Related papers: Finding low-complexity DNA sequences with longdust
The ever-increasing fine-tuning cost of large-scale pre-trained models gives rise to the importance of dataset pruning, which aims to reduce dataset size while maintaining task performance. However, existing dataset pruning methods require…
Lung cancer is the leading cause of cancer deaths. Early detection through low-dose computed tomography (CT) screening has been shown to significantly reduce mortality but suffers from a high false positive rate that leads to unnecessary…
This article introduces a new DNA sequence compression algorithm which is based on LUT and LZ77 algorithm. Combined a LUT-based pre-coding routine and LZ77 compression routine,this algorithm can approach a compression ratio of 1.9bits…
In forensic genetics, short tandem repeats (STRs) are used for human identification (HID). Degraded biological trace samples with low amounts of short DNA fragments (low-quality DNA samples) pose a challenge for STR typing. Predefined…
Recently, lattice-reduction-aided detectors have been proposed for multiple-input multiple-output (MIMO) systems to give performance with full diversity like maximum likelihood receiver, and yet with complexity similar to linear receivers.…
We propose a recursive lattice reduction framework for finding short non-zero vectors or dense sublattices of a lattice. The framework works by recursively searching for dense sublattices of dense sublattices (or their duals) with…
Trained on massive cross-species DNA corpora, DNA large language models (LLMs) learn the fundamental "grammar" and evolutionary patterns of genomic sequences. This makes them powerful priors for DNA sequence modeling, particularly over long…
In the recent years, DNA has emerged as a potentially viable storage technology. DNA synthesis, which refers to the task of writing the data into DNA, is perhaps the most costly part of existing storage systems. Accordingly, this high cost…
This paper demonstrates the utility of organized numerical representations of genes in research involving flat string gene formats (i.e., FASTA/FASTQ5). FASTA/FASTQ files have several current limitations, such as their large file sizes,…
Data represented as strings abounds in biology, linguistics, document mining, web search and many other fields. Such data often have a hierarchical structure, either because they were artificially designed and composed in a hierarchical…
We propose a low-complexity method to find quasi-cyclic low-density parity-check block codes with girth 10 or 12 and shorter length than those designed through classical approaches. The method is extended to time-invariant spatially coupled…
Existing benchmarks for evaluating long-context language models (LCLMs) primarily focus on long-context recall, requiring models to produce short responses based on a few critical snippets while processing thousands of irrelevant tokens. We…
Text line detection is a key task in historical document analysis facing many challenges of arbitrary-shaped text lines, dense texts, and text lines with high aspect ratios, etc. In this paper, we propose a general framework for historical…
Fast and effective unsupervised anomaly detection algorithms have been proposed for categorical data based on the minimum description length (MDL) principle. However, they can be ineffective when detecting anomalies in heterogeneous…
Due to their sequential nature, traditional DNA synthesis methods are expensive in terms of time and resources. They also fabricate multiple copies of the same strand, introducing redundancy. This redundancy can be leveraged to enhance the…
The determination of block-entropies is a well established method for the investigation of discrete data, also called symbols (7). There is a large variety of such symbolic sequences, ranging from texts written in natural languages,…
Tools that effectively analyze and compare sequences are of great importance in various areas of applied computational research, especially in the framework of molecular biology. In the present paper, we introduce simple geometric criteria…
At the core of high throughput DNA sequencing platforms lies a bio-physical surface process that results in a random geometry of clusters of homogenous short DNA fragments typically hundreds of base pairs long - bridge amplification. The…
The explosive growth of large language models (LLMs) has created a vast but opaque landscape: millions of models exist, yet their evolutionary relationships through fine-tuning, distillation, or adaptation are often undocumented or unclear,…
An ideal outcome of pattern mining is a small set of informative patterns, containing no redundancy or noise, that identifies the key structure of the data at hand. Standard frequent pattern miners do not achieve this goal, as due to the…