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Post-training quantization (PTQ) of large language models (LLMs) holds the promise in reducing the prohibitive computational cost at inference time. Quantization of all weight, activation and key-value (KV) cache tensors to 4-bit without…
Deep neural networks based on linear RNNs interleaved with position-wise MLPs are gaining traction as competitive approaches for sequence modeling. Examples of such architectures include state-space models (SSMs) like S4, LRU, and Mamba:…
Quantization of Deep Neural Network (DNN) activations is a commonly used technique to reduce compute and memory demands during DNN inference, which can be particularly beneficial on resource-constrained devices. To achieve high accuracy,…
For $q$-ary $n$-sequences, we develop the concept of similarity functions that can be used (for $q=4$) to model a thermodynamic similarity on DNA sequences. A similarity function is identified by the length of a longest common subsequence…
High dimensionality poses many challenges to the use of data, from visualization and interpretation, to prediction and storage for historical preservation. Techniques abound to reduce the dimensionality of fixed-length sequences, yet these…
Recurrence Quantification Analysis (RQA) is a widely used method for capturing the dynamical structure embedded in time series data, relying on the analysis of recurrence patterns in the reconstructed phase space via recurrence plots (RPs).…
Question Answering (QA) has proved to be an arduous challenge in the area of natural language processing (NLP) and artificial intelligence (AI). Many attempts have been made to develop complete solutions for QA as well as improving…
In this paper we treat some fractal and statistical features of the DNA sequences. First, a fractal record model of DNA sequence is proposed by mapping DNA sequences to integer sequences, followed by R/S analysis of the model and…
Non-coding RNA are functional molecules that are not translated into proteins. Their function comes as important regulators of biological function. Because they are not translated, they need not be as stable as other types of RNA. The TKF91…
A recent study by one of the authors has demonstrated the importance of profile vectors in DNA-based data storage. We provide exact values and lower bounds on the number of profile vectors for finite values of alphabet size $q$, read length…
The recurrence times between extreme events have been the central point of statistical analyses in many different areas of science. Simultaneously, the Poincar\'e recurrence time has been extensively used to characterize nonlinear dynamical…
Recurrence rate, determinism, average line length, and entropy of line lengths are measures of complexity in recurrence quantification analysis, that help to understand the structure, predictability and complexity of dynamical systems. In…
The emerging field of epigenetics has recently unveiled a dynamic landscape in which gene expression is not determined solely by genetic sequences but also by intricate regulatory mechanisms. This review examines the interactions between…
Recurrent Neural Networks (RNNs), and specifically a variant with Long Short-Term Memory (LSTM), are enjoying renewed interest as a result of successful applications in a wide range of machine learning problems that involve sequential data.…
Nowadays, when crashes and crises are rather frequent events, an effective monitoring system for the international financial market is needed. Modern nonlinear methods, such as Recurrence Quantification Analysis (RQA), demonstrate the…
Recent work has sought to understand the behavior of neural networks by comparing representations between layers and between different trained models. We examine methods for comparing neural network representations based on canonical…
Generalizing beyond the experiences has a significant role in developing practical AI systems. It has been shown that current Visual Question Answering (VQA) models are over-dependent on the language-priors (spurious correlations between…
High-throughput mRNA sequencing (RNA-Seq) is widely used for transcript quantification of gene isoforms. Since RNA-Seq data alone is often not sufficient to accurately identify the read origins from the isoforms for quantification, we…
During the last couple of years, Recurrent Neural Networks (RNN) have reached state-of-the-art performances on most of the sequence modelling problems. In particular, the "sequence to sequence" model and the neural CRF have proved to be…
DNA is subject to large deformations in a wide range of biological processes. Two key examples illustrate how such deformations influence the readout of the genetic information: the sequestering of eukaryotic genes by nucleosomes, and DNA…