Related papers: New strategies to improve minimap2 alignment accur…
Behavioral alignment in large language models (LLMs) is often achieved through broad fine-tuning, which can result in undesired side effects like distributional shift and low interpretability. We propose a method for alignment that…
Summary: BWA-MEM is a new alignment algorithm for aligning sequence reads or long query sequences against a large reference genome such as human. It automatically chooses between local and end-to-end alignments, supports paired-end reads…
We outline a procedure for jointly sampling substitution matrices and multiple sequence alignments, according to an approximate posterior distribution, using an MCMC-based algorithm. This procedure provides an efficient and simple method by…
Deep features have been proven powerful in building accurate dense semantic correspondences in various previous works. However, the multi-scale and pyramidal hierarchy of convolutional neural networks has not been well studied to learn…
We study the relation between streaming algorithms and linear sketching algorithms, in the context of binary updates. We show that for inputs in $n$ dimensions, the existence of efficient streaming algorithms which can process $\Omega(n^2)$…
Various methods have been developed to analyze the association between organisms and their genomic sequences. Among them, sequence alignment is the most frequently used for comparative analysis of biological genomes. However, the…
Learning in the reproducing kernel Hilbert space (RKHS) such as the support vector machine has been recognized as a promising technique. It continues to be highly effective and competitive in numerous prediction tasks, particularly in…
Collecting large-scale medical datasets with fine-grained annotations is time-consuming and requires experts. For this reason, weakly supervised learning aims at optimising machine learning models using weaker forms of annotations, such as…
In the last decade a number of algorithms and associated software have been developed to align next generation sequencing (NGS) reads with relevant reference genomes. The accuracy of these programs may vary significantly, especially when…
Pyro-Align is a multiple alignment program specifically designed for pyrosequencing reads of huge number. Multiple sequence alignment is shown to be NP-hard and heuristics are designed for approximate solutions. Multiple sequence alignment…
Prior to deep learning the semantic parsing community has been interested in understanding and modeling the range of possible word alignments between natural language sentences and their corresponding meaning representations.…
The proliferation of high-throughput sequencing machines ensures rapid generation of up to billions of short nucleotide fragments in a short period of time. This massive amount of sequence data can quickly overwhelm today's storage and…
Although massive pre-trained vision-language models like CLIP show impressive generalization capabilities for many tasks, still it often remains necessary to fine-tune them for improved performance on specific datasets. When doing so, it is…
The way for performing multiple sequence alignment is based on the criterion of the maximum scored information content computed from a weight matrix, but it is possible to have two or more alignments to have the same highest score leading…
In this work, we aim to calibrate the score outputs of an estimator for the binary classification problem by finding an 'optimal' mapping to class probabilities, where the 'optimal' mapping is in the sense that minimizes the classification…
In this paper, we present an adaptive bitextual alignment system called AIlign. This aligner relies on sentence embeddings to extract reliable anchor points that can guide the alignment path, even for texts whose parallelism is fragmentary…
To tackle the exponentially increasing throughput of Next-Generation Sequencing (NGS), most of the existing short-read aligners can be configured to favor speed in trade of accuracy and sensitivity. SOAP3-dp, through leveraging the…
In this paper, we present a novel algorithm to address the Network Alignment problem. It is inspired from a previous message passing framework of Bayati et al. [2] and includes several modifications designed to significantly speed up the…
In the fast developing countries it is hard to trace new buildings construction or old structures destruction and, as a result, to keep the up-to-date cadastre maps. Moreover, due to the complexity of urban regions or inconsistency of data…
The rapidly changing landscape of sequencing technologies brings new opportunities to genomics research. Longer sequence reads and higher sequence throughput coupled with ever-improving base accuracy and decreasing per-base cost is now…