Daniel E. Platt
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View article: Examples of real stable bundles on K3 surfaces
Examples of real stable bundles on K3 surfaces Open
Motivated by gauge theory on manifolds with exceptional holonomy, we construct examples of stable bundles on K3 surfaces that are invariant under two involutions: one is holomorphic; and the other is anti-holomorphic. These bundles are obt…
View article: Human migration from the Levant and Arabia into Yemen since Last Glacial Maximum
Human migration from the Levant and Arabia into Yemen since Last Glacial Maximum Open
While a broad consensus about the first successful migration modern humans out of Africa seems established, the peopling of Arabia remains somewhat enigmatic. Identifying the ancestral populations that contributed to the gene pool of the c…
View article: Informational rescaling of PCA maps with application to genetic distance
Informational rescaling of PCA maps with application to genetic distance Open
Principal Component Analysis (PCA) is a powerful multivariate tool allowing the projection of data in low-dimensional representations. Nevertheless, datapoint distances on these low-dimensional projections are challenging to interpret. Her…
View article: Multi-view biomedical foundation models for molecule-target and property prediction
Multi-view biomedical foundation models for molecule-target and property prediction Open
Quality molecular representations are key to foundation model development in bio-medical research. Previous efforts have typically focused on a single representation or molecular view, which may have strengths or weaknesses on a given task…
View article: Multimodal predictions of end stage chronic kidney disease from asymptomatic individuals for discovery of genomic biomarkers
Multimodal predictions of end stage chronic kidney disease from asymptomatic individuals for discovery of genomic biomarkers Open
Chronic kidney disease (CKD) is a complex condition where the kidneys are damaged and progressively lose their ability to filter blood, 10% of the world population have the disease that often goes undetected until it is too late for interv…
View article: Epidemiological topology data analysis links severe COVID-19 to RAAS and hyperlipidemia associated metabolic syndrome conditions
Epidemiological topology data analysis links severe COVID-19 to RAAS and hyperlipidemia associated metabolic syndrome conditions Open
Motivation The emergence of COVID-19 (C19) created incredible worldwide challenges but offers unique opportunities to understand the physiology of its risk factors and their interactions with complex disease conditions, such as metabolic s…
View article: K3 surfaces with two involutions and low Picard number
K3 surfaces with two involutions and low Picard number Open
Let X be a complex algebraic K3 surface of degree 2 d and with Picard number $$\rho $$ . Assume that X admits two commuting involutions: one holomorphic and one anti-holomorphic. In that case, $$\rho \ge 1$$ when $$d=1$$ and $$\rho \ge …
View article: AI-enabled evaluation of genome-wide association relevance and polygenic risk score prediction in Alzheimer's disease
AI-enabled evaluation of genome-wide association relevance and polygenic risk score prediction in Alzheimer's disease Open
GWAS focuses on significance loosing false positives; machine learning probes sub-significant features relying on predictivity. Yet, these are far from orthogonal. We sought to explore how these inform each other in sub-genome-wide signifi…
View article: Effectiveness of Generative Artificial Intelligence for Scientific Content Analysis
Effectiveness of Generative Artificial Intelligence for Scientific Content Analysis Open
Generative artificial intelligence (GenAI) in general, and large language models (LLMs) in particular, are highly fashionable. As they have the ability to generate coherent output based on prompts in natural language, they are promoted as …
View article: Towards quantum-enabled cell-centric therapeutics
Towards quantum-enabled cell-centric therapeutics Open
In recent years, there has been tremendous progress in the development of quantum computing hardware, algorithms and services leading to the expectation that in the near future quantum computers will be capable of performing simulations fo…
View article: The impact of forced displacement: trauma, increased levels of inflammation and early presentation of diabetes in women Syrian refugees
The impact of forced displacement: trauma, increased levels of inflammation and early presentation of diabetes in women Syrian refugees Open
Background Forced displacement and war trauma cause high rates of post-traumatic stress, anxiety disorders and depression in refugee populations. We investigated the impact of forced displacement on mental health status, gender, presentati…
View article: Informational Rescaling of PCA Maps with Application to Genetic Distance
Informational Rescaling of PCA Maps with Application to Genetic Distance Open
We discuss the inadequacy of covariances/correlations and other measures in L2 as relative distance metrics under some conditions. We propose a computationally simple heuristic to transform a map based on standard principal component analy…
View article: Role of genetics in capturing racial disparities in cardiovascular disease
Role of genetics in capturing racial disparities in cardiovascular disease Open
The role of race in medical decision-making has been a contentious issue. Insights from history and population genetics suggest considering race as a differentiating marker for medical practices can be influenced by systemic bias, leading …
View article: Elevated Lp(a) Levels Correlate with Severe and Multiple Coronary Artery Stenotic Lesions
Elevated Lp(a) Levels Correlate with Severe and Multiple Coronary Artery Stenotic Lesions Open
Cynthia Al Hageh,1,* Stephanie Chacar,2,* Michella Ghassibe-Sabbagh,3 Daniel E Platt,4 Andreas Henschel,5 Hamdan Hamdan,2 Dominique Gauguier,6,7 Yara El Murr,3 Eman Alefishat,8,9 Elie Chammas,10 Siobhán O’Sullivan,1 An…
