Related papers: Reducing Boolean Networks with Backward Boolean Eq…
Boolean networks are dynamical models of disease development in which the activation levels of genes are represented by binary variables. Given a Boolean network, controls represent mutations or medical treatments that fix the activation…
Since their introduction, Boolean networks have been traditionally studied in view of their rich dynamical behavior under different update protocols and for their qualitative analogy with cell regulatory networks. More recently, tools…
Bayesian networks (BN) are used in a big range of applications but they have one issue concerning parameter learning. In real application, training data are always incomplete or some nodes are hidden. To deal with this problem many learning…
Annotating the right data for training deep neural networks is an important challenge. Active learning using uncertainty estimates from Bayesian Neural Networks (BNNs) could provide an effective solution to this. Despite being theoretically…
Boolean control networks (BCNs) are discrete-time dynamical systems with Boolean state-variables and inputs that are interconnected via Boolean functions. BCNs are recently attracting considerable interest as computational models for…
In this work, we study scaling limits of shallow Bayesian neural networks (BNNs) via their connection to Gaussian processes (GPs), with an emphasis on statistical modeling, identifiability, and scalable inference. We first establish a…
Progress in cell type reprogramming has revived the interest in Waddington's concept of the epigenetic landscape. Recently researchers developed the quasi-potential theory to represent the Waddington's landscape. The Quasi-potential U(x),…
Modern neural networks have proven to be powerful function approximators, providing state-of-the-art performance in a multitude of applications. They however fall short in their ability to quantify confidence in their predictions - this is…
Restricted Boltzmann Machines (RBMs) are a class of generative neural network that are typically trained to maximize a log-likelihood objective function. We argue that likelihood-based training strategies may fail because the objective does…
Variational Bayesian neural networks (BNNs) perform variational inference over weights, but it is difficult to specify meaningful priors and approximate posteriors in a high-dimensional weight space. We introduce functional variational…
A Bayesian Network (BN) is a probabilistic model that represents a set of variables using a directed acyclic graph (DAG). Current algorithms for learning BN structures from data focus on estimating the edges of a specific DAG, and often…
We introduce a new method for learning Bayesian neural networks, treating them as a stack of multivariate Bayesian linear regression models. The main idea is to infer the layerwise posterior exactly if we know the target outputs of each…
We apply a Gaussian variational approximation to model reduction in large biochemical networks of unary and binary reactions. We focus on a small subset of variables (subnetwork) of interest, e.g. because they are accessible experimentally,…
Compared to point estimates calculated by standard neural networks, Bayesian neural networks (BNN) provide probability distributions over the output predictions and model parameters, i.e., the weights. Training the weight distribution of a…
Batch Normalization (BN) techniques have been proposed to reduce the so-called Internal Covariate Shift (ICS) by attempting to keep the distributions of layer outputs unchanged. Experiments have shown their effectiveness on training deep…
A Bayesian network is a widely used probabilistic graphical model with applications in knowledge discovery and prediction. Learning a Bayesian network (BN) from data can be cast as an optimization problem using the well-known…
While deep neural networks are highly performant and successful in a wide range of real-world problems, estimating their predictive uncertainty remains a challenging task. To address this challenge, we propose and implement a loss function…
Convolutional neural networks (CNNs) work well on large datasets. But labelled data is hard to collect, and in some applications larger amounts of data are not available. The problem then is how to use CNNs with small data -- as CNNs…
Fragmentation methods such as the many-body expansion (MBE) are a common strategy to model large systems by partitioning energies into a hierarchy of decreasingly significant contributions. The number of fragments required for chemical…
Many complex systems in biology, physics, and engineering include a large number of state-variables, and measuring the full state of the system is often impossible. Typically, a set of sensors is used to measure part of the state-variables.…