Abstract
This paper presents two computable functions, \(\omega \) and \(\varepsilon \), that map networks into networks. If all cognition occurs as an active neural network, then it is thought that \(\omega \) models long-term memory consolidation and \(\varepsilon \) models memory recall. A derived, intermediate network form, consisting of chordless cycles, could be the structural substrate of long-term memory; just as the double helix is the necessary substrate for genomic memory.
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Notes
- 1.
This is primarily for mathematical convenience.
- 2.
Probably essential. If \(\eta \) is not monotone, we can prove very few mathematical results of interest.
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- 4.
In [24], this was called the “spine” of \(\mathcal{N}\).
- 5.
Cord Hockemeyer, http://www.uni-graz.at/cord.hockemeyer/KST_Bibliographie/kst-bib.html, maintains a bibliography of over 400 related references.
- 6.
This network, \(\mathcal{N}\), that we received from a lab at Johns Hopkins Univ. was only identified as GrN2. We believe it is an natively unfolded phenylalanine-glycine (FG)-repeat [15].
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A Appendix
A Appendix
Too much formal mathematics makes a paper hard to read. Yet, it is important to be able to check some of the statements made in the body of the paper. In this appendix we provide a few propositions to formally prove some of our assertions.
The order in which nodes, or more accurately the singleton subsets, of \(\mathcal{N}\) are encountered can alter which points are subsumed and subsequently deleted. Nevertheless, we show below that the reduced trace \(\mathcal{T}= \mathcal{N}.\omega \) will be unique, up to isomorphism.
Proposition 1
Let \(\mathcal{T}= \mathcal{N}.\omega \) and \(\mathcal{T}' = \mathcal{N}.\omega '\) be irreducible subsets of a finite network \(\mathcal{N}\), then \(\mathcal{T}\cong \mathcal{T}'\).
Proof
Let \(y_0 \in \mathcal{T}\), \(y_0 \not \in \mathcal{T}'\). Then \(y_0\) can be subsumed by some point \(y_1\) in \(\mathcal{T}'\) and \(y_1 \not \in \mathcal{T}\) else because \(y_0.\eta \subseteq y_1.\eta \) implies \(y_0 \in \{y_1\}.\varphi \) and \(\mathcal{T}\) would not be irreducible.
Similarly, since \(y_1 \in \mathcal{T}'\) and \(y_1 \not \in \mathcal{T}\), there exists \(y_2 \in \mathcal{T}\) such that \(y_1\) is subsumed by \(y_2\). So, \(y_1.\eta \subseteq y_2.\eta \).
Now we have two possible cases; either \(y_2 = y_0\), or not.
Suppose \(y_2 = y_0\) (which is often the case), then \(y_0.\eta \subseteq y_1.\eta \) and \(y_1.\eta \subseteq y_2.\eta \) or \(y_0.\eta = y_1.\eta \). Hence \(i(y_0) = y_1\) is part of the desired isometry, i.
Now suppose \(y_2 \ne y_0\). There exists \(y_3 \ne y_1 \in \mathcal{T}'\) such that \(y_2.\eta \subseteq y_3.\eta \), and so forth. Since \(\mathcal{T}\) is finite this construction must halt with some \(y_n\). The points \(\{ y_0, y_1, y_2, \dots y_n \}\) constitute a complete graph \(Y_n\) with \(\{y_i\}.\eta = Y_n.\eta \), for \(i \in [0, n]\). In any reduction all \(y_i \in Y_n\) reduce to a single point. All possibilities lead to mutually isomorphic maps. \(\square \)
In addition to \(\mathcal{N}.\omega \) being unique, we may observe that the transformation \(\omega \) is functional because \(\omega \) maps all subsets of N onto \(N_{\omega }\). So we can have , thus “deleting” z. Similarly, \(\varepsilon \) is functional because provides for the inclusion of new elements. Both \(\omega \) and \(\varepsilon \) are monotone, if we only modify its definition to be \(X \subseteq Y\) implies \(X.\varepsilon \subseteq Y.\varepsilon \), provided .
