Computational complexity of the landscape I

We study the computational complexity of the physical problem of finding vacua of string theory which agree with data, such as the cosmological constant, and show that such problems are typically NP hard. In particular, we prove that in the Bousso-Polchinski model, the problem is NP complete. We discuss the issues this raises and the possibility that, even if we were to find compelling evidence that some vacuum of string theory describes our universe, we might never be able to find that vacuum explicitly. In a companion paper, we apply this point of view to the question of how early cosmology might select a vacuum.Comment: JHEP3 Latex, 53 pp, 2 .eps figure

Computational strategies for dissecting the high-dimensional complexity of adaptive immune repertoires

The adaptive immune system recognizes antigens via an immense array of antigen-binding antibodies and T-cell receptors, the immune repertoire. The interrogation of immune repertoires is of high relevance for understanding the adaptive immune response in disease and infection (e.g., autoimmunity, cancer, HIV). Adaptive immune receptor repertoire sequencing (AIRR-seq) has driven the quantitative and molecular-level profiling of immune repertoires thereby revealing the high-dimensional complexity of the immune receptor sequence landscape. Several methods for the computational and statistical analysis of large-scale AIRR-seq data have been developed to resolve immune repertoire complexity in order to understand the dynamics of adaptive immunity. Here, we review the current research on (i) diversity, (ii) clustering and network, (iii) phylogenetic and (iv) machine learning methods applied to dissect, quantify and compare the architecture, evolution, and specificity of immune repertoires. We summarize outstanding questions in computational immunology and propose future directions for systems immunology towards coupling AIRR-seq with the computational discovery of immunotherapeutics, vaccines, and immunodiagnostics.Comment: 27 pages, 2 figure

Subclasses of Presburger Arithmetic and the Weak EXP Hierarchy

It is shown that for any fixed $i>0$, the $\Sigma_{i+1}$-fragment of Presburger arithmetic, i.e., its restriction to $i+1$ quantifier alternations beginning with an existential quantifier, is complete for $\mathsf{\Sigma}^{\mathsf{EXP}}_{i}$, the $i$-th level of the weak EXP hierarchy, an analogue to the polynomial-time hierarchy residing between $\mathsf{NEXP}$ and $\mathsf{EXPSPACE}$. This result completes the computational complexity landscape for Presburger arithmetic, a line of research which dates back to the seminal work by Fischer & Rabin in 1974. Moreover, we apply some of the techniques developed in the proof of the lower bound in order to establish bounds on sets of naturals definable in the $\Sigma_1$-fragment of Presburger arithmetic: given a $\Sigma_1$-formula $\Phi(x)$, it is shown that the set of non-negative solutions is an ultimately periodic set whose period is at most doubly-exponential and that this bound is tight.Comment: 10 pages, 2 figure

Complexity of evolutionary equilibria in static fitness landscapes

A fitness landscape is a genetic space -- with two genotypes adjacent if they differ in a single locus -- and a fitness function. Evolutionary dynamics produce a flow on this landscape from lower fitness to higher; reaching equilibrium only if a local fitness peak is found. I use computational complexity to question the common assumption that evolution on static fitness landscapes can quickly reach a local fitness peak. I do this by showing that the popular NK model of rugged fitness landscapes is PLS-complete for K >= 2; the reduction from Weighted 2SAT is a bijection on adaptive walks, so there are NK fitness landscapes where every adaptive path from some vertices is of exponential length. Alternatively -- under the standard complexity theoretic assumption that there are problems in PLS not solvable in polynomial time -- this means that there are no evolutionary dynamics (known, or to be discovered, and not necessarily following adaptive paths) that can converge to a local fitness peak on all NK landscapes with K = 2. Applying results from the analysis of simplex algorithms, I show that there exist single-peaked landscapes with no reciprocal sign epistasis where the expected length of an adaptive path following strong selection weak mutation dynamics is $e^{O(n^{1/3})}$ even though an adaptive path to the optimum of length less than n is available from every vertex. The technical results are written to be accessible to mathematical biologists without a computer science background, and the biological literature is summarized for the convenience of non-biologists with the aim to open a constructive dialogue between the two disciplines.Comment: 14 pages, 3 figure

Fast optimization algorithms and the cosmological constant

Denef and Douglas have observed that in certain landscape models the problem of finding small values of the cosmological constant is a large instance of an NP-hard problem. The number of elementary operations (quantum gates) needed to solve this problem by brute force search exceeds the estimated computational capacity of the observable universe. Here we describe a way out of this puzzling circumstance: despite being NP-hard, the problem of finding a small cosmological constant can be attacked by more sophisticated algorithms whose performance vastly exceeds brute force search. In fact, in some parameter regimes the average-case complexity is polynomial. We demonstrate this by explicitly finding a cosmological constant of order $10^{-120}$ in a randomly generated $10^9$-dimensional ADK landscape.Comment: 19 pages, 5 figure

Physical portrayal of computational complexity

Computational complexity is examined using the principle of increasing entropy. To consider computation as a physical process from an initial instance to the final acceptance is motivated because many natural processes have been recognized to complete in non-polynomial time (NP). The irreversible process with three or more degrees of freedom is found intractable because, in terms of physics, flows of energy are inseparable from their driving forces. In computational terms, when solving problems in the class NP, decisions will affect subsequently available sets of decisions. The state space of a non-deterministic finite automaton is evolving due to the computation itself hence it cannot be efficiently contracted using a deterministic finite automaton that will arrive at a solution in super-polynomial time. The solution of the NP problem itself is verifiable in polynomial time (P) because the corresponding state is stationary. Likewise the class P set of states does not depend on computational history hence it can be efficiently contracted to the accepting state by a deterministic sequence of dissipative transformations. Thus it is concluded that the class P set of states is inherently smaller than the set of class NP. Since the computational time to contract a given set is proportional to dissipation, the computational complexity class P is a subset of NP.Comment: 16, pages, 7 figure

Artificial Neural Network in Cosmic Landscape

In this paper we propose that artificial neural network, the basis of machine learning, is useful to generate the inflationary landscape from a cosmological point of view. Traditional numerical simulations of a global cosmic landscape typically need an exponential complexity when the number of fields is large. However, a basic application of artificial neural network could solve the problem based on the universal approximation theorem of the multilayer perceptron. A toy model in inflation with multiple light fields is investigated numerically as an example of such an application.Comment: v2, add some new content