Related papers: Fast Exact String to D-Texts Alignments
Recent work shows that Sparse Autoencoders (SAE) applied to large language model (LLM) layers have neurons corresponding to interpretable concepts. These SAE neurons can be modified to align generated outputs, but only towards…
Domain adaptive retrieval aims to transfer knowledge from a labeled source domain to an unlabeled target domain, enabling effective retrieval while mitigating domain discrepancies. However, existing methods encounter several fundamental…
Recently, a compressed index for similar strings, called the FM-index of alignment (FMA), has been proposed with the functionalities of pattern search and random access. The FMA is quite efficient in space requirement and pattern search…
State-of-the-art text-to-image models produce visually impressive results but often struggle with precise alignment to text prompts, leading to missing critical elements or unintended blending of distinct concepts. We propose a novel…
Currently, third-generation sequencing techniques, which allow to obtain much longer DNA reads compared to the next-generation sequencing technologies, are becoming more and more popular. There are many possibilities to combine data from…
One of the most computationally intensive tasks in computational biology is de novo genome assembly, the decoding of the sequence of an unknown genome from redundant and erroneous short sequences. A common assembly paradigm identifies…
We propose a new linear-size data structure which provides a fast access to all palindromic substrings of a string or a set of strings. This structure inherits some ideas from the construction of both the suffix trie and suffix tree. Using…
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…
The alignment of biological networks has the potential to teach us as much about biology and disease as has sequence alignment. Sequence alignment can be optimally solved in polynomial time. In contrast, network alignment is $NP$-hard,…
In this paper we present $LCSk$++: a new metric for measuring the similarity of long strings, and provide an algorithm for its efficient computation. With ever increasing size of strings occuring in practice, e.g. large genomes of plants…
We introduce string2string, an open-source library that offers a comprehensive suite of efficient algorithms for a broad range of string-to-string problems. It includes traditional algorithmic solutions as well as recent advanced neural…
Genomic data I used in many fields but, it has become known that most of the platforms used in the sequencing process produce significant errors. This means that the analysis and inferences generated from these data may have some errors…
Earlier formulations of the DNA assembly problem were all in the context of perfect assembly; i.e., given a set of reads from a long genome sequence, is it possible to perfectly reconstruct the original sequence? In practice, however, it is…
In the String Matching in Labeled Graphs (SMLG) problem, we need to determine whether a pattern string appears on a given labeled graph or a given automaton. Under the Orthogonal Vectors hypothesis, the SMLG problem cannot be solved in…
Heterogeneous domain adaptation (HDA) transfers knowledge across source and target domains that present heterogeneities e.g., distinct domain distributions and difference in feature type or dimension. Most previous HDA methods tackle this…
Since the completion of the human genome sequencing project in 2001, significant progress has been made in areas such as gene regulation editing and protein structure prediction. However, given the vast amount of genomic data, the segments…
We revisit classic string problems considered in the area of parameterized complexity, and study them through the lens of dynamic data structures. That is, instead of asking for a static algorithm that solves the given instance efficiently,…
Graph-based learning excels at capturing interaction patterns in diverse domains like recommendation, fraud detection, and particle physics. However, its performance often degrades under distribution shifts, especially those altering…
The main goal of this research is to produce a useful software for United Nations (UN), that could help to speed up the process of qualifying the UN documents following the Sustainable Development Goals (SDGs) in order to monitor the…
DNA read mapping is a computationally expensive bioinformatics task, required for genome assembly and consensus polishing. It requires to find the best-fitting location for each DNA read on a long reference sequence. A novel resistive…