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Register a new userHow do some Bayesian Network machine learned graphs compare to causal knowledge?
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Anthony Constantinou
Publication date
2021
fields
Informatics Engineering
and research's language is
English
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The graph of a Bayesian Network (BN) can be machine learned, determined by causal knowledge, or a combination of both. In disciplines like bioinformatics, applying BN structure learning algorithms can reveal new insights that would otherwise remain unknown. However, these algorithms are less effective when the input data are limited in terms of sample size, which is often the case when working with real data. This paper focuses on purely machine learned and purely knowledge-based BNs and investigates their differences in terms of graphical structure and how well the implied statistical models explain the data. The tests are based on four previous case studies whose BN structure was determined by domain knowledge. Using various metrics, we compare the knowledge-based graphs to the machine learned graphs generated from various algorithms implemented in TETRAD spanning all three classes of learning. The results show that, while the algorithms produce graphs with much higher model selection score, the knowledge-based graphs are more accurate predictors of variables of interest. Maximising score fitting is ineffective in the presence of limited sample size because the fitting becomes increasingly distorted with limited data, guiding algorithms towards graphical patterns that share higher fitting scores and yet deviate considerably from the true graph. This highlights the value of causal knowledge in these cases, as well as the need for more appropriate fitting scores suitable for limited data. Lastly, the experiments also provide new evidence that support the notion that results from simulated data tell us little about actual real-world performance.
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Bayesian Networks (BNs) have become a powerful technology for reasoning under uncertainty, particularly in areas that require causal assumptions that enable us to simulate the effect of intervention. The graphical structure of these models can be determined by causal knowledge, learnt from data, or a combination of both. While it seems plausible that the best approach in constructing a causal graph involves combining knowledge with machine learning, this approach remains underused in practice. We implement and evaluate 10 knowledge approaches with application to different case studies and BN structure learning algorithms available in the open-source Bayesys structure learning system. The approaches enable us to specify pre-existing knowledge that can be obtained from heterogeneous sources, to constrain or guide structure learning. Each approach is assessed in terms of structure learning effectiveness and efficiency, including graphical accuracy, model fitting, complexity, and runtime; making this the first paper that provides a comparative evaluation of a wide range of knowledge approaches for BN structure learning. Because the value of knowledge depends on what data are available, we illustrate the results both with limited and big data. While the overall results show that knowledge becomes less important with big data due to higher learning accuracy rendering knowledge less important, some of the knowledge approaches are actually found to be more important with big data. Amongst the main conclusions is the observation that reduced search space obtained from knowledge does not always imply reduced computational complexity, perhaps because the relationships implied by the data and knowledge are in tension.
Knowledge bases (KB) constructed through information extraction from text play an important role in query answering and reasoning. In this work, we study a particular reasoning task, the problem of discovering causal relationships between entities, known as causal discovery. There are two contrasting types of approaches to discovering causal knowledge. One approach attempts to identify causal relationships from text using automatic extraction techniques, while the other approach infers causation from observational data. However, extractions alone are often insufficient to capture complex patterns and full observational data is expensive to obtain. We introduce a probabilistic method for fusing noisy extractions with observational data to discover causal knowledge. We propose a principled approach that uses the probabilistic soft logic (PSL) framework to encode well-studied constraints to recover long-range patterns and consistent predictions, while cheaply acquired extractions provide a proxy for unseen observations. We apply our method gene regulatory networks and show the promise of exploiting KB signals in causal discovery, suggesting a critical, new area of research.
N-body simulations are widely used to simulate the dynamical evolution of a variety of systems, among them star clusters. Much of our understanding of their evolution rests on the results of such direct N-body simulations. They provide insight in the structural evolution of star clusters, as well as into the occurrence of stellar exotica. Although the major pure N-body codes STARLAB/KIRA and NBODY4 are widely used for a range of applications, there is no thorough comparison study yet. Here we thoroughly compare basic quantities as derived from simulations performed either with STARLAB/KIRA or NBODY4. We construct a large number of star cluster models for various stellar mass function settings (but without stellar/binary evolution, primordial binaries, external tidal fields etc), evolve them in parallel with STARLAB/KIRA and NBODY4, analyse them in a consistent way and compare the averaged results quantitatively. For this quantitative comparison we develop a bootstrap algorithm for functional dependencies. We find an overall excellent agreement between the codes, both for the clusters structural and energy parameters as well as for the properties of the dynamically created binaries. However, we identify small differences, like in the energy conservation before core collapse and the energies of escaping stars, which deserve further studies. Our results reassure the comparability and the possibility to combine results from these two major N-body codes, at least for the purely dynamical models (i.e. without stellar/binary evolution) we performed. (abridged)
Commonsense knowledge acquisition is a key problem for artificial intelligence. Conventional methods of acquiring commonsense knowledge generally require laborious and costly human annotations, which are not feasible on a large scale. In this paper, we explore a practical way of mining commonsense knowledge from linguistic graphs, with the goal of transferring cheap knowledge obtained with linguistic patterns into expensive commonsense knowledge. The result is a conversion of ASER [Zhang et al., 2020], a large-scale selectional preference knowledge resource, into TransOMCS, of the same representation as ConceptNet [Liu and Singh, 2004] but two orders of magnitude larger. Experimental results demonstrate the transferability of linguistic knowledge to commonsense knowledge and the effectiveness of the proposed approach in terms of quantity, novelty, and quality. TransOMCS is publicly available at: https://github.com/HKUST-KnowComp/TransOMCS.
We address in this study the problem of learning a summary causal graph on time series with potentially different sampling rates. To do so, we first propose a new temporal mutual information measure defined on a window-based representation of time series. We then show how this measure relates to an entropy reduction principle that can be seen as a special case of the Probabilistic Raising Principle. We finally combine these two ingredients in a PC-like algorithm to construct the summary causal graph. This algorithm is evaluated on several datasets that shows both its efficacy and efficiency.
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