Related papers: Finding low-complexity DNA sequences with longdust
We argue that there are two major distinct capabilities in long context understanding: retrieval and holistic understanding. Understanding and further improving LLMs' long context capabilities would not be possible without knowing the…
This commentary discusses a recently proposed measure of heterogeneity of DNA sequences and compares with the measures of complexity.
Relation classification is associated with many potential applications in the artificial intelligence area. Recent approaches usually leverage neural networks based on structure features such as syntactic or dependency features to solve…
DNA storage technology offers new possibilities for addressing massive data storage due to its high storage density, long-term preservation, low maintenance cost, and compact size. To improve the reliability of stored information, base…
The so called long range correlation properties of DNA sequences are studied using the variance analyses of the density distribution of a single or a group of nucleotides in a model independent way. This new method which was suggested…
Discovering fine-grained categories from coarsely labeled data is a practical and challenging task, which can bridge the gap between the demand for fine-grained analysis and the high annotation cost. Previous works mainly focus on…
We study the sample complexity of learning one-hidden-layer convolutional neural networks (CNNs) with non-overlapping filters. We propose a novel algorithm called approximate gradient descent for training CNNs, and show that, with high…
Feature selection is an important and challenging task in high dimensional clustering. For example, in genomics, there may only be a small number of genes that are differentially expressed, which are informative to the overall clustering…
In this paper we address the problem of discovering a small set of frequent serial episodes from sequential data so as to adequately characterize or summarize the data. We discuss an algorithm based on the Minimum Description Length (MDL)…
Finding the densest subgraph (DS) from a graph is a fundamental problem in graph databases. The DS obtained, which reveals closely related entities, has been found to be useful in various application domains such as e-commerce, social…
DNA synthesis is considered as one of the most expensive components in current DNA storage systems. In this paper, focusing on a common synthesis machine, which generates multiple DNA strands in parallel following a fixed supersequence,we…
Length generalization remains a persistent challenge for neural networks: recurrent models tend to suffer from positional biases, while transformers are constrained by fixed computational depth. Regular languages provide a frequently used…
Current advanced long-context language models offer great potential for real-world software engineering applications. However, progress in this critical domain remains hampered by a fundamental limitation: the absence of a rigorous…
We define the complexity of DNA sequences as the information content per nucleotide, calculated by means of some Lempel-Ziv data compression algorithm. It is possible to use the statistics of the complexity values of the functional regions…
In computational biology and bioinformatics, the manner to understand evolution processes within various related organisms paid a lot of attention these last decades. However, accurate methodologies are still needed to discover genes…
Large Language Models (LLMs) have demonstrated remarkable capabilities in comprehending and analyzing lengthy sequential inputs, owing to their extensive context windows that allow processing millions of tokens in a single forward pass.…
Due to its higher data density, longevity, energy efficiency, and ease of generating copies, DNA is considered a promising storage technology for satisfying future needs. However, a diverse set of errors including deletions, insertions,…
Research on text simplification has primarily focused on lexical and sentence-level changes. Long document-level simplification (DS) is still relatively unexplored. Large Language Models (LLMs), like ChatGPT, have excelled in many natural…
In this paper, we investigate the complexity of one-dimensional dynamic programming, or more specifically, of the Least-Weight Subsequence (LWS) problem: Given a sequence of $n$ data items together with weights for every pair of the items,…
This note provides very simple, efficient algorithms for computing the number of distinct longest common subsequences of two input strings and for computing the number of LCS embeddings.