View article: Topology and redescriptions detect multiple alternative biological pathways from clinical phenotypes
Topology and redescriptions detect multiple alternative biological pathways from clinical phenotypes Open
Biological pathways play a crucial role in the properties of diseases and are important in drug discovery. Identifying the logical relationships among distinctive phenotypic clusters could reveal possible connections to the underlying path…
View article: K3 surfaces with two involutions and low Picard number
K3 surfaces with two involutions and low Picard number Open
Let $X$ be a complex algebraic K3 surface of degree $2d$ and with Picard number $ρ$. Assume that $X$ admits two commuting involutions: one holomorphic and one anti-holomorphic. In that case, $ρ\geq 1$ when $d=1$ and $ρ\geq 2$ when $d \geq …
View article: Observational study of factors associated with morbidity and mortality from COVID-19 in Lebanon, 2020–2021
Observational study of factors associated with morbidity and mortality from COVID-19 in Lebanon, 2020–2021 Open
Background The COVID-19 pandemic claimed millions of lives worldwide without clear signs of abating despite several mitigation efforts and vaccination campaigns. There have been tremendous interests in understanding the etiology of the dis…
View article: Creatinine levels on admission are main modulators of COVID-19 severity
Creatinine levels on admission are main modulators of COVID-19 severity Open
Background: The COVID-19 pandemic claimed millions of lives worldwide without clear signs of abating. There have been tremendous interests in understanding the etiology of the disease particularly in what makes it fatal in certain patients…
View article: Epidemiological topology data analysis links severe COVID-19 to RAAS and hyperlipidemia associated metabolic syndrome conditions
Epidemiological topology data analysis links severe COVID-19 to RAAS and hyperlipidemia associated metabolic syndrome conditions Open
The emergence of COVID19 created incredible worldwide challenges but offers unique opportunities to understand the physiology of its risk factors and their interactions with complex disease conditions, such as metabolic syndrome. Epidemiol…
View article: Group invariant machine learning by fundamental domain projections
Group invariant machine learning by fundamental domain projections Open
We approach the well-studied problem of supervised group invariant and equivariant machine learning from the point of view of geometric topology. We propose a novel approach using a pre-processing step, which involves projecting the input …
View article: K-Mer Analyses Reveal Different Evolutionary Histories of Alpha, Beta, and Gamma Papillomaviruses
K-Mer Analyses Reveal Different Evolutionary Histories of Alpha, Beta, and Gamma Papillomaviruses Open
Papillomaviruses (PVs) are a heterogeneous group of DNA viruses that can infect fish, birds, reptiles, and mammals. PVs infecting humans (HPVs) phylogenetically cluster into five genera (Alpha-, Beta-, Gamma-, Mu- and Nu-PV), with differen…
View article: CuNA: Cumulant-based Network Analysis of genotype-phenotype associations in Parkinson’s Disease
CuNA: Cumulant-based Network Analysis of genotype-phenotype associations in Parkinson’s Disease Open
Parkinson’s Disease (PD) is a progressive neurodegenerative movement disorder characterized by loss of striatal dopaminergic neurons. Progression of PD is usually captured by a host of clinical features represented in different rating scal…
View article: Multiple Loci Selection with Multi-Way Epistasis in Coalescence with Recombination
Multiple Loci Selection with Multi-Way Epistasis in Coalescence with Recombination Open
As studies move into deeper characterization of the impact of selection through non-neutral mutations in whole genome population genetics, modeling for selection becomes crucial. Moreover, epistasis has long been recognized as a significan…
View article: RubricOE: a learning framework for genetic epidemiology
RubricOE: a learning framework for genetic epidemiology Open
Genetic epidemiology is a growing area of interest in the past years due to the availability of genetic data with the decreasing cost of sequencing. Machine learning (ML) algorithms can be a very useful tool to study the genetic factors on…
View article: Multiple Loci Selection with Multi-way Epistasis in Coalescence with Recombination
Multiple Loci Selection with Multi-way Epistasis in Coalescence with Recombination Open
As studies move into deeper characterization of the impact of selection through non-neutral mutations in whole genome population genetics, modeling for selection becomes crucial. Moreover, epistasis has long been recognized as a significan…
View article: Inferring COVID-19 Biological Pathways from Clinical Phenotypes via Topological Analysis
Inferring COVID-19 Biological Pathways from Clinical Phenotypes via Topological Analysis Open
COVID-19 has caused thousands of deaths around the world and also resulted in a large international economic disruption. Identifying the pathways associated with this illness can help medical researchers to better understand the properties…
View article: Integrating Linguistics, Social Structure, and Geography to Model Genetic Diversity within India
Integrating Linguistics, Social Structure, and Geography to Model Genetic Diversity within India Open
India represents an intricate tapestry of population substructure shaped by geography, language, culture, and social stratification. Although geography closely correlates with genetic structure in other parts of the world, the strict endog…
View article: Lies, Gosh Darn Lies, and not enough good statistics: why epidemic model parameter estimation fails
Lies, Gosh Darn Lies, and not enough good statistics: why epidemic model parameter estimation fails Open
We sought to investigate whether epidemiological parameters that define epidemic models could be determined from the epidemic trajectory of infections, recovery, and hospitalizations prior to peak, and also to evaluate the comparability of…