arXiv research

CNMs detect tipping points in complex systems using causal network markers.

We describe a method that infers whether statistical dependences between two observed variables X and Y are due to a "direct" causal link or only due to a connecting causal path that contains an unobserved variable of low complexity, e.g., a binary variable. This problem is motivated by statistical genetics. Given a ge…

Many complex disease syndromes such as asthma consist of a large number of highly related, rather than independent, clinical phenotypes, raising a new technical challenge in identifying genetic variations associated simultaneously with correlated traits. In this study, we propose a new statistical framework called grap…

Summary statistics of genome-wide association studies (GWAS) teach causal relationship between millions of genetic markers and tens and thousands of phenotypes. However, underlying biological mechanisms are yet to be elucidated. We can achieve necessary interpretation of GWAS in a causal mediation framework, looking to…

Novel method identifies proteomic risk markers for Alzheimer disease.

We target modeling latent dynamics in high-dimension marked event sequences without any prior knowledge about marker relations. Such problem has been rarely studied by previous works which would have fundamental difficulty to handle the arisen challenges: 1) the high-dimensional markers and unknown relation network amo…

Discovering causal genetic variants from large genetic association studies poses many difficult challenges. Assessing which genetic markers are involved in determining trait status is a computationally demanding task, especially in the presence of gene-gene interactions. A non-parametric Bayesian approach in the form o…

Estimates vaccine effectiveness and immune correlates in TND studies with missing data.

We consider the hypothesis testing problem of detecting conditional dependence, with a focus on high-dimensional feature spaces. Our contribution is a new test statistic based on samples from a generative adversarial network designed to approximate directly a conditional distribution that encodes the null hypothesis, i…

Preterm birth is the most common cause of neonatal death. Current diagnostic methods that assess the risk of preterm birth involve the collection of maternal characteristics and transvaginal ultrasound imaging conducted in the first and second trimester of pregnancy. Analysis of the ultrasound data is based on visual i…

Study uses DNM theory to detect early warning signals of market instability.

Neural network training entails heavy computation with obvious bottlenecks. The Compute Unified Device Architecture (CUDA) programming model allows us to accelerate computation by passing the processing workload from the CPU to the graphics processing unit (GPU). In this paper, we leveraged the power of Nvidia GPUs to …

New method uses kernel deviance measures to discover causal relationships in heterogeneous data.

As societies around the world are ageing, the number of Alzheimer's disease (AD) patients is rapidly increasing. To date, no low-cost, non-invasive biomarkers have been established to advance the objectivization of AD diagnosis and progression assessment. Here, we utilize Bayesian neural networks to develop a multivari…

SCIENCE improves prediction intervals for individual causal effects.

Improves disease progression prediction using auxiliary surrogate labels and health markers.

AR app visualizes Quranic Surah al-Fil for Islamic education.

Quantifying behavior is crucial for many applications in neuroscience. Videography provides easy methods for the observation and recording of animal behavior in diverse settings, yet extracting particular aspects of a behavior for further analysis can be highly time consuming. In motor control studies, humans or other …

For precision medicine and personalized treatment, we need to identify predictive markers of disease. We focus on Alzheimer's disease (AD), where magnetic resonance imaging scans provide information about the disease status. By combining imaging with genome sequencing, we aim at identifying rare genetic markers associa…

Microbial clades modeling is a challenging problem in biology based on microarray genome sequences, especially in new species gene isolates discovery and category. Marker family genome sequences play important roles in describing specific microbial clades within species, a framework of support vector machine (SVM) base…

MarkerMap selects key genes for cell type analysis in single-cell RNA-seq.

Predicts clinical events using a landmark approach with machine learning for large biomarker histories.

This paper introduces the factorial marked temporal point process model and presents efficient learning methods. In conventional (multi-dimensional) marked temporal point process models, event is often encoded by a single discrete variable i.e. a marker. In this paper, we describe the factorial marked point processes w…

The diagnosis of Alzheimer's disease (AD) in routine clinical practice is most commonly based on subjective clinical interpretations. Quantitative electroencephalography (QEEG) measures have been shown to reflect neurodegenerative processes in AD and might qualify as affordable and thereby widely available markers to f…

Proposes a two-stage method for estimating heterogeneous treatment effects using gradient boosting trees.

fiBAG integrates multiplatform genomic data to identify disease markers.

Understanding cell identity is an important task in many biomedical areas. Expression patterns of specific marker genes have been used to characterize some limited cell types, but exclusive markers are not available for many cell types. A second approach is to use machine learning to discriminate cell types based on th…

Reinterprets Granger causality with causal Bayesian networks and Reichenbach's principles.

Proposes DCNAR for dynamic causal inference from neural time series.

New method quantifies intrinsic causal contributions in neural networks.

Graph neural networks help infer causal effects from partially observable data.

CRN learns causal models using neural networks, scaling with variables and leveraging prior knowledge.

CgNN uses network structure as IVs to estimate causal effects in networks.

The paper proposes a method to integrate prior information into penalized regression.

Blog post comparing neural network methods for causal inference.

Causal deep learning tackles causal inference using tensor factor analysis.

Falls prevention, especially in older people, becomes an increasingly important topic in the times of aging societies. In this work, we present Gated Recurrent Unit-based neural networks models designed for predicting falls (syncope). The cardiovascular systems signals used in the study come from Gravitational Physiolo…

Interpretable model for Granger causality using neural networks.

New neural network approach for optimizing latent variable models.

Deep Causal Graphs model complex causal relationships using neural networks.

A neural network finds causal relationships among latent variables.

New method uses entropy to generate multiple plausible causal maps.

While the prevalence of Autism Spectrum Disorder (ASD) is increasing, research continues in an effort to identify common etiological and pathophysiological bases. In this regard, modern machine learning and network science pave the way for a better understanding of the neuropathology and the development of diagnosis ai…

A new algorithm infers causal networks from data using topological thresholds.

We consider the task of detecting regulatory elements in the human genome directly from raw DNA. Past work has focused on small snippets of DNA, making it difficult to model long-distance dependencies that arise from DNA's 3-dimensional conformation. In order to study long-distance dependencies, we develop and release …

Paper develops a method to learn causal networks with non-invertible functions.

BaMANI uses ensemble learning to improve Bayesian network inference.

We consider testing and learning problems on causal Bayesian networks as defined by Pearl (Pearl, 2009). Given a causal Bayesian network $\mathcal{M}$ on a graph with $n$ discrete variables and bounded in-degree and bounded `confounded components', we show that $O(\log n)$ interventions on an unknown causal Bayesian ne…