相关论文: HAlign-II: efficient ultra-large multiple sequence…
Quantifying axon and myelin properties (e.g., axon diameter, myelin thickness, g-ratio) in histology images can provide useful information about microstructural changes caused by neurodegenerative diseases. Automatic tissue segmentation is…
We develop a method for improving the parallel scalability of the recently developed parallel selected inversion algorithm [Jacquelin, Lin and Yang 2014], named PSelInv, on massively parallel distributed memory machines. In the PSelInv…
Multiple Sequence Alignment (MSA) plays a pivotal role in unveiling the evolutionary trajectories of protein families. The accuracy of protein structure predictions is often compromised for protein sequences that lack sufficient homologous…
The rising demand for Large Language Model (LLM) inference services has intensified pressure on computational resources, resulting in latency and cost challenges. This paper introduces a novel routing algorithm based on the Non-dominated…
One approach in phylogenomics to infer the tree of life is based on concatenated multiple sequence alignments from many genes. Unfortunately, the resulting so-called supermatrix is usually sparse, that is, not every gene sequence is…
Innovations in Next-Generation Sequencing are enabling generation of DNA sequence data at ever faster rates and at very low cost. Large sequencing centers typically employ hundreds of such systems. Such high-throughput and low-cost…
We present a generative framework for inverse design of five-layer transmissive Huygens' metasurfaces (HMSs), addressing a longstanding challenge in achieving full-phase, high-efficiency unit cell designs with minimal full-wave simulations.…
Multiple sequence alignment is a basic procedure in molecular biology, and it is often treated as being essentially a solved computational problem. However, this is not so, and here I review the evidence for this claim, and outline the…
The reconstruction of phylogenetic networks is an important but challenging problem in phylogenetics and genome evolution, as the space of phylogenetic networks is vast and cannot be sampled well. One approach to the problem is to solve the…
Multiple sequence alignments (MSAs) of proteins encode rich biological information and have been workhorses in bioinformatic methods for tasks like protein design and protein structure prediction for decades. Recent breakthroughs like…
The translation of comparative genomics into clinical decision support tools often depends on the quality of sequence alignments. However, currently used methods of multiple sequence alignments suffer from significant biases and problems…
We compare different methods for sampling from discrete probability distributions and introduce a new algorithm which is especially efficient on massively parallel processors, such as GPUs. The scheme preserves the distribution properties…
Recently, a framework considering RNA sequences and their RNA secondary structures as pairs, led to some information-theoretic perspectives on how the semantics encoded in RNA sequences can be inferred. In this context, the pairing arises…
A Supertree synthesizes the topologies of a set of phylogenetic trees carrying overlapping taxa set. In process, conflicts in the tree topologies are aimed to be resolved with the consensus clades. Such a problem is proved to be NP-hard.…
Multitask learning is a widely recognized technique in the field of computer vision and deep learning domain. However, it is still a research question in remote sensing, particularly for hyperspectral imaging. Moreover, most of the research…
In this paper, we study the parallel query complexity of reconstructing biological and digital phylogenetic trees from simple queries involving their nodes. This is motivated from computational biology, data protection, and computer…
Heterogeneous information networks (HIN) have gained increasing popularity in recent years for capturing complex relations between diverse types of nodes. Meta-structures are proposed as a useful tool to identify the important patterns in…
Computational pathology (CPath) has significantly advanced the clinical practice of pathology. Despite the progress made, Multiple Instance Learning (MIL), a promising paradigm within CPath, continues to face challenges, particularly…
This paper presents an efficient method to perform Structured Matrix Approximation by Separation and Hierarchy (SMASH), when the original dense matrix is associated with a kernel function. Given points in a domain, a tree structure is first…
We present an Evolutionary Placement Algorithm (EPA) for the rapid assignment of sequence fragments (short reads) to branches of a given phylogenetic tree under the Maximum Likelihood (ML) model. The accuracy of the algorithm is evaluated…