H = HH CThe homology of a 2-fold factorization $H$ is defined by ker dd^C/image dd^C. The differential of the homology complex is the zero map. If the differentials of the factorization do not compose to 0, then the homology is not defined. Similarly, in order to make sense of the homology of a d-fold factorization for d > 3, one should use the fullCollapse command.
An easy way to construct complexes from factorizations is to use the End command, which computes the endomorphisms of the factorization. In general, if $F$ is a factorization of some polynomial $f$ and $G$ is a factorization of some polynomial $g$, then $\operatorname{Hom} (F,G)$ is a factorization of $g-f$.
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Thus $E$ is a $2$-periodic complex. This means that the homology is well-defined:
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In the above case, the homology of the endomorphism factorization is computing the stable Ext of the residue field over the hypersurface $R/(f)$, ie, the Ext module obtained by taking sufficiently high Ext values.
The source of this document is in MatrixFactorizations/MatrixFactorizationsDOC.m2:1067:0.