e.g., clinical notes, etc.). However, synthesizing rich information from both of them still needs to be explored. Firstly, the heterogeneous semantic biases across them heavily hinder the synthesis of representation spaces, which is critical for diagnosis prediction. Secondly, the intermingled quality of partial clinical notes leads to inadequate representations of to-be-predicted patients. Thirdly, typical attention mechanisms mainly focus on aggregating information from similar patients, ignoring important auxiliary information from others. To tackle these challenges, we propose a novel visit sequences-clinical notes joint learning approach, dubbed VecoCare. It performs a Gromov-Wasserstein Distance (GWD)-based contrastive learning task and an adaptive masked language model task in a sequential pre-training manner to reduce heterogeneous semantic biases. After pre-training, VecoCare further aggregates information from both similar and dissimilar patients through a dual-channel retrieval mechanism. We conduct diagnosis prediction experiments on two real-world datasets, which indicates that VecoCare outperforms state-of-the-art approaches. Moreover, the findings discovered by VecoCare are consistent with the medical researches.

Deep learning techniques are capable of capturing complex input-output relationships, and have been widely applied to the diagnosis prediction task based on web-based patient electronic health records (EHR) data. To improve the prediction and interpretability of pure data-driven deep learning with only a limited amount of labeled data, a pervasive trend is to assist the model training with knowledge priors from online medical knowledge graphs. However, they marginally investigated the label imbalance and the task-irrelevant noise in the external knowledge graph. The imbalanced label distribution would bias the learning and knowledge extraction towards the majority categories. The task-irrelevant noise introduces extra uncertainty to the model performance. To this end, aiming at by-passing the bias-variance trade-off dilemma, we introduce a new sequential learning framework, dubbed SeqCare, for diagnosis prediction with online medical knowledge graphs. Concretely, in the first step, SeqCare learns a bias-reduced space through a self-supervised graph contrastive learning task. Secondly, SeqCare reduces the learning uncertainty by refining the supervision signal and the graph structure of the knowledge graph simultaneously. Lastly, SeqCare trains the model in the bias-variance reduced space with a self-distillation to further filter out irrelevant information in the data. Experimental evaluations on two real-world datasets show that SeqCare outperforms state-of-the-art approaches. Case studies exemplify the interpretability of SeqCare. Moreover, the medical findings discovered by SeqCare are consistent with experts and medical literature.

While recent developments of neural network (NN) models have led to a series of record-breaking achievements in many applications, the lack of sufficiently good datasets remains a problem for some applications. For such a problem, we can however exploit a large number of unstructured text corpora as an external knowledge to complement the training data, and most prevailing neural network solutions employ word embedding methods for such purposes. In this paper, we propose LDA-Reg, a novel knowledge driven regularization framework based on Latent Dirichlet Allocation (LDA) as an alternative to the word embedding methods to adaptively utilize abundant external knowledge and to interpret the NN model. For the joint learning of the parameters, we propose EM-SGD, an effective update method which incorporates Expectation Maximization (EM) and Stochastic Gradient Descent (SGD) to update parameters iteratively. Moreover, we also devise a lazy update and sparse update method for the high-dimensional inputs and sparse inputs respectively. We validate the effectiveness of our regularization framework through an extensive experimental study over real world and standard benchmark datasets. The results show that our proposed framework not only achieves significant improvement over state-of-the-art word embedding methods but also learns interpretable and significant topics for various tasks.

Entity alignment is a fundamental and vital task in Knowledge Graph (KG) construction and fusion. Previous works mainly focus on capturing the structural semantics of entities by learning the entity embeddings on the relational triples and pre-aligned "seed entities". Some works also seek to incorporate the attribute information to assist refining the entity embeddings. However, there are still many problems not considered, which dramatically limits the utilization of attribute information in the entity alignment. Different KGs may have lots of different attribute types, and even the same attribute may have diverse data structures and value granularities. Most importantly, attributes may have various "contributions" to the entity alignment. To solve these problems, we propose COTSAE that combines the structure and attribute information of entities by co-training two embedding learning components, respectively. We also propose a joint attention method in our model to learn the attentions of attribute types and values cooperatively. We verified our COTSAE on several datasets from real-world KGs, and the results showed that it is significantly better than the latest entity alignment methods. The structure and attribute information can complement each other and both contribute to performance improvement.

With the better availability of healthcare data, such as Electronic Health Records (EHR), more and more data analytics methodologies are developed aiming at digging insights from them to improve the quality of care delivery. There are many challenges on analyzing EHR, such as high dimensionality and event sparsity. Moreover, different from other application domains, the EHR analysis algorithms need to be highly interpretable to make them clinically useful. This makes representation learning from EHRs of key importance. In this paper, we propose an algorithm called Predictive Task Guided Tensor Decomposition (TaGiTeD), to analyze EHRs. Specifically, TaGiTeD learns event interaction patterns that are highly predictive for certain tasks from EHRs with supervised tensor decomposition. Compared with unsupervised methods, TaGiTeD can learn effective EHR representations in a more focused way. This is crucial because most of the medical problems have very limited patient samples, which are not enough for unsupervised algorithms to learn meaningful representations form. We apply TaGiTeD on real world EHR data warehouse and demonstrate that TaGiTeD can learn representations that are both interpretable and predictive.