arXiv research

We present PubMed 200k RCT, a new dataset based on PubMed for sequential sentence classification. The dataset consists of approximately 200,000 abstracts of randomized controlled trials, totaling 2.3 million sentences. Each sentence of each abstract is labeled with their role in the abstract using one of the following …

This paper presents our system details and results of participation in the RDoC Tasks of BioNLP-OST 2019. Research Domain Criteria (RDoC) construct is a multi-dimensional and broad framework to describe mental health disorders by combining knowledge from genomics to behaviour. Non-availability of RDoC labelled dataset …

System automates identification of cancer drug repurposing from PubMed.

Drug-drug interaction (DDI) is a major cause of morbidity and mortality and a subject of intense scientific interest. Biomedical literature mining can aid DDI research by extracting evidence for large numbers of potential interactions from published literature and clinical databases. Though DDI is investigated in domai…

A new GCN model learns higher-order neighbors without explicit adjacency matrix computation.

This paper explores the recently proposed Graph Convolutional Network architecture proposed in (Kipf & Welling, 2016) The key points of their work is summarized and their results are reproduced. Graph regularization and alternative graph convolution approaches are explored. I find that explicit graph regularization was…

We present graph wavelet neural network (GWNN), a novel graph convolutional neural network (CNN), leveraging graph wavelet transform to address the shortcomings of previous spectral graph CNN methods that depend on graph Fourier transform. Different from graph Fourier transform, graph wavelet transform can be obtained …

To scale non-parametric extensions of probabilistic topic models such as Latent Dirichlet allocation to larger data sets, practitioners rely increasingly on parallel and distributed systems. In this work, we study data-parallel training for the hierarchical Dirichlet process (HDP) topic model. Based upon a representati…

In this paper, we study the problem of node representation learning with graph neural networks. We present a graph neural network class named recurrent graph neural network (RGNN), that address the shortcomings of prior methods. By using recurrent units to capture the long-term dependency across layers, our methods can…

It has been recently shown that sparse, nonnegative tensor factorization of multi-modal electronic health record data is a promising approach to high-throughput computational phenotyping. However, such approaches typically do not leverage available domain knowledge while extracting the phenotypes; hence, some of the su…

We present batch virtual adversarial training (BVAT), a novel regularization method for graph convolutional networks (GCNs). BVAT addresses the shortcoming of GCNs that do not consider the smoothness of the model's output distribution against local perturbations around the input. We propose two algorithms, sample-based…

Node embeddings have become an ubiquitous technique for representing graph data in a low dimensional space. Graph autoencoders, as one of the widely adapted deep models, have been proposed to learn graph embeddings in an unsupervised way by minimizing the reconstruction error for the graph data. However, its reconstruc…

We present graph attention networks (GATs), novel neural network architectures that operate on graph-structured data, leveraging masked self-attentional layers to address the shortcomings of prior methods based on graph convolutions or their approximations. By stacking layers in which nodes are able to attend over thei…

Graph Convolutional Networks (GCNs) have shown significant improvements in semi-supervised learning on graph-structured data. Concurrently, unsupervised learning of graph embeddings has benefited from the information contained in random walks. In this paper, we propose a model: Network of GCNs (N-GCN), which marries th…

We present GraphMix, a regularization method for Graph Neural Network based semi-supervised object classification, whereby we propose to train a fully-connected network jointly with the graph neural network via parameter sharing and interpolation-based regularization. Further, we provide a theoretical analysis of how G…

New graph representation learning network improves scalability and feature integration.

Graph autoencoders (AE) and variational autoencoders (VAE) recently emerged as powerful node embedding methods, with promising performances on challenging tasks such as link prediction and node clustering. Graph AE, VAE and most of their extensions rely on graph convolutional networks (GCN) to learn vector space repres…

Curating labeled training data has become the primary bottleneck in machine learning. Recent frameworks address this bottleneck with generative models to synthesize labels at scale from weak supervision sources. The generative model's dependency structure directly affects the quality of the estimated labels, but select…

Graph Neural Networks (GNNs) have been popularly used for analyzing non-Euclidean data such as social network data and biological data. Despite their success, the design of graph neural networks requires a lot of manual work and domain knowledge. In this paper, we propose a Graph Neural Architecture Search method (Grap…

Eliciting semantic similarity between concepts in the biomedical domain remains a challenging task. Recent approaches founded on embedding vectors have gained in popularity as they risen to efficiently capture semantic relationships The underlying idea is that two words that have close meaning gather similar contexts. …

Relational learning deals with data that are characterized by relational structures. An important task is collective classification, which is to jointly classify networked objects. While it holds a great promise to produce a better accuracy than non-collective classifiers, collective classification is computational cha…

Estimates binary labels from dependent data using Markov Random Fields.

