scholarly journals Graphical models for machine learning and digital communication

1999 ◽  
Vol 37 (3) ◽  
pp. 133
2011 ◽  
Vol 37 (1) ◽  
pp. 231-248 ◽  
Author(s):  
Daniel Gildea

We describe the application of the graph-theoretic property known as treewidth to the problem of finding efficient parsing algorithms. This method, similar to the junction tree algorithm used in graphical models for machine learning, allows automatic discovery of efficient algorithms such as the O(n4) algorithm for bilexical grammars of Eisner and Satta. We examine the complexity of applying this method to parsing algorithms for general Linear Context-Free Rewriting Systems. We show that any polynomial-time algorithm for this problem would imply an improved approximation algorithm for the well-studied treewidth problem on general graphs.


2021 ◽  
Vol 9 (3) ◽  
pp. 283
Author(s):  
Rafaela C. Cruz ◽  
Pedro Reis Costa ◽  
Susana Vinga ◽  
Ludwig Krippahl ◽  
Marta B. Lopes

Harmful algal blooms (HABs) are among the most severe ecological marine problems worldwide. Under favorable climate and oceanographic conditions, toxin-producing microalgae species may proliferate, reach increasingly high cell concentrations in seawater, accumulate in shellfish, and threaten the health of seafood consumers. There is an urgent need for the development of effective tools to help shellfish farmers to cope and anticipate HAB events and shellfish contamination, which frequently leads to significant negative economic impacts. Statistical and machine learning forecasting tools have been developed in an attempt to better inform the shellfish industry to limit damages, improve mitigation measures and reduce production losses. This study presents a synoptic review covering the trends in machine learning methods for predicting HABs and shellfish biotoxin contamination, with a particular focus on autoregressive models, support vector machines, random forest, probabilistic graphical models, and artificial neural networks (ANN). Most efforts have been attempted to forecast HABs based on models of increased complexity over the years, coupled with increased multi-source data availability, with ANN architectures in the forefront to model these events. The purpose of this review is to help defining machine learning-based strategies to support shellfish industry to manage their harvesting/production, and decision making by governmental agencies with environmental responsibilities.


2008 ◽  
Vol 33 ◽  
pp. 259-283 ◽  
Author(s):  
I. Rezek ◽  
D. S. Leslie ◽  
S. Reece ◽  
S. J. Roberts ◽  
A. Rogers ◽  
...  

In this paper, we elucidate the equivalence between inference in game theory and machine learning. Our aim in so doing is to establish an equivalent vocabulary between the two domains so as to facilitate developments at the intersection of both fields, and as proof of the usefulness of this approach, we use recent developments in each field to make useful improvements to the other. More specifically, we consider the analogies between smooth best responses in fictitious play and Bayesian inference methods. Initially, we use these insights to develop and demonstrate an improved algorithm for learning in games based on probabilistic moderation. That is, by integrating over the distribution of opponent strategies (a Bayesian approach within machine learning) rather than taking a simple empirical average (the approach used in standard fictitious play) we derive a novel moderated fictitious play algorithm and show that it is more likely than standard fictitious play to converge to a payoff-dominant but risk-dominated Nash equilibrium in a simple coordination game. Furthermore we consider the converse case, and show how insights from game theory can be used to derive two improved mean field variational learning algorithms. We first show that the standard update rule of mean field variational learning is analogous to a Cournot adjustment within game theory. By analogy with fictitious play, we then suggest an improved update rule, and show that this results in fictitious variational play, an improved mean field variational learning algorithm that exhibits better convergence in highly or strongly connected graphical models. Second, we use a recent advance in fictitious play, namely dynamic fictitious play, to derive a derivative action variational learning algorithm, that exhibits superior convergence properties on a canonical machine learning problem (clustering a mixture distribution).


