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Article
Open AccessAlterations in colorectal cancer virome and its persistence after surgery
Viruses are a key component of the colon microbiome, but the relationship between virome and colorectal cancer (CRC) remains poorly understood. We seek to identify alterations in the viral community that is ch...
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Article
Open AccessEvolutionary shift detection with ensemble variable selection
Abrupt environmental changes can lead to evolutionary shifts in trait evolution. Identifying these shifts is an important step in understanding the evolutionary history of phenotypes. The detection performance...
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Article
Adaptive group Lasso neural network models for functions of few variables and time-dependent data
Learning nonlinear functions from time-varying measurements is always difficult due to the high correlation among observations. This task is more challenging when the target function is high dimensional. In th...
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Article
SPADE4: Sparsity and Delay Embedding Based Forecasting of Epidemics
Predicting the evolution of diseases is challenging, especially when the data availability is scarce and incomplete. The most popular tools for modelling and predicting infectious disease epidemics are compart...
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Article
When can we reconstruct the ancestral state? Beyond Brownian motion
Reconstructing the ancestral state of a group of species helps answer many important questions in evolutionary biology. Therefore, it is crucial to understand when we can estimate the ancestral state accuratel...
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Article
Ancestral state reconstruction with large numbers of sequences and edge-length estimation
Likelihood-based methods are widely considered the best approaches for reconstructing ancestral states. Although much effort has been made to study properties of these methods, previous works often assume that...
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Article
Open AccessCharacterization of oral virome and microbiome revealed distinctive microbiome disruptions in paediatric patients with hand, foot and mouth disease
While the underlying determinants are unclear, hand, foot and mouth disease (HFMD) presents a wide spectrum of clinical manifestations with varying severity in different individuals. Recently, many studies ide...
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Article
On the convergence of the maximum likelihood estimator for the transition rate under a 2-state symmetric model
Maximum likelihood estimators are used extensively to estimate unknown parameters of stochastic trait evolution models on phylogenetic trees. Although the MLE has been proven to converge to the true value in t...
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Article
Birth/birth-death processes and their computable transition probabilities with biological applications
Birth-death processes track the size of a univariate population, but many biological systems involve interaction between populations, necessitating models for two or more populations simultaneously. A lack of ...
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Article
Phase transition on the convergence rate of parameter estimation under an Ornstein–Uhlenbeck diffusion on a tree
Diffusion processes on trees are commonly used in evolutionary biology to model the joint distribution of continuous traits, such as body mass, across species. Estimating the parameters of such processes from ...
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Chapter and Conference Paper
Naturalistic Human-Robot Interaction Design for Control of Unmanned Ground Vehicles
This study explored the effectiveness of multi-modal interaction techniques to enable dismounted soldiers to manage their digital information systems and Unmanned Ground Vehicles (UGV) in urban environments. T...
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Chapter and Conference Paper
Learning from Non-iid Data: Fast Rates for the One-vs-All Multiclass Plug-in Classifiers
We prove new fast learning rates for the one-vs-all multiclass plug-in classifiers trained either from exponentially strongly mixing data or from data generated by a converging drifting distribution. These are...
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Chapter and Conference Paper
Correlation of Aberrant Methylation of APC Gene to MTHFR C677T Genetic Polymorphisms in Hepatic Carcinoma
Object To investigate the relationship between aberrant hypermethylation of APC gene and methylenetetrahydrofolate reductase (MTHFR) C677T genetic polymorphisms in Hepatic Carcinoma. Method Hepatic...
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Chapter and Conference Paper
Generalization and Robustness of Batched Weighted Average Algorithm with V-Geometrically Ergodic Markov Data
We analyze the generalization and robustness of the batched weighted average algorithm for V-geometrically ergodic Markov data. This algorithm is a good alternative to the empirical risk minimization algorithm...
