120 research outputs found
Learning AMP Chain Graphs under Faithfulness
This paper deals with chain graphs under the alternative
Andersson-Madigan-Perlman (AMP) interpretation. In particular, we present a
constraint based algorithm for learning an AMP chain graph a given probability
distribution is faithful to. We also show that the extension of Meek's
conjecture to AMP chain graphs does not hold, which compromises the development
of efficient and correct score+search learning algorithms under assumptions
weaker than faithfulness
Identifiability of Causal Graphs using Functional Models
This work addresses the following question: Under what assumptions on the
data generating process can one infer the causal graph from the joint
distribution? The approach taken by conditional independence-based causal
discovery methods is based on two assumptions: the Markov condition and
faithfulness. It has been shown that under these assumptions the causal graph
can be identified up to Markov equivalence (some arrows remain undirected)
using methods like the PC algorithm. In this work we propose an alternative by
defining Identifiable Functional Model Classes (IFMOCs). As our main theorem we
prove that if the data generating process belongs to an IFMOC, one can identify
the complete causal graph. To the best of our knowledge this is the first
identifiability result of this kind that is not limited to linear functional
relationships. We discuss how the IFMOC assumption and the Markov and
faithfulness assumptions relate to each other and explain why we believe that
the IFMOC assumption can be tested more easily on given data. We further
provide a practical algorithm that recovers the causal graph from finitely many
data; experiments on simulated data support the theoretical findings
Application of new probabilistic graphical models in the genetic regulatory networks studies
This paper introduces two new probabilistic graphical models for
reconstruction of genetic regulatory networks using DNA microarray data. One is
an Independence Graph (IG) model with either a forward or a backward search
algorithm and the other one is a Gaussian Network (GN) model with a novel
greedy search method. The performances of both models were evaluated on four
MAPK pathways in yeast and three simulated data sets. Generally, an IG model
provides a sparse graph but a GN model produces a dense graph where more
information about gene-gene interactions is preserved. Additionally, we found
two key limitations in the prediction of genetic regulatory networks using DNA
microarray data, the first is the sufficiency of sample size and the second is
the complexity of network structures may not be captured without additional
data at the protein level. Those limitations are present in all prediction
methods which used only DNA microarray data.Comment: 38 pages, 3 figure
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