Related papers: Temporal Positive-unlabeled Learning for Biomedica…

Analysis of longitudinal Electronic Health Record (EHR) data is an important goal for precision medicine. Difficulty in applying Machine Learning (ML) methods, either predictive or unsupervised, stems in part from the heterogeneity and…

This paper frames causal structure estimation as a machine learning task. The idea is to treat indicators of causal relationships between variables as `labels' and to exploit available data on the variables of interest to provide features…

Adoption of recently developed methods from machine learning has given rise to creation of drug-discovery knowledge graphs (KG) that utilize the interconnected nature of the domain. Graph-based modelling of the data, combined with KG…

Learning from positive and unlabeled data is known as positive-unlabeled (PU) learning in literature and has attracted much attention in recent years. One common approach in PU learning is to sample a set of pseudo-negatives from the…

Automatic phenotype concept recognition from unstructured text remains a challenging task in biomedical text mining research. Previous works that address the task typically use dictionary-based matching methods, which can achieve high…

In many scenarios of binary classification, only positive instances are provided in the training data, leaving the rest of the data unlabeled. This setup, known as positive-unlabeled (PU) learning, is addressed here with a network…

This article proposes methods to model nonstationary temporal graph processes. This corresponds to modelling the observation of edge variables (relationships between objects) indicating interactions between pairs of nodes (or objects)…

Temporal information extraction from unstructured text is essential for contextualizing events and deriving actionable insights, particularly in the medical domain. We address the task of extracting clinical events and their temporal…

Computational prediction of in-hospital mortality in the setting of an intensive care unit can help clinical practitioners to guide care and make early decisions for interventions. As clinical data are complex and varied in their structure…

In recent years, significant progress has been made in the field of learning from positive and unlabeled examples (PU learning), particularly in the context of advancing image and text classification tasks. However, applying PU learning to…

Deep learning-based predictive models, leveraging Electronic Health Records (EHR), are receiving increasing attention in healthcare. An effective representation of a patient's EHR should hierarchically encompass both the temporal…

Biomedical Knowledge Graphs (BKGs) integrate diverse datasets to elucidate complex relationships within the biomedical field. Effective link prediction on these graphs can uncover valuable connections, such as potential novel drug-disease…

Learning from positive and unlabeled data or PU learning is the setting where a learner only has access to positive examples and unlabeled data. The assumption is that the unlabeled data can contain both positive and negative examples. This…

Traditional machine learning methods face two main challenges in dealing with healthcare predictive analytics tasks. First, the high-dimensional nature of healthcare data needs labor-intensive and time-consuming processes to select an…

Research on link prediction in knowledge graphs has mainly focused on static multi-relational data. In this work we consider temporal knowledge graphs where relations between entities may only hold for a time interval or a specific point in…

Learning binary classifiers from positive and unlabeled data (PUL) is vital in many real-world applications, especially when verifying negative examples is difficult. Despite the impressive empirical performance of recent PUL methods,…

This study proposes a risk prediction method based on a Multi-Scale Temporal Alignment Network (MSTAN) to address the challenges of temporal irregularity, sampling interval differences, and multi-scale dynamic dependencies in Electronic…

This paper presents a novel benchmarking framework Dyport for evaluating biomedical hypothesis generation systems. Utilizing curated datasets, our approach tests these systems under realistic conditions, enhancing the relevance of our…

This paper presents a probabilistic model for reasoning about the state of a system as it changes over time, both due to exogenous and endogenous influences. Our target domain is a class of medical prediction problems that are neither so…

We propose a novel generative model to explore both local and global context for joint learning topics and topic-specific word embeddings. In particular, we assume that global latent topics are shared across documents, a word is generated…