Related papers: Minimum error correction-based haplotype assembly:…
Scanning Transmission Electron Microscopy (STEM) offers high-resolution images that are used to quantify the nanoscale atomic structure and composition of materials and biological specimens. In many cases, however, the resolution is limited…
Reproducibility in genome-wide association studies (GWAS) is crucial for ensuring reliable genomic research outcomes. However, limited access to original genomic datasets (mainly due to privacy concerns) prevents researchers from…
Realizing the full potential of quantum computation requires Quantum Error Correction (QEC). QEC reduces error rates by encoding logical information across redundant physical qubits, enabling errors to be detected and corrected. A common…
The electrical property (EP) of human tissues is a quantitative biomarker that facilitates early diagnosis of cancerous tissues. Magnetic resonance electrical properties tomography (MREPT) is an imaging modality that reconstructs EPs by the…
Microarray technology is known as one of the most important tools for collecting DNA expression data. This technology allows researchers to investigate and examine types of diseases and their origins. However, microarray data are often…
De novo genome assembly is challenging in highly repetitive regions; however, reference-guided assemblers often suffer from bias. We propose a framework for pangenome-guided sequence assembly, which can resolve short-read data in complex…
Microfluidic devices offer numerous advantages in medical applications, including the capture of single cells in microwell-based platforms for genomic analysis. As the cost of sequencing decreases, the demand for high-throughput single-cell…
Uncertainty quantification in deep-learning (DL) based image reconstruction models is critical for reliable clinical decision making based on the reconstructed images. We introduce "NPB-REC", a non-parametric fully Bayesian framework for…
Reliable inference from complex survey samples can be derailed by outliers and high-leverage observations induced by unequal inclusion probabilities and calibration. We develop a minimum Hellinger distance estimator (MHDE) for parametric…
Sparse Autoencoders (SAEs) are a prominent tool in mechanistic interpretability (MI) for decomposing neural network activations into interpretable features. However, the aspiration to identify a canonical set of features is challenged by…
The Linear Representation Hypothesis asserts that the embeddings learned by neural networks can be understood as linear combinations of features corresponding to high-level concepts. Based on this ansatz, sparse autoencoders (SAEs) have…
Convolutional network-error correcting codes (CNECCs) are known to provide error correcting capability in acyclic instantaneous networks within the network coding paradigm under small field size conditions. In this work, we investigate the…
We present two results about using allele-count (AC) burdens of rare SNPs discovered in a case-control sequencing study for prediction or validation in an external prospective study. When genotyping only the SNPs polymorphic in the sequence…
Low-dimensional embeddings for data from disparate sources play critical roles in multi-modal machine learning, multimedia information retrieval, and bioinformatics. In this paper, we propose a supervised dimensionality reduction method…
Nested sampling is a promising tool for Bayesian statistical analysis because it simultaneously performs parameter estimation and facilitates model comparison. MultiNest is one of the most popular nested sampling implementations, and has…
Compressed sensing, which involves the reconstruction of sparse signals from an under-determined linear system, has been recently used to solve problems in group testing. In a public health context, group testing aims to determine the…
The paper studies the problem of recovering a spectrally sparse object from a small number of time domain samples. Specifically, the object of interest with ambient dimension $n$ is assumed to be a mixture of $r$ complex multi-dimensional…
Understanding genetic variation, e.g., through mutations, in organisms is crucial to unravel their effects on the environment and human health. A fundamental characterization can be obtained by solving the haplotype assembly problem, which…
In this study, we propose HOPER (HOlistic ProtEin Representation), a novel multimodal learning framework designed to enhance protein function prediction (PFP) in low-data settings. The challenge of predicting protein functions is compounded…
As feature sizes shrink to the nanometer scale, accurately transferring circuit patterns from photomasks to silicon wafers becomes increasingly challenging. Optical proximity correction (OPC) is widely used to ensure pattern fidelity and…