Graph structures are ubiquitous throughout the natural sciences. Here we develop an approach that exploits the quantum source's graph structure to improve learning via an arbitrary quantum neural network (QNN) ansatz. In particular, we devise and optimize a self-supervised objective to capture the information-theoretic closeness of the quantum states in the training of a QNN. Numerical simulations show that our approach improves the learning efficiency and the generalization behavior of the base QNN. On a practical note, scalable quantum implementations of the learning procedure described in this paper are likely feasible on the next generation of quantum computing devices.

Growing evidence from recent studies implies that microRNAs or miRNAs could serve as biomarkers in various complex human diseases. Since wet-lab experiments for detecting miRNAs associated with a disease are expensive and time-consuming, machine learning techniques for miRNA-disease association prediction have attracted much attention in recent years. A big challenge in building reliable machine learning models is that of data scarcity. In particular, existing approaches trained on the available small datasets, even when combined with precalculated handcrafted input features, often suffer from bad generalization and data leakage problems. We overcome the limitations of existing works by proposing a novel multitask graph convolution-based approach, which we refer to as MuCoMiD. MuCoMiD allows automatic feature extraction while incorporating knowledge from five heterogeneous biological information sources (associations between miRNAs/diseases and protein-coding genes (PCGs), interactions between protein-coding genes, miRNA family information, and disease ontology) in a multitask setting which is a novel perspective and has not been studied before. To effectively test the generalization capability of our model, we conduct large-scale experiments on the standard benchmark datasets as well as on our proposed large independent testing sets and case studies. MuCoMiD obtains significantly higher Average Precision (AP) scores than all benchmarked models on three large independent testing sets, especially those with many new miRNAs, as well as in the detection of false positives. Thanks to its capability of learning directly from raw input information, MuCoMiD is easier to maintain and update than handcrafted feature-based methods, which would require recomputation of features every time there is a change in the original information sources (e.g., disease ontology, miRNA/disease-PCG associations, etc.). We share our code for reproducibility and future research at https://git.l3s.uni-hannover.de/dong/cmtt.

Background: Viral infections are causing significant morbidity and mortality worldwide. Understanding the interaction patterns between a particular virus and human proteins plays a crucial role in unveiling the underlying mechanism of viral infection and pathogenesis. This could further help in prevention and treatment of virus-related diseases. However, the task of predicting protein–protein interactions between a new virus and human cells is extremely challenging due to scarce data on virus-human interactions and fast mutation rates of most viruses. Results: We developed a multitask transfer learning approach that exploits the information of around 24 million protein sequences and the interaction patterns from the human interactome to counter the problem of small training datasets. Instead of using hand-crafted protein features, we utilize statistically rich protein representations learned by a deep language modeling approach from a massive source of protein sequences. Additionally, we employ an additional objective which aims to maximize the probability of observing human protein–protein interactions. This additional task objective acts as a regularizer and also allows to incorporate domain knowledge to inform the virus-human protein–protein interaction prediction model. Conclusions: Our approach achieved competitive results on 13 benchmark datasets and the case study for the SARS-CoV-2 virus receptor. Experimental results show that our proposed model works effectively for both virus-human and bacteria-human protein–protein interaction prediction tasks. We share our code for reproducibility and future research at https://git.l3s.uni-hannover.de/dong/multitask-transfer.

There has been significant progress in unsupervised network representation learning (UNRL) approaches over graphs recently with flexible random-walk approaches, new optimization objectives, and deep architectures. However, there is no common ground for systematic comparison of embeddings to understand their behavior for different graphs and tasks. We argue that most of the UNRL approaches either model and exploit neighborhood or what we call context information of a node. These methods largely differ in their definitions and exploitation of context. Consequently, we propose a framework that casts a variety of approaches-random walk based, matrix factorization and deep learning based-into a unified context-based optimization function. We systematically group the methods based on their similarities and differences. We study their differences which we later use to explain their performance differences (on downstream tasks). We conduct a large-scale empirical study considering nine popular and recent UNRL techniques and 11 real-world datasets with varying structural properties and two common tasks-node classification and link prediction. We find that for non-attributed graphs there is no single method that is a clear winner and that the choice of a suitable method is dictated by certain properties of the embedding methods, task and structural properties of the underlying graph. In addition, we also report the common pitfalls in evaluation of UNRL methods and come up with suggestions for experimental design and interpretation of results.

The extraction of main content from web pages is an important task for numerous applications, ranging from usability aspects, like reader views for news articles in web browsers, to information retrieval or natural language processing. Existing approaches are lacking as they rely on large amounts of hand-crafted features for classification. This results in models that are tailored to a specific distribution of web pages, e.g. from a certain time frame, but lack in generalization power. We propose a neural sequence labeling model that does not rely on any hand-crafted features but takes only the HTML tags and words that appear in a web page as input. This allows us to present a browser extension which highlights the content of arbitrary web pages directly within the browser using our model. In addition, we create a new, more current dataset to show that our model is able to adapt to changes in the structure of web pages and outperform the state-of-the-art model.

We propose a novel approach for learning node representations in directed graphs, which maintains separate views or embedding spaces for the two distinct node roles induced by the directionality of the edges. We argue that the previous approaches either fail to encode the edge directionality or their encodings cannot be generalized across tasks. With our simple alternating random walk strategy, we generate role specific vertex neighborhoods and train node embeddings in their corresponding source/target roles while fully exploiting the semantics of directed graphs. We also unearth the limitations of evaluations on directed graphs in previous works and propose a clear strategy for evaluating link prediction and graph reconstruction in directed graphs. We conduct extensive experiments to showcase our effectiveness on several real-world datasets on link prediction, node classification and graph reconstruction tasks. We show that the embeddings from our approach are indeed robust, generalizable and well performing across multiple kinds of tasks and graphs. We show that we consistently outperform all baselines for node classification task. In addition to providing a theoretical interpretation of our method we also show that we are considerably more robust than the other directed graph approaches.

Hash tables are ubiquitous in computer science for efficient access to large datasets. However, there is always a need for approaches that offer compact memory utilisation without substantial degradation of lookup performance. Cuckoo hashing is an efficient technique of creating hash tables with high space utilisation and offer a guaranteed constant access time. We are given n locations and m items. Each item has to be placed in one of the k≥ 2 locations chosen by k random hash functions. By allowing more than one choice for a single item, cuckoo hashing resembles multiple choice allocations schemes. In addition it supports dynamically changing the location of an item among its possible locations. We propose and analyse an insertion algorithm for cuckoo hashing that runs in linear time with high probability and in expectation. Previous work on total allocation time has analysed breadth first search, and it was shown to be linear only in expectation. Our algorithm finds an assignment (with probability 1) whenever it exists. In contrast, the other known insertion method, known as random walk insertion, may run indefinitely even for a solvable instance. We also present experimental results comparing the performance of our algorithm with the random walk method, also for the case when each location can hold more than one item. As a corollary we obtain a linear time algorithm (with high probability and in expectation) for finding perfect matchings in a special class of sparse random bipartite graphs. We support this by performing experiments on a real world large dataset for finding maximum matchings in general large bipartite graphs. We report an order of magnitude improvement in the running time as compared to the Hopkraft–Karp matching algorithm.