Related papers: GENEOnet: Statistical analysis supporting explaina…

Structural changes in a network representation of a system (e.g.,different experimental conditions, time evolution), can provide insight on its organization, function and on how it responds to external perturbations. The deeper…

Many physical processes in science and engineering are naturally represented by operators between infinite-dimensional function spaces. The problem of operator learning, in this context, seeks to extract these physical processes from…

As the societal impact of Deep Neural Networks (DNNs) grows, the goals for advancing DNNs become more complex and diverse, ranging from improving a conventional model accuracy metric to infusing advanced human virtues such as fairness,…

While machine learning techniques have been successfully applied in several fields, the black-box nature of the models presents challenges for interpreting and explaining the results. We develop a new framework called Adaptive Explainable…

Explainable Artificial Intelligence (xAI) has the potential to enhance the transparency and trust of AI-based systems. Although accurate predictions can be made using Deep Neural Networks (DNNs), the process used to arrive at such…

Gene expression-based heterogeneity analysis has been extensively conducted. In recent studies, it has been shown that network-based analysis, which takes a system perspective and accommodates the interconnections among genes, can be more…

Although very successfully used in conventional machine learning, convolution based neural network architectures -- believed to be inconsistent in function space -- have been largely ignored in the context of learning solution operators of…

There has recently been a surge of work in explanatory artificial intelligence (XAI). This research area tackles the important problem that complex machines and algorithms often cannot provide insights into their behavior and thought…

Ensemble learning is a general technique to improve accuracy in machine learning. However, the heavy computation of a ConvNets ensemble limits its usage in deep learning. In this paper, we present Group Ensemble Network (GENet), an…

Explainable artificial intelligence (XAI) can help foster trust in and acceptance of intelligent and autonomous systems. Moreover, understanding the motivation for an agent's behavior results in better and more successful collaborations…

Group equivariant neural networks have been explored in the past few years and are interesting from theoretical and practical standpoints. They leverage concepts from group representation theory, non-commutative harmonic analysis and…

Graph Neural Networks (GNNs) are powerful models that can manage complex data sources and their interconnection links. One of GNNs' main drawbacks is their lack of interpretability, which limits their application in sensitive fields. In…

The traditional role of the network layer is to create an end-to-end route, through which the intermediate nodes replicate and forward the packets towards the destination. This role can be radically redefined by exploiting the power of…

Artificial intelligence methods are being increasingly applied across various domains, but their often opaque nature has raised concerns about accountability and trust. In response, the field of explainable AI (XAI) has emerged to address…

Deep learning-based AI models have been extensively applied in genomics, achieving remarkable success across diverse applications. As these models gain prominence, there exists an urgent need for interpretability methods to establish…

The last decade has witnessed a surge of theoretical and computational models to describe the dynamics of complex gene regulatory networks, and how these interactions can give rise to multistable and heterogeneous cell populations. As the…

Bioinformatics tools have been developed to interpret gene expression data at the gene set level, and these gene set based analyses improve the biologists' capability to discover functional relevance of their experiment design. While…

Graph Neural Networks (GNNs) excel in graph-based learning tasks, but their complex, non-linear operations often render them as opaque "black boxes". This opacity hinders user trust, complicates debugging, bias detection, and adoption in…

The application of deep learning methods, particularly foundation models, in biological research has surged in recent years. These models can be text-based or trained on underlying biological data, especially omics data of various types.…

Generative Adversarial Networks (GANs) have been used in many different applications to generate realistic synthetic data. We introduce a novel GAN with Autoencoder (GAN-AE) architecture to generate synthetic samples for variable length,…