The following proposition characterizes the structure of irreducible traces.
Proposition 2
Let \(\mathcal{N}\) be a finite symmetric network with \(\mathcal{T}= \mathcal{N}.\omega \) being its irreducible trace. If \(y \in \mathcal{T}\) is not an isolated point then either
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(1) there exists a chordless k-cycle C, \(k \ge 4\) such that \(y \in C\), or
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(2) there exist chordless k-cycles \(C_1, C_2\) each of length \(\ge 4\) with \(x \in C_1\) \(z \in C_2\) and y lies on a path from x to z.
Proof
-
(1)
Let \(y \in N_{\mathcal{T}}\). Since y is not isolated, we let \(y = y_0\) with \(y_1 \in y_0.\eta \), so \((y_0, y_1) \in E\). Since \(y_1\) is not subsumed by \(y_0\), \(\exists y_2 \in y_1.\eta , y_2 \not \in y_0.\eta \), and since \(y_2\) is not subsumed by \(y_1\), \(\exists y_3 \in y_2.\eta \), \(y_3 \not \in y_1.\eta \). Since \(y_2 \not \in y_0.\eta \), \(y_3 \ne y_0\). Suppose \(y_3 \in y_0.\eta \), then \(< y_0, y_1, y_2, y_3, y_0>\) constitutes a k-cycle \(k \ge 4\), and we are done. Suppose \(y_3 \not \in y_0.\eta \). We repeat the same path extension. \(y_3.\eta \not \subseteq y_2.\eta \) implies \(\exists y_4 \in y_3.\eta \), \(y_4 \not \in y_2.\eta \). If \(y_4 \in y_0.\eta \) or \(y_4 \in y_1.\eta \), we have the desired cycle. If not \(\exists \ y_5, \ldots \) and so forth. Because \(\mathcal{N}\) is finite, this path extension must terminate with \(y_k \in y_i.\eta \), where \(0 \le i \le n-3\), \(n = |N|\). Let \(x = y_0, z = y_k\).
-
(2)
follows naturally. \(\square \)
Finally, we show that \(\omega \) preserves the shortest paths between all elements of the trace, \(\mathcal{T}\).
Proposition 3
Let \(\sigma (x, z)\) denote a shortest path between x and z in \(\mathcal{N}\). Then for all \(y \ne x, z, \in \sigma (x, z)\), if y can be subsumed by \(y'\), then there exists a shortest path \(\sigma '(x, z)\) through \(y'\).
Proof
We may assume without loss of generality that y is adjacent to z in \(\sigma (x, z)\).
Let \(< x, \ldots , x_n, y, z>\) constitute \(\sigma (x, z)\). If y is subsumed by \(y'\), then \(y.\eta = \{x_n, y, z\} \subseteq y'.\eta \). So we have \(\sigma '(x, z) = < x. \ldots , x_n, y', z>\) of equal length. (Also proven in [23].) \(\square \)
In other words, z can be removed from \(\mathcal{N}\) with the certainty that if there was a path from some node x to z through y, there will still exist a path of equal length from x to z after y’s removal.
Figure 9 visually illustrates the situation described in Proposition 3, which we call a diamond. There may, or may not, be a connection between y and \(y'\) as indicated by the dashed line. If there is, as assumed in Proposition 3, then either \(y'\) subsumes y or vice versa, depending on the order in which y and \(y'\) are encountered by \(\omega \). This provides one example of the isomorphism described in Proposition 1. If there is no connection between y and \(y'\) then we have two distinct paths between x and z of the same length.
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Pfaltz, J.L. (2017). Computational Processes that Appear to Model Human Memory. In: Figueiredo, D., Martín-Vide, C., Pratas, D., Vega-Rodríguez, M. (eds) Algorithms for Computational Biology. AlCoB 2017. Lecture Notes in Computer Science(), vol 10252. Springer, Cham. https://doi.org/10.1007/978-3-319-58163-7_6
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