The identification of compound-protein interactions (CPI) plays a critical role in drug screening, drug repurposing, and combination therapy studies. The effectiveness of CPI prediction relies heavily on the features extracted from both compounds and target proteins. While various prediction methods employ different feature combinations, both molecular-based and network-based models encounter the common obstacle of incomplete feature representations. Thus, a promising solution to this issue is to fully integrate all relevant CPI features. This study proposed a novel model named MCPI, which is designed to improve the prediction performance of CPI by integrating multiple sources of information, including the PPI network, CCI network, and structural features of CPI. The results of the study indicate that the MCPI model outperformed other existing methods for predicting CPI on public datasets. Furthermore, the study has practical implications for drug development, as the model was applied to search for potential inhibitors among FDA-approved drugs in response to the SARS-CoV-2 pandemic. The prediction results were then validated through the literature, suggesting that the MCPI model could be a useful tool for identifying potential drug candidates. Overall, this study has the potential to advance our understanding of CPI and guide drug development efforts.
In this work, we establish a method for abstracting information from Computer Aided Engineering (CAE) into graphs. Such graph representations of CAE data can improve design guidelines and support recommendation systems by enabling the comparison of simulations, highlighting unexplored experimental designs, and correlating different designs. We focus on the load-path in crashworthiness analysis, a complex sub-discipline in vehicle design. The load-path is the sequence of parts that absorb most of the energy caused by the impact. To detect the load-path, we generate a directed weighted graph from the CAE data. The vertices represent the vehicle's parts, and the edges are an abstraction of the connectivity of the parts. The edge direction follows the temporal occurrence of the collision, where the edge weights reflect aspects of the energy absorption. We introduce and assess three methods for graph extraction and an additional method for further updating each graph with the sequences of absorption. Based on longest-path calculations, we introduce an automated detection of the load-path, which we analyse for the different graph extraction methods and weights. Finally, we show how our method for the detection of load-paths helps in the classification and labelling of CAE simulations.
Graph coarsening is a technique for solving large-scale graph problems by working on a smaller version of the original graph, and possibly interpolating the results back to the original graph. It has a long history in scientific computing and has recently gained popularity in machine learning, particularly in methods that preserve the graph spectrum. This work studies graph coarsening from a different perspective, developing a theory for preserving graph distances and proposing a method to achieve this. The geometric approach is useful when working with a collection of graphs, such as in graph classification and regression. In this study, we consider a graph as an element on a metric space equipped with the Gromov--Wasserstein (GW) distance, and bound the difference between the distance of two graphs and their coarsened versions. Minimizing this difference can be done using the popular weighted kernel $K$-means method, which improves existing spectrum-preserving methods with the proper choice of the kernel. The study includes a set of experiments to support the theory and method, including approximating the GW distance, preserving the graph spectrum, classifying graphs using spectral information, and performing regression using graph convolutional networks. Code is available at https://github.com/ychen-stat-ml/GW-Graph-Coarsening .
With the quick proliferation of extended reality (XR) services, the mobile communications networks are faced with gigantic challenges to meet the diversified and challenging service requirements. A tight coordination or even convergence of applications and mobile networks is highly motivated. In this paper, a multi-domain (e.g. application layer, transport layer, the core network, radio access network, user equipment) coordination scheme is first proposed, which facilitates a tight coordination between applications and networks based on the current 5G networks. Toward the convergence of applications and networks, a network architectures with cross-domain joint processing capability is further proposed for 6G mobile communications and beyond. Both designs are able to provide more accurate information of the quality of experience (QoE) and quality of service (QoS), thus paving the path for the joint optimization of applications and networks. The benefits of the QoE assisted scheduling are further investigated via simulations. A new QoE-oriented fairness metric is further proposed, which is capable of ensuring better fairness when different services are scheduled. Future research directions and their standardization impacts are also identified. Toward optimized end-to-end service provision, the paradigm shift from loosely coupled to converged design of applications and wireless communication networks is indispensable.
Clinical data is often affected by clinically irrelevant factors such as discrepancies between measurement devices or differing processing methods between sites. In the field of machine learning (ML), these factors are known as domains and the distribution differences they cause in the data are known as domain shifts. ML models trained using data from one domain often perform poorly when applied to data from another domain, potentially leading to wrong predictions. As such, developing machine learning models that can generalise well across multiple domains is a challenging yet essential task in the successful application of ML in clinical practice. In this paper, we propose a novel disentangled autoencoder (Dis-AE) neural network architecture that can learn domain-invariant data representations for multi-label classification of medical measurements even when the data is influenced by multiple interacting domain shifts at once. The model utilises adversarial training to produce data representations from which the domain can no longer be determined. We evaluate the model's domain generalisation capabilities on synthetic datasets and full blood count (FBC) data from blood donors as well as primary and secondary care patients, showing that Dis-AE improves model generalisation on multiple domains simultaneously while preserving clinically relevant information.
