相关论文: Waiting for regulatory sequences to appear

Eukaryotic DNA replication follows a specific temporal program, with some genomic regions consistently replicating earlier than others, yet what determines this program is largely unknown. Highly transcribed regions have been observed to…

The inverse relationship between the length of a word and the frequency of its use, first identified by G.K. Zipf in 1935, is a classic empirical law that holds across a wide range of human languages. We demonstrate that length is one…

It is staggering that words of the English language, which are on average represented by 5--6 bytes of ASCII, require as much as 24 kilobytes when served to large language models. We show that there is room for more information in every…

Word frequency is assumed to correlate with word familiarity, but the strength of this correlation has not been thoroughly investigated. In this paper, we report on our analysis of the correlation between a word familiarity rating list…

We show that confidence intervals in a variance component model, with asymptotically correct uniform coverage probability, can be obtained by inverting certain test-statistics based on the score for the restricted likelihood. The results…

Designing short DNA words is a problem of constructing a set (i.e., code) of n DNA strings (i.e., words) with the minimum length such that the Hamming distance between each pair of words is at least k and the n words satisfy a set of…

The genome-wide recombination rate ($RR$) of a species is often described by one parameter, the ratio between total genetic map length ($G$) and physical map length ($P$), measured in centiMorgans per Megabase (cM/Mb). The value of this…

Standard decoding strategies for text generation, including top-k, nucleus sampling, and contrastive search, select tokens based on likelihood, restricting selection to high-probability regions. Human language production operates…

We investigate how neural language models acquire individual words during training, extracting learning curves and ages of acquisition for over 600 words on the MacArthur-Bates Communicative Development Inventory (Fenson et al., 2007).…

Using human evaluation of 100,000 words spread across 24 corpora in 10 languages diverse in origin and culture, we present evidence of a deep imprint of human sociality in language, observing that (1) the words of natural human language…

We refine a uniform algebraic approach for deriving upper bounds on reset thresholds of synchronizing automata. We express the condition that an automaton is synchronizing in terms of linear algebra, and obtain upper bounds for the reset…

The emergence of discourse-like tokens such as "wait" and "therefore" in large language models (LLMs) has offered a unique window into their reasoning processes. However, systematic analyses of how such signals vary across training…

We analyze the occurrence frequencies of over 15 million words recorded in millions of books published during the past two centuries in seven different languages. For all languages and chronological subsets of the data we confirm that two…

Fix two words over the binary alphabet $\{0,1\}$, and generate iid Bernoulli$(p)$ bits until one of the words occurs in sequence. This setup, commonly known as Penney's ante, was popularized by Conway, who found (in unpublished work) a…

Recursive processing in sentence comprehension is considered a hallmark of human linguistic abilities. However, its underlying neural mechanisms remain largely unknown. We studied whether a modern artificial neural network trained with…

We study here the so called subsequence pattern matching also known as hidden pattern matching in which one searches for a given pattern $w$ of length $m$ as a subsequence in a random text of length $n$. The quantity of interest is the…

We study the complexity of the problem of searching for a set of patterns that separate two given sets of strings. This problem has applications in a wide variety of areas, most notably in data mining, computational biology, and in…

To maintain coherence in language, the brain must satisfy key competing temporal demands: the gradual accumulation of meaning across extended context (drift) and the rapid reconfiguration of representations at event boundaries (shift). How…

Language models, especially transformer-based ones, have achieved colossal success in NLP. To be precise, studies like BERT for NLU and works like GPT-3 for NLG are very important. If we consider DNA sequences as a text written with an…

Motivated by DNA data storage, we study the expected number of coded symbols drawn from a linear code until a desired information symbol can be decoded - the random access expectation. We focus on generator matrices with a type of symmetry,…