News media has been utilized as a political tool to stray from facts, presenting biased claims without evidence. Amid the COVID-19 pandemic, politically biased news (PBN) has significantly undermined public trust in vaccines, despite strong medical evidence supporting their efficacy. In this paper, we analyze: (i) how inherent vaccine stances subtly influence individuals' selection of news sources and participation in social media discussions; and (ii) the impact of exposure to PBN on users' attitudes toward vaccines. In doing so, we first curate a comprehensive dataset that connects PBN with related social media discourse. Utilizing advanced deep learning and causal inference techniques, we reveal distinct user behaviors between social media groups with various vaccine stances. Moreover, we observe that individuals with moderate stances, particularly the vaccine-hesitant majority, are more vulnerable to the influence of PBN compared to those with extreme views. Our findings provide critical insights to foster this line of research.

Cellular reprogramming can be used for both the prevention and cure of different diseases. However, the efficiency of discovering reprogramming strategies with classical wet-lab experiments is hindered by lengthy time commitments and high costs. In this study, we develop a novel computational framework based on deep reinforcement learning that facilitates the identification of reprogramming strategies. For this aim, we formulate a control problem in the context of cellular reprogramming for the frameworks of BNs and PBNs under the asynchronous update mode. Furthermore, we introduce the notion of a pseudo-attractor and a procedure for identification of pseudo-attractor state during training. Finally, we devise a computational framework for solving the control problem, which we test on a number of different models.

The projected belief network (PBN) is a generative stochastic network with tractable likelihood function based on a feed-forward neural network (FFNN). The generative function operates by "backing up" through the FFNN. The PBN is two networks in one, a FFNN that operates in the forward direction, and a generative network that operates in the backward direction. Both networks co-exist based on the same parameter set, have their own cost functions, and can be separately or jointly trained. The PBN therefore has the potential to possess the best qualities of both discriminative and generative classifiers. To realize this potential, a separate PBN is trained on each class, maximizing the generative likelihood function for the given class, while minimizing the discriminative cost for the FFNN against "all other classes". This technique, called discriminative alignment (PBN-DA), aligns the contours of the likelihood function to the decision boundaries and attains vastly improved classification performance, rivaling that of state of the art discriminative networks. The method may be further improved using a hidden Markov model (HMM) as a component of the PBN, called PBN-DA-HMM. This paper provides a comprehensive treatment of PBN, PBN-DA, and PBN-DA-HMM. In addition, the results of two new classification experiments are provided. The first experiment uses air-acoustic events, and the second uses underwater acoustic data consisting of marine mammal calls. In both experiments, PBN-DA-HMM attains comparable or better performance as a state of the art CNN, and attain a factor of two error reduction when combined with the CNN.

The problem of Novel Class Discovery (NCD) consists in extracting knowledge from a labeled set of known classes to accurately partition an unlabeled set of novel classes. While NCD has recently received a lot of attention from the community, it is often solved on computer vision problems and under unrealistic conditions. In particular, the number of novel classes is usually assumed to be known in advance, and their labels are sometimes used to tune hyperparameters. Methods that rely on these assumptions are not applicable in real-world scenarios. In this work, we focus on solving NCD in tabular data when no prior knowledge of the novel classes is available. To this end, we propose to tune the hyperparameters of NCD methods by adapting the $k$-fold cross-validation process and hiding some of the known classes in each fold. Since we have found that methods with too many hyperparameters are likely to overfit these hidden classes, we define a simple deep NCD model. This method is composed of only the essential elements necessary for the NCD problem and performs impressively well under realistic conditions. Furthermore, we find that the latent space of this method can be used to reliably estimate the number of novel classes. Additionally, we adapt two unsupervised clustering algorithms ($k$-means and Spectral Clustering) to leverage the knowledge of the known classes. Extensive experiments are conducted on 7 tabular datasets and demonstrate the effectiveness of the proposed method and hyperparameter tuning process, and show that the NCD problem can be solved without relying on knowledge from the novel classes.

Downstream applications often require text classification models to be accurate, robust, and interpretable. While the accuracy of the stateof-the-art language models approximates human performance, they are not designed to be interpretable and often exhibit a drop in performance on noisy data. The family of PrototypeBased Networks (PBNs) that classify examples based on their similarity to prototypical examples of a class (prototypes) is natively interpretable and shown to be robust to noise, which enabled its wide usage for computer vision tasks. In this paper, we study whether the robustness properties of PBNs transfer to text classification tasks. We design a modular and comprehensive framework for studying PBNs, which includes different backbone architectures, backbone sizes, and objective functions. Our evaluation protocol assesses the robustness of models against character-, word-, and sentence-level perturbations. Our experiments on three benchmarks show that the robustness of PBNs transfers to NLP classification tasks facing realistic perturbations. Moreover, the robustness of PBNs is supported mostly by the objective function that keeps prototypes interpretable, while the robustness superiority of PBNs over vanilla models becomes more salient as datasets get more complex.

