Machine learning-guided directed evolution for protein engineering

Machine learning (ML)-guided directed evolution is a new paradigm for biological design that enables optimization of complex functions. ML methods use data to predict how sequence maps to function without requiring a detailed model of the underlying physics or biological pathways. To demonstrate ML-guided directed evolution, we introduce the steps required to build ML sequence-function models and use them to guide engineering, making recommendations at each stage. This review covers basic concepts relevant to using ML for protein engineering as well as the current literature and applications of this new engineering paradigm. ML methods accelerate directed evolution by learning from information contained in all measured variants and using that information to select sequences that are likely to be improved. We then provide two case studies that demonstrate the ML-guided directed evolution process. We also look to future opportunities where ML will enable discovery of new protein functions and uncover the relationship between protein sequence and function.Comment: Made significant revisions to focus on aspects most relevant to applying machine learning to speed up directed evolutio

The origin of large amplitude oscillations of dust particles in a plasma sheath

Micron-size charged particles can be easily levitated in low-density plasma environments. At low pressures, suspended particles have been observed to spontaneously oscillate around an equilibrium position. In systems of many particles, these oscillations can catalyze a variety of nonequilibrium, collective behaviors. Here, we report spontaneous oscillations of single particles that remain stable for minutes with striking regularity in amplitude and frequency. The oscillation amplitude can also exceed 1 cm, nearly an order of magnitude larger than previously observed. Using an integrated experimental and numerical approach, we show how the motion of an individual particle can be used to extract the electrostatic force and equilibrium charge variation in the plasma sheath. Additionally, using a delayed-charging model, we are able to accurately capture the nonlinear dynamics of the particle motion, and estimate the particle's equilibrium charging time in the plasma environment

Hierarchies of Predominantly Connected Communities

We consider communities whose vertices are predominantly connected, i.e., the vertices in each community are stronger connected to other community members of the same community than to vertices outside the community. Flake et al. introduced a hierarchical clustering algorithm that finds such predominantly connected communities of different coarseness depending on an input parameter. We present a simple and efficient method for constructing a clustering hierarchy according to Flake et al. that supersedes the necessity of choosing feasible parameter values and guarantees the completeness of the resulting hierarchy, i.e., the hierarchy contains all clusterings that can be constructed by the original algorithm for any parameter value. However, predominantly connected communities are not organized in a single hierarchy. Thus, we develop a framework that, after precomputing at most $2(n-1)$ maximum flows, admits a linear time construction of a clustering \C(S) of predominantly connected communities that contains a given community $S$ and is maximum in the sense that any further clustering of predominantly connected communities that also contains $S$ is hierarchically nested in \C(S). We further generalize this construction yielding a clustering with similar properties for $k$ given communities in $O(kn)$ time. This admits the analysis of a network's structure with respect to various communities in different hierarchies.Comment: to appear (WADS 2013

Data-Driven Protein Engineering

Directed evolution has enabled the adaptation of natural protein sequences for an endless variety of human applications. Given a starting point - a sequence with measurable activity - directed evolution is able to improve protein sequences by iteratively accumulating beneficial mutations. However, directed evolution requires investing large experimental effort, which continues to be the major bottleneck in efficient protein optimization. To this end, we describe a framework for incorporating machine learning in the directed evolution process to maximize the utility of generated experimental data in Chapter 2. In Chapter 3, we then show that this framework outperforms traditional directed evolution methods on an empirical fitness landscape. However, directed evolution is fundamentally limited by its need for a starting point, or a sequence with measurable activity. To tackle this issue, we test the ability of nascent deep learning techniques for generating short, functional amino acid sequences in Chapter 4. Encouraged by this success, we attempted to generate full length enzymatic sequences for desired substrates without success. However, we were able to apply this deep learning approach to model other aspects of enzymatic protein sequences in Chapter 5. Finally, the field of data-driven protein sequence generation is enjoying a recent surge in interest, and we provide an updated review of protein engineering with machine learning, focusing on recent work in deep generative modeling in Chapter 1.</p