Goto

Collaborating Authors

Causal Queries from Observational Data in Biological Systems via Bayesian Networks: An Empirical Study in Small Networks

arXiv.org Machine Learning

Biological networks are a very convenient modelling and visualisation tool to discover knowledge from modern high-throughput genomics and postgenomics data sets. Indeed, biological entities are not isolated, but are components of complex multi-level systems. We go one step further and advocate for the consideration of causal representations of the interactions in living systems.We present the causal formalism and bring it out in the context of biological networks, when the data is observational. We also discuss its ability to decipher the causal information flow as observed in gene expression. We also illustrate our exploration by experiments on small simulated networks as well as on a real biological data set.


The Big Three: A Methodology to Increase Data Science ROI by Answering the Questions Companies Care About

arXiv.org Machine Learning

Companies may be achieving only a third of the value they could be getting from data science in industry applications. In this paper, we propose a methodology for categorizing and answering 'The Big Three' questions (what is going on, what is causing it, and what actions can I take that will optimize what I care about) using data science. The applications of data science seem to be nearly endless in today's modern landscape, with each company jockeying for position in the new data and insights economy. Yet, data scientists seem to be solely focused on using classification, regression, and clustering methods to answer the question 'what is going on'. Answering questions about why things are happening or how to take optimal actions to improve metrics are relegated to niche fields of research and generally neglected in industry data science analysis. We survey technical methods to answer these other important questions, describe areas in which some of these methods are being applied, and provide a practical example of how to apply our methodology and selected methods to a real business use case.


A Primer on Causal Analysis

arXiv.org Machine Learning

We provide a conceptual map to navigate causal analysis problems. Focusing on the case of discrete random variables, we consider the case of causal effect estimation from observational data. The presented approaches apply also to continuous variables, but the issue of estimation becomes more complex. We then introduce the four schools of thought for causal analysis


Playing against Nature: causal discovery for decision making under uncertainty

arXiv.org Artificial Intelligence

We consider decision problems under uncertainty where the options available to a decision maker and the resulting outcome are related through a causal mechanism which is unknown to the decision maker. We ask how a decision maker can learn about this causal mechanism through sequential decision making as well as using current causal knowledge inside each round in order to make better choices had she not considered causal knowledge and propose a decision making procedure in which an agent holds \textit{beliefs} about her environment which are used to make a choice and are updated using the observed outcome. As proof of concept, we present an implementation of this causal decision making model and apply it in a simple scenario. We show that the model achieves a performance similar to the classic Q-learning while it also acquires a causal model of the environment.


The Cognitive Processing of Causal Knowledge

arXiv.org Artificial Intelligence

There is a brief description of the probabilistic causal graph model for representing, reasoning with, and learning causal structure using Bayesian networks. It is then argued that this model is closely related to how humans reason with and learn causal structure. It is shown that studies in psychology on discounting (reasoning concerning how the presence of one cause of an effect makes another cause less probable) support the hypothesis that humans reach the same judgments as algorithms for doing inference in Bayesian networks. Next, it is shown how studies by Piaget indicate that humans learn causal structure by observing the same independencies and dependencies as those used by certain algorithms for learning the structure of a Bayesian network. Based on this indication, a subjective definition of causality is forwarded. Finally, methods for further testing the accuracy of these claims are discussed.