Author(s):  
Shyamala G. Nadathur

Large datasets are regularly collected in biomedicine and healthcare (here referred to as the ‘health domain’). These datasets have some unique characteristics and problems. Therefore there is a need for methods which allow modelling in spite of the uniqueness of the datasets, capable of dealing with missing data, allow integrating data from various sources, explicitly indicate statistical dependence and independence and allow modelling with uncertainties. These requirements have given rise to an influx of new methods, especially from the fields of machine learning and probabilistic graphical models. In particular, Bayesian Networks (BNs), which are a type of graphical network model with directed links that offer a general and versatile approach to capturing and reasoning with uncertainty. In this chapter some background mathematics/statistics, description and relevant aspects of building the networks are given to better understand s and appreciate BN’s potential. There are also brief discussions of their applications, the unique value and the challenges of this modelling technique for the domain. As will be seen in this chapter, with the additional advantages the BNs can offer, it is not surprising that it is becoming an increasingly popular modelling tool in the health domain.


2021 ◽  
Vol 39 (6_suppl) ◽  
pp. 162-162
Author(s):  
Raquel Reisinger ◽  
Sergiusz Wesolowski ◽  
Umang Swami ◽  
Pedro C. Barata ◽  
Edgar Javier Hernandez ◽  
...  

162 Background: PARP inhibitors (PARPi) provide significant clinical benefit for men with aPC with BRCA 1 and BRCA 2 mutations. However, in clinical trials, pts with BRCA1 mutations appeared to derive less benefit than pts with BRCA2 (De Bono et al., 2020). Probabilistic Graphical Models (PGMs) are artificial intelligence (AI) algorithms that capture multivariate, multi-level dependencies in complex patterns in large datasets while retaining human interpretability. We hypothesize that PGMs can reveal variants in BRCA1 and 2 that co-segregate with other known pathogenic variants and may explain the difference in response to PARPi therapy. Methods: Multilevel gene interdependencies between BRCA1 or BRCA2 were assessed using a Bayesian Network (BN) machine learning approach and Fisher’s exact test. CGP was performed by a validated cfDNA NGS panel that sequenced 74 clinically relevant cancer genes (Guardant360, Redwood City, CA). Only variants of known significance and those of unknown significance with a pathogenic REVEL score were included in the analysis. Results: Of 4671 men with aPC undergoing cfDNA CGP, 1248 men with somatic mutations in BRCA1, BRCA2, ATM, or combinations of the three were included in the analysis. The Bayesian network analysis demonstrated positive interdependencies between pathogenic variants in BRCA1 and 7 other genes. A positive interdependency between BRCA2 and 2 genes was present (table). ATM displayed negative interdependency with both BRCA 1 and 2. Conclusions: Our results demonstrate a decreased association of BRCA2 versus BRCA1 with known or predicted pathogenic variants at other loci. This may explain increased sensitivity of aPC with BRCA2 mutations to PARPi due to fewer concurrent resistance pathways. For example, alteration of ERBB2, which segregates strongly with BRCA1, is known to induce tumor progression and invasion in aPC and is associated with castration-resistance. These hypothesis-generating data reveal differential genomic signatures associated with BRCA1 as compared to BRCA2 and may inform development of future combinatorial treatment regimens for these pts. [Table: see text]


Entropy ◽  
2021 ◽  
Vol 23 (8) ◽  
pp. 986
Author(s):  
Marcus Harris ◽  
Martin Zwick

Reconstructability Analysis (RA) and Bayesian Networks (BN) are both probabilistic graphical modeling methodologies used in machine learning and artificial intelligence. There are RA models that are statistically equivalent to BN models and there are also models unique to RA and models unique to BN. The primary goal of this paper is to unify these two methodologies via a lattice of structures that offers an expanded set of models to represent complex systems more accurately or more simply. The conceptualization of this lattice also offers a framework for additional innovations beyond what is presented here. Specifically, this paper integrates RA and BN by developing and visualizing: (1) a BN neutral system lattice of general and specific graphs, (2) a joint RA-BN neutral system lattice of general and specific graphs, (3) an augmented RA directed system lattice of prediction graphs, and (4) a BN directed system lattice of prediction graphs. Additionally, it (5) extends RA notation to encompass BN graphs and (6) offers an algorithm to search the joint RA-BN neutral system lattice to find the best representation of system structure from underlying system variables. All lattices shown in this paper are for four variables, but the theory and methodology presented in this paper are general and apply to any number of variables. These methodological innovations are contributions to machine learning and artificial intelligence and more generally to complex systems analysis. The paper also reviews some relevant prior work of others so that the innovations offered here can be understood in a self-contained way within the context of this paper.


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