Network embedding, a graph representation learning method illustrating network topology by mapping nodes into lower-dimension vectors, is challenging to accommodate the ever-changing dynamic graphs in practice. Existing research is mainly based on node-by-node embedding modifications, which falls into the dilemma of efficient calculation and accuracy. Observing that the embedding dimensions are usually much smaller than the number of nodes, we break this dilemma with a novel dynamic network embedding paradigm that rotates and scales the axes of embedding space instead of a node-by-node update. Specifically, we propose the Dynamic Adjacency Matrix Factorization (DAMF) algorithm, which achieves an efficient and accurate dynamic network embedding by rotating and scaling the coordinate system where the network embedding resides with no more than the number of edge modifications changes of node embeddings. Moreover, a dynamic Personalized PageRank is applied to the obtained network embeddings to enhance node embeddings and capture higher-order neighbor information dynamically. Experiments of node classification, link prediction, and graph reconstruction on different-sized dynamic graphs suggest that DAMF advances dynamic network embedding. Further, we unprecedentedly expand dynamic network embedding experiments to billion-edge graphs, where DAMF updates billion-level parameters in less than 10ms.
Recent advances in the healthcare industry have led to an abundance of unstructured data, making it challenging to perform tasks such as efficient and accurate information retrieval at scale. Our work offers an all-in-one scalable solution for extracting and exploring complex information from large-scale research documents, which would otherwise be tedious. First, we briefly explain our knowledge synthesis process to extract helpful information from unstructured text data of research documents. Then, on top of the knowledge extracted from the documents, we perform complex information retrieval using three major components- Paragraph Retrieval, Triplet Retrieval from Knowledge Graphs, and Complex Question Answering (QA). These components combine lexical and semantic-based methods to retrieve paragraphs and triplets and perform faceted refinement for filtering these search results. The complexity of biomedical queries and documents necessitates using a QA system capable of handling queries more complex than factoid queries, which we evaluate qualitatively on the COVID-19 Open Research Dataset (CORD-19) to demonstrate the effectiveness and value-add.
Language models of code (LMs) work well when the surrounding code in the vicinity of generation provides sufficient context. This is not true when it becomes necessary to use types or functionality defined in another module or library, especially those not seen during training. LMs suffer from limited awareness of such global context and end up hallucinating, e.g., using types defined in other files incorrectly. Recent work tries to overcome this issue by retrieving global information to augment the local context. However, this bloats the prompt or requires architecture modifications and additional training. Integrated development environments (IDEs) assist developers by bringing the global context at their fingertips using static analysis. We extend this assistance, enjoyed by developers, to the LMs. We propose a notion of monitors that use static analysis in the background to guide the decoding. Unlike a priori retrieval, static analysis is invoked iteratively during the entire decoding process, providing the most relevant suggestions on demand. We demonstrate the usefulness of our proposal by monitoring for type-consistent use of identifiers whenever an LM generates code for object dereference. To evaluate our approach, we curate PragmaticCode, a dataset of open-source projects with their development environments. On models of varying parameter scale, we show that monitor-guided decoding consistently improves the ability of an LM to not only generate identifiers that match the ground truth but also improves compilation rates and agreement with ground truth. We find that LMs with fewer parameters, when guided with our monitor, can outperform larger LMs. With monitor-guided decoding, SantaCoder-1.1B achieves better compilation rate and next-identifier match than the much larger text-davinci-003 model. The datasets and code will be released at https://aka.ms/monitors4codegen .
Translation models tend to ignore the rich semantic information in triads in the process of knowledge graph complementation. To remedy this shortcoming, this paper constructs a knowledge graph complementation method that incorporates adaptively enhanced semantic information. The hidden semantic information inherent in the triad is obtained by fine-tuning the BERT model, and the attention feature embedding method is used to calculate the semantic attention scores between relations and entities in positive and negative triads and incorporate them into the structural information to form a soft constraint rule for semantic information. The rule is added to the original translation model to realize the adaptive enhancement of semantic information. In addition, the method takes into account the effect of high-dimensional vectors on the effect, and uses the BERT-whitening method to reduce the dimensionality and generate a more efficient semantic vector representation. After experimental comparison, the proposed method performs better on both FB15K and WIN18 datasets, with a numerical improvement of about 2.6% compared with the original translation model, which verifies the reasonableness and effectiveness of the method.
Reinforcement learning can effectively learn amortised design policies for designing sequences of experiments. However, current methods rely on contrastive estimators of expected information gain, which require an exponential number of contrastive samples to achieve an unbiased estimation. We propose an alternative lower bound estimator, based on the cross-entropy of the joint model distribution and a flexible proposal distribution. This proposal distribution approximates the true posterior of the model parameters given the experimental history and the design policy. Our estimator requires no contrastive samples, can achieve more accurate estimates of high information gains, allows learning of superior design policies, and is compatible with implicit probabilistic models. We assess our algorithm's performance in various tasks, including continuous and discrete designs and explicit and implicit likelihoods.