Related papers: Recurrent Neural Network Based Modeling of Gene Re…

The behaviour of gene regulatory networks (GRNs) is typically analysed using simulation-based statistical testing-like methods. In this paper, we demonstrate that we can replace this approach by a formal verification-like method that gives…

Binary neural networks (BNNs) have received ever-increasing popularity for their great capability of reducing storage burden as well as quickening inference time. However, there is a severe performance drop compared with real-valued…

We propose a genetic algorithm (GA) for hyperparameter optimization of artificial neural networks which includes chromosomal crossover as well as a decoupling of parameters (i.e., weights and biases) from hyperparameters (e.g., learning…

We introduce Active Tuning, a novel paradigm for optimizing the internal dynamics of recurrent neural networks (RNNs) on the fly. In contrast to the conventional sequence-to-sequence mapping scheme, Active Tuning decouples the RNN's…

A genetic algorithm (GA) is a search method that optimises a population of solutions by simulating natural evolution. Good solutions reproduce together to create better candidates. The standard GA assumes that any two solutions can mate.…

This paper presents a new algorithm, Evolutionary eXploration of Augmenting Memory Models (EXAMM), which is capable of evolving recurrent neural networks (RNNs) using a wide variety of memory structures, such as Delta-RNN, GRU, LSTM, MGU…

Recurrent Neural Networks are powerful machine learning frameworks that allow for data to be saved and referenced in a temporal sequence. This opens many new possibilities in fields such as handwriting analysis and speech recognition. This…

It has been estimated that about 30% of the genes in the human genome are regulated by microRNAs (miRNAs). These are short RNA sequences that can down-regulate the levels of mRNAs or proteins in animals and plants. Genes regulated by miRNAs…

Understanding, predicting, and generating object motions and transformations is a core problem in artificial intelligence. Modeling sequences of evolving images may provide better representations and models of motion and may ultimately be…

We introduce a deep residual recurrent neural network (DR-RNN) as an efficient model reduction technique for nonlinear dynamical systems. The developed DR-RNN is inspired by the iterative steps of line search methods in finding the residual…

Data are often sampled irregularly in time. Dealing with this using Recurrent Neural Networks (RNNs) traditionally involved ignoring the fact, feeding the time differences as additional inputs, or resampling the data. All these methods have…

A recurrent Neural Network (RNN) is trained to predict sound samples based on audio input augmented by control parameter information for pitch, volume, and instrument identification. During the generative phase following training, audio…

In this work, we present a quantum circuit model for inferring gene regulatory networks (GRNs). The model is based on the idea of using qubit-qubit entanglement to simulate interactions between genes. We provide preliminary results that…

Recurrent Neural Networks (RNNs) are commonly used for real-time processing, streaming data, and cases where the amount of training samples is limited. Backpropagation Through Time (BPTT) is the predominant algorithm for training RNNs;…

Reconstructing transcriptional regulatory networks is an important task in functional genomics. Data obtained from experiments that perturb genes by knockouts or RNA interference contain useful information for addressing this reconstruction…

The goal of this tutorial is to promote interest in the study of random Boolean networks (RBNs). These can be very interesting models, since one does not have to assume any functionality or particular connectivity of the networks to study…

Transformers have surpassed RNNs in popularity due to their superior abilities in parallel training and long-term dependency modeling. Recently, there has been a renewed interest in using linear RNNs for efficient sequence modeling. These…

How to properly model graphs is a long-existing and important problem in NLP area, where several popular types of graphs are knowledge graphs, semantic graphs and dependency graphs. Comparing with other data structures, such as sequences…

Reconstructing the causal network in a complex dynamical system plays a crucial role in many applications, from sub-cellular biology to economic systems. Here we focus on inferring gene regulation networks (GRNs) from perturbation or gene…

Gene Regulatory Network (GRN) inference is essential for understanding complex cellular mechanisms, rendered tractable through single-cell transcriptomic data. With the emergence of single-cell Foundation Models (scFMs), enhanced…