This paper presents alternative techniques for inference on classical Bayesian networks in which all probabilities are fixed, and for synthesis problems when conditional probability tables (CPTs) in such networks contain symbolic parameters rather than concrete probabilities. The key idea is to exploit probabilistic model checking as well as its recent extension to parameter synthesis techniques for parametric Markov chains. To enable this, the Bayesian networks are transformed into Markov chains and their objectives are mapped onto probabilistic temporal logic formulas. For exact inference, we compare probabilistic model checking to weighted model counting on various Bayesian network benchmarks. We contrast symbolic model checking using multi-terminal binary (aka: algebraic) decision diagrams to symbolic inference using proba- bilistic sentential decision diagrams, symbolic data structures that are tailored to Bayesian networks. For the parametric setting, we describe how our techniques can be used for various synthesis problems such as computing sensitivity functions (and values), simple and difference parameter tuning and ratio parameter tuning. Our parameter synthesis techniques are applicable to arbitrarily many, possibly dependent, parameters that may occur in multiple CPTs. This lifts restrictions, e.g., on the number of parametrized CPTs, or on parameter dependencies between several CPTs, that exist in the literature. Experiments on several benchmarks show that our parameter synthesis techniques can treat parameter synthesis for Bayesian networks (with hundreds of unknown parameters) that are out of reach for existing techniques.

This paper addresses the $\epsilon$-close parameter tuning problem for Bayesian Networks (BNs): find a minimal $\epsilon$-close amendment of probability entries in a given set of (rows in) conditional probability tables that make a given quantitative constraint on the BN valid. Based on the state-of-the-art "region verification" techniques for parametric Markov chains, we propose an algorithm whose capabilities go beyond any existing techniques. Our experiments show that $\epsilon$-close tuning of large BN benchmarks with up to 8 parameters is feasible. In particular, by allowing (i) varied parameters in multiple CPTs and (ii) inter-CPT parameter dependencies, we treat subclasses of parametric BNs that have received scant attention so far.

Probabilistic Boolean Networks have been proposed for estimating the behaviour of dynamical systems as they combine rule-based modelling with uncertainty principles. Inferring PBNs directly from gene data is challenging however, especially when data is costly to collect and/or noisy, e.g., in the case of gene expression profile data. In this paper, we present a reproducible method for inferring PBNs directly from real gene expression data measurements taken when the system was at a steady state. The steady-state dynamics of PBNs is of special interest in the analysis of biological machinery. The proposed approach does not rely on reconstructing the state evolution of the network, which is computationally intractable for larger networks. We demonstrate the method on samples of real gene expression profiling data from a well-known study on metastatic melanoma. The pipeline is implemented using Python and we make it publicly available.

The ability to direct a Probabilistic Boolean Network (PBN) to a desired state is important to applications such as targeted therapeutics in cancer biology. Reinforcement Learning (RL) has been proposed as a framework that solves a discrete-time optimal control problem cast as a Markov Decision Process. We focus on an integrative framework powered by a model-free deep RL method that can address different flavours of the control problem (e.g., with or without control inputs; attractor state or a subset of the state space as the target domain). The method is agnostic to the distribution of probabilities for the next state, hence it does not use the probability transition matrix. The time complexity is linear on the time steps, or interactions between the agent (deep RL) and the environment (PBN), during training. Indeed, we explore the scalability of the deep RL approach to (set) stabilization of large-scale PBNs and demonstrate successful control on large networks, including a metastatic melanoma PBN with 200 nodes.

This paper proposes various new analysis techniques for Bayes networks in which conditional probability tables (CPTs) may contain symbolic variables. The key idea is to exploit scalable and powerful techniques for synthesis problems in parametric Markov chains. Our techniques are applicable to arbitrarily many, possibly dependent parameters that may occur in various CPTs. This lifts the severe restrictions on parameters, e.g., by restricting the number of parametrized CPTs to one or two, or by avoiding parameter dependencies between several CPTs, in existing works for parametric Bayes networks (pBNs). We describe how our techniques can be used for various pBN synthesis problems studied in the literature such as computing sensitivity functions (and values), simple and difference parameter tuning, ratio parameter tuning, and minimal change tuning. Experiments on several benchmarks show that our prototypical tool built on top of the probabilistic model checker Storm can handle several hundreds of parameters.