Related papers: Lightweight merging of compressed indices based on…
Advances in DNA sequencing technology have stimulated the development of algorithms and tools for processing very large collections of short strings (reads). Short-read alignment and assembly are among the most well-studied problems. Many…
Given a weighted bipartite graph $G = (L, R, E, w)$, the maximum weight matching (MWM) problem seeks to find a matching $M \subseteq E$ that maximizes the total weight $\sum_{e \in M} w(e)$. This paper presents a novel algorithm with a time…
Model merging aims to build a multi-task learner by combining the parameters of individually fine-tuned models without additional training. While a straightforward approach is to average model parameters across tasks, this often results in…
Data-centric ML pipelines extend traditional machine learning (ML) pipelines -- of feature transformations and ML model training -- by outer loops for data cleaning, augmentation, and feature engineering to create high-quality input data.…
Bitmap indexes must be compressed to reduce input/output costs and minimize CPU usage. To accelerate logical operations (AND, OR, XOR) over bitmaps, we use techniques based on run-length encoding (RLE), such as Word-Aligned Hybrid (WAH)…
This paper explores learned image compression based on traditional and learned discrete wavelet transform (DWT) architectures and learned entropy models for coding DWT subband coefficients. A learned DWT is obtained through the lifting…
A standard format used for storing the output of high-throughput sequencing experiments is the FASTQ format. It comprises three main components: (i) headers, (ii) bases (nucleotide sequences), and (iii) quality scores. FASTQ files are…
Constructing the Burrows-Wheeler transform (BWT) for long strings poses significant challenges regarding construction time and memory usage. We use a prefix of the suffix array to partition a long string into shorter substrings, thereby…
Fitting mixed models to complex survey data is a challenging problem. Most methods in the literature, including the most widely used one, require a close relationship between the model structure and the survey design. In this paper we…
The compression of highly repetitive strings (i.e., strings with many repetitions) has been a central research topic in string processing, and quite a few compression methods for these strings have been proposed thus far. Among them, an…
Biomedical entity linking aims to map biomedical mentions, such as diseases and drugs, to standard entities in a given knowledge base. The specific challenge in this context is that the same biomedical entity can have a wide range of names,…
Multivariate polynomials arise in many different disciplines. Representing such a polynomial as a vector of univariate polynomials can offer useful insight, as well as more intuitive understanding. For this, techniques based on tensor…
In this paper, we consider the problem of compressing a trie while supporting the powerful \emph{locate} queries: to return the pre-order identifiers of all nodes reached by a path labeled with a given query pattern. Our result builds on…
We introduce a simple yet effective method of integrating contextual embeddings with commonsense graph embeddings, dubbed BERT Infused Graphs: Matching Over Other embeDdings. First, we introduce a preprocessing method to improve the speed…
Directional interpolation is a fast and efficient compression technique for high-frequency Helmholtz boundary integral equations, but it requires a very large amount of storage in its original form. Algebraic recompression can significantly…
The Lempel-Ziv factorization (LZ77) and the Run-Length encoded Burrows-Wheeler Transform (RLBWT) are two important tools in text compression and indexing, being their sizes $z$ and $r$ closely related to the amount of text…
Bearing data compression is vital to manage the large volumes of data generated during condition monitoring. In this paper, a novel asymmetrical autoencoder with a lifting wavelet transform (LWT) layer is developed to compress bearing…
Finding low-weight multiples of a binary polynomial is a difficult problem arising in the context of stream ciphers cryptanalysis. The classical algorithm to solve this problem is based on a time memory trade-off. We will present an…
Inverted indexes are vital in providing fast key-word-based search. For every term in the document collection, a list of identifiers of documents in which the term appears is stored, along with auxiliary information such as term frequency,…
This paper proposes a clustering and merging approach for the Poisson multi-Bernoulli mixture (PMBM) filter to lower its computational complexity and make it suitable for multiple target tracking with a high number of targets. We define a…