Related papers: Human Genome Book: Words, Sentences and Paragraphs
Recent advances in DNA sequencing technologies have put ubiquitous availability of fully sequenced human genomes within reach. It is no longer hard to imagine the day when everyone will have the means to obtain and store one's own DNA…
DNA language models are increasingly used to represent genomic sequence, yet their effectiveness depends critically on how raw nucleotides are converted into model inputs. Unlike natural language, DNA offers no canonical boundaries, making…
The amount of sequence data obtained from ancient samples has dramatically expanded in the last decade, and so have the types of questions that can now be addressed using ancient DNA. In the field of human history, while ancient DNA has…
In recent years, the sequencing, assembling and annotation of prokaryotic genomes has become increasingly easy and cheap. Thus it becomes increasingly feasible and interesting to perform comparative genomics analyses of new genomes to those…
We present a novel corpus of 445 human- and computer-generated documents, comprising about 27,000 clauses, annotated for semantic clause types and coherence relations that allow for nuanced comparison of artificial and natural discourse…
This research introduces a novel psychometric method for analyzing textual data using large language models. By leveraging contextual embeddings to create contextual scores, we transform textual data into response data suitable for…
It takes several years for the developing brain of a baby to fully master word repetition-the task of hearing a word and repeating it aloud. Repeating a new word, such as from a new language, can be a challenging task also for adults.…
Machine-translated text plays an important role in modern life by smoothing communication from various communities using different languages. However, unnatural translation may lead to misunderstanding, a detector is thus needed to avoid…
This study evaluates the performance of Recurrent Neural Network (RNN) and Transformer models in replicating cross-language structural priming, a key indicator of abstract grammatical representations in human language processing. Focusing…
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…
Over the past several years, DNA sequencing has emerged as one of the driving forces in life-sciences, paving the way for affordable and accurate whole genome sequencing. As genomes represent the entirety of an organism's hereditary…
The comparative genomics revolution of the past decade has enabled the discovery of functional elements in the human genome via sequence comparison. While that is so, an important class of elements, those specific to humans, is entirely…
Emerging topics in biomedical research are continuously expanding, providing a wealth of information about genes and their function. This rapid proliferation of knowledge presents unprecedented opportunities for scientific discovery and…
The present article is the first of a series whose goal is to define a logical formalism in which it is possible to reason about genetics. In this paper, we introduce the main concepts of our language whose domain of discourse consists of a…
Language modeling has seen impressive progress over the last years, mainly prompted by the invention of the Transformer architecture, sparking a revolution in many fields of machine learning, with breakthroughs in chemistry and biology. In…
Sentence Embedding stands as a fundamental task within the realm of Natural Language Processing, finding extensive application in search engines, expert systems, and question-and-answer platforms. With the continuous evolution of large…
Genome sequencing is the basis for many modern biological and medicinal studies. With recent technological advances, metagenomics has become a problem of interest. This problem entails the analysis and reconstruction of multiple DNA…
Gene enhancers control when and where genes switch on, yet their sequence diversity and tissue specificity make them hard to pinpoint in colorectal cancer. We take a sequence-only route and fine-tune DNABERT-2, a transformer genomic…
De novo assembly is the process of reconstructing the genome sequence of an organism from sequencing reads. Genome sequences are essential to biology, and assembly has been a central problem in bioinformatics for four decades. Until…
Recent advances in large language models (LLMs) have made significant progress across multiple biomedical tasks, including biomedical question answering, lay-language summarization of the biomedical literature, and clinical note…