Method predicts rarity of image features to support research integrity investigations.

New G-GNN models learn global graph info for better node learning.

In this paper, we propose guaranteed spectral methods for learning a broad range of topic models, which generalize the popular Latent Dirichlet Allocation (LDA). We overcome the limitation of LDA to incorporate arbitrary topic correlations, by assuming that the hidden topic proportions are drawn from a flexible class o…

In dynamic topic modeling, the proportional contribution of a topic to a document depends on the temporal dynamics of that topic's overall prevalence in the corpus. We extend the Dynamic Topic Model of Blei and Lafferty (2006) by explicitly modeling document level topic proportions with covariates and dynamic structure…

Graph convolutional network (GCN) provides a powerful means for graph-based semi-supervised tasks. However, as a localized first-order approximation of spectral graph convolution, the classic GCN can not take full advantage of unlabeled data, especially when the unlabeled node is far from labeled ones. To capitalize on…

Background: In this paper we present the approaches and methods employed in order to deal with a large scale multi-label semantic indexing task of biomedical papers. This work was mainly implemented within the context of the BioASQ challenge of 2014. Methods: The main contribution of this work is a multi-label ensemble…

Suffering from the multi-view data diversity and complexity for semi-supervised classification, most of existing graph convolutional networks focus on the networks architecture construction or the salient graph structure preservation, and ignore the the complete graph structure for semi-supervised classification contri…

Extracts roles of authors from biomedical papers.

Proposes GIL for semi-supervised graph classification.

Split-Merge MCMC (Monte Carlo Markov Chain) is one of the essential and popular variants of MCMC for problems when an MCMC state consists of an unknown number of components. It is well known that state-of-the-art methods for split-merge MCMC do not scale well. Strategies for rapid mixing requires smart and informative …

Convolutional neural networks (CNNs) have achieved great success on grid-like data such as images, but face tremendous challenges in learning from more generic data such as graphs. In CNNs, the trainable local filters enable the automatic extraction of high-level features. The computation with filters requires a fixed …

Study repurposes open data to find potential COVID-19 drugs.

GUIDE detects anomalies in attributed networks by reconstructing node attributes and higher-order structures.

Topic modeling, a method for extracting the underlying themes from a collection of documents, is an increasingly important component of the design of intelligent systems enabling the sense-making of highly dynamic and diverse streams of text data. Traditional methods such as Dynamic Topic Modeling (DTM) do not lend the…

GG-SAGE predicts links in directed graphs with attributes, outperforming existing methods.

Machine learning models for COVID-19 detection and prognosis from chest images are flawed and unreliable.

Review of childhood data for predicting overweight and obesity in later life.

Topic models have been extensively used to organize and interpret the contents of large, unstructured corpora of text documents. Although topic models often perform well on traditional training vs. test set evaluations, it is often the case that the results of a topic model do not align with human interpretation. This …

New method scales Gaussian processes with derivatives using variational inference.

Extends feature selection to GNNs, improving accuracy and feature ranking.

HGCN uses hyperbolic geometry to improve graph node embeddings.

MAGNA improves graph neural networks by incorporating multi-hop context information.

Aim: To review how machine learning (ML) is applied to imaging biomarkers in neuro-oncology, in particular for diagnosis, prognosis, and treatment response monitoring. Materials and Methods: The PubMed and MEDLINE databases were searched for articles published before September 2018 using relevant search terms. The sear…

Background. Drug-drug interaction (DDI) is a major cause of morbidity and mortality. [...] Biomedical literature mining can aid DDI research by extracting relevant DDI signals from either the published literature or large clinical databases. However, though drug interaction is an ideal area for translational research, …

Machine learning aids in diagnosing Parkinson's disease with higher accuracy.

Deep learning has shown outstanding performance in identifying intricate structures in complex high-dimensional data, especially in the domain of computer vision. The application of deep learning to early detection and automated classification of Alzheimer's disease (AD) has recently gained considerable attention, as r…