Related papers: Recurrent Neural Network Based Hybrid Model of Gen…

In the last few years, Recurrent Neural Networks (RNNs) have proved effective on several NLP tasks. Despite such great success, their ability to model \emph{sequence labeling} is still limited. This lead research toward solutions where RNNs…

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…

Model discovery based on existing data has been one of the major focuses of mathematical modelers for decades. Despite tremendous achievements of model identification from adequate data, how to unravel the models from limited data is less…

Dynamic treatment recommendation systems based on large-scale electronic health records (EHRs) become a key to successfully improve practical clinical outcomes. Prior relevant studies recommend treatments either use supervised learning…

In many real-world applications, fully-differentiable RNNs such as LSTMs and GRUs have been widely deployed to solve time series learning tasks. These networks train via Backpropagation Through Time, which can work well in practice but…

Gene regulatory relationships can be abstracted as a gene regulatory network (GRN), which plays a key role in characterizing complex cellular processes and pathways. Recently, graph neural networks (GNNs), as a class of deep learning…

Delays in protein synthesis cause a confounding effect when constructing Gene Regulatory Networks (GRNs) from RNA-sequencing time-series data. Accurate GRNs can be very insightful when modelling development, disease pathways, and drug…

The main goal of Systems Biology research is to reconstruct biological networks for its topological analysis so that reconstructed networks can be used for the identification of various kinds of disease. The availability of high-throughput…

A core technology that has emerged from the artificial intelligence revolution is the recurrent neural network (RNN). Its unique sequence-based architecture provides a tractable likelihood estimate with stable training paradigms, a…

The recent development of artificial intelligence (AI) technology, especially the advance of deep neural network (DNN) technology, has revolutionized many fields. While DNN plays a central role in modern AI technology, it has been rarely…

This paper presents a novel approach to advancing artificial intelligence (AI) through the development of the Complex Recurrent Spectral Network ($\mathbb{C}$-RSN), an innovative variant of the Recurrent Spectral Network (RSN) model. The…

Recurrent neural networks (RNNs) are a popular choice for modeling sequential data. Modern RNN architectures assume constant time-intervals between observations. However, in many datasets (e.g. medical records) observation times are…

Recurrent neural networks (RNNs) are known to be difficult to train due to the gradient vanishing and exploding problems and thus difficult to learn long-term patterns and construct deep networks. To address these problems, this paper…

Recurrent Neural Networks (RNNs) are a class of machine learning algorithms used for applications with time-series and sequential data. Recently, there has been a strong interest in executing RNNs on embedded devices. However, difficulties…

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…

Data-driven control methods need to be sample-efficient and lightweight, especially when data acquisition and computational resources are limited -- such as during learning on hardware. Most modern data-driven methods require large datasets…

Obesity is a serious public health concern world-wide, which increases the risk of many diseases, including hypertension, stroke, and type 2 diabetes. To tackle this problem, researchers across the health ecosystem are collecting diverse…

Gene regulatory networks (GRNs) orchestrate cellular decision making and survival strategies. Inferring the structure of these networks from high-dimensional transcriptomics data is a central challenge in systems biology. Traditional…

This paper presents the Jump Markov Filtering Network (JMFNet), a novel model-based deep learning framework for real-time state-state estimation in jump Markov systems with unknown noise statistics and mode transition dynamics. A hybrid…

Recurrent Neural Networks (RNNs) are popular models of brain function. The typical training strategy is to adjust their input-output behavior so that it matches that of the biological circuit of interest. Even though this strategy ensures…