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Register a new userHigher-order interactions in fitness landscapes are sparse
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Biological fitness arises from interactions between molecules, genes, and organisms. To discover the causative mechanisms of this complexity, we must differentiate the significant interactions from a large number of possibilities. Epistasis is the standard way to identify interactions in fitness landscapes. However, this intuitive approach breaks down in higher dimensions for example because the sign of epistasis takes on an arbitrary meaning, and the false discovery rate becomes high. These limitations make it difficult to evaluate the role of epistasis in higher dimensions. Here we develop epistatic filtrations, a dimensionally-normalized approach to define fitness landscape topography for higher dimensional spaces. We apply the method to higher-dimensional datasets from genetics and the gut microbiome. This reveals a sparse higher-order structure that often arises from lower-order. Despite sparsity, these higher-order effects carry significant effects on biological fitness and are consequential for ecology and evolution.
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Ordinary differential equations (ODE) are widely used for modeling in Systems Biology. As most commonly only some of the kinetic parameters are measurable or precisely known, parameter estimation techniques are applied to parametrize the model to experimental data. A main challenge for the parameter estimation is the complexity of the parameter space, especially its high dimensionality and local minima. Parameter estimation techniques consist of an objective function, measuring how well a certain parameter set describes the experimental data, and an optimization algorithm that optimizes this objective function. A lot of effort has been spent on developing highly sophisticated optimization algorithms to cope with the complexity in the parameter space, but surprisingly few articles address the influence of the objective function on the computational complexity in finding global optima. We extend a recently developed multiple shooting for stochastic systems (MSS) objective function for parameter estimation of stochastic models and apply it to parameter estimation of ODE models. This MSS objective function treats the intervals between measurement points separately. This separate treatment allows the ODE trajectory to stay closer to the data and we show that it reduces the complexity of the parameter space. We use examples from Systems Biology, namely a Lotka-Volterra model, a FitzHugh-Nagumo oscillator and a Calcium oscillation model, to demonstrate the power of the MSS approach for reducing the complexity and the number of local minima in the parameter space. The approach is fully implemented in the COPASI software package and, therefore, easily accessible for a wide community of researchers.
This Letter studies the quasispecies dynamics of a population capable of genetic repair evolving on a time-dependent fitness landscape. We develop a model that considers an asexual population of single-stranded, conservatively replicating genomes, whose only source of genetic variation is due to copying errors during replication. We consider a time-dependent, single-fitness-peak landscape where the master sequence changes by a single point mutation every time $ tau $. We are able to analytically solve for the evolutionary dynamics of the population in the point-mutation limit. In particular, our model provides an analytical expression for the fraction of mutators in the dynamic fitness landscape that agrees well with results from stochastic simulations.
Genetic pathways usually encode molecular mechanisms that can inform targeted interventions. It is often challenging for existing machine learning approaches to jointly model genetic pathways (higher-order features) and variants (atomic features), and present to clinicians interpretable models. In order to build more accurate and better interpretable machine learning models for genetic medicine, we introduce Pathway Augmented Nonnegative Tensor factorization for HighER-order feature learning (PANTHER). PANTHER selects informative genetic pathways that directly encode molecular mechanisms. We apply genetically motivated constrained tensor factorization to group pathways in a way that reflects molecular mechanism interactions. We then train a softmax classifier for disease types using the identified pathway groups. We evaluated PANTHER against multiple state-of-the-art constrained tensor/matrix factorization models, as well as group guided and Bayesian hierarchical models. PANTHER outperforms all state-of-the-art comparison models significantly (p<0.05). Our experiments on large scale Next Generation Sequencing (NGS) and whole-genome genotyping datasets also demonstrated wide applicability of PANTHER. We performed feature analysis in predicting disease types, which suggested insights and benefits of the identified pathway groups.
The issue of opinion sharing and formation has received considerable attention in the academic literature, and a few models have been proposed to study this problem. However, existing models are limited to the interactions among nearest neighbors, ignoring those second, third, and higher-order neighbors, despite the fact that higher-order interactions occur frequently in real social networks. In this paper, we develop a new model for opinion dynamics by incorporating long-range interactions based on higher-order random walks. We prove that the model converges to a fixed opinion vector, which may differ greatly from those models without higher-order interactions. Since direct computation of the equilibrium opinion is computationally expensive, which involves the operations of huge-scale matrix multiplication and inversion, we design a theoretically convergence-guaranteed estimation algorithm that approximates the equilibrium opinion vector nearly linearly in both space and time with respect to the number of edges in the graph. We conduct extensive experiments on various social networks, demonstrating that the new algorithm is both highly efficient and effective.
Magnetism in recently discovered van der Waals materials has opened new avenues in the study of fundamental spin interactions in truly two-dimensions. A paramount question is what effect higher-order interactions beyond bilinear Heisenberg exchange have on the magnetic properties of few-atom thick compounds. Here we demonstrate that biquadratic exchange interactions, which is the simplest and most natural form of non-Heisenberg coupling, assume a key role in the magnetic properties of layered magnets. Using a combination of nonperturbative analytical techniques, non-collinear first-principles methods and classical Monte Carlo calculations that incorporate higher-order exchange, we show that several quantities including magnetic anisotropies, spin-wave gaps and topological spin-excitations are intrinsically renormalized leading to further thermal stability of the layers. We develop a spin Hamiltonian that also contains antisymmetric exchanges (e.g. Dzyaloshinskii-Moriya interactions) to successfully rationalize numerous observations currently under debate, such as the non-Ising character of several compounds despite a strong magnetic anisotropy, peculiarities of the magnon spectrum of 2D magnets, and the discrepancy between measured and calculated Curie temperatures. Our results lay the foundation of a universal higher-order exchange theory for novel 2D magnetic design strategies.
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