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

Two-layer classification and distinguished representations of users and documents for grouping and authorship identification

Most studies on authorship identification reported a drop in the identification result when the number of authors exceeds 20-25. In this paper, we introduce a new user representation to address this problem and split classification across two layers. There are at least 3 novelties in this paper. First, the two-layer approach allows applying authorship identification over larger number of authors (tested over 100 authors), and it is extendable. The authors are divided into groups that contain smaller number of authors. Given an anonymous document, the primary layer detects the group to which the document belongs. Then, the secondary layer determines the particular author inside the selected group. In order to extract the groups linking similar authors, clustering is applied over users rather than documents. Hence, the second novelty of this paper is introducing a new user representation that is different from document representation. Without the proposed user representation, the clustering over documents will result in documents of author(s) distributed over several clusters, instead of a single cluster membership for each author. Third, the extracted clusters are descriptive and meaningful of their users as the dimensions have psychological backgrounds. For authorship identification, the documents are labelled with the extracted groups and fed into machine learning to build classification models that predicts the group and author of a given document. The results show that the documents are highly correlated with the extracted corresponding groups, and the proposed model can be accurately trained to determine the group and the author identity

Interacting Attention-gated Recurrent Networks for Recommendation

Capturing the temporal dynamics of user preferences over items is important for recommendation. Existing methods mainly assume that all time steps in user-item interaction history are equally relevant to recommendation, which however does not apply in real-world scenarios where user-item interactions can often happen accidentally. More importantly, they learn user and item dynamics separately, thus failing to capture their joint effects on user-item interactions. To better model user and item dynamics, we present the Interacting Attention-gated Recurrent Network (IARN) which adopts the attention model to measure the relevance of each time step. In particular, we propose a novel attention scheme to learn the attention scores of user and item history in an interacting way, thus to account for the dependencies between user and item dynamics in shaping user-item interactions. By doing so, IARN can selectively memorize different time steps of a user's history when predicting her preferences over different items. Our model can therefore provide meaningful interpretations for recommendation results, which could be further enhanced by auxiliary features. Extensive validation on real-world datasets shows that IARN consistently outperforms state-of-the-art methods.Comment: Accepted by ACM International Conference on Information and Knowledge Management (CIKM), 201

CHR(PRISM)-based Probabilistic Logic Learning

PRISM is an extension of Prolog with probabilistic predicates and built-in support for expectation-maximization learning. Constraint Handling Rules (CHR) is a high-level programming language based on multi-headed multiset rewrite rules. In this paper, we introduce a new probabilistic logic formalism, called CHRiSM, based on a combination of CHR and PRISM. It can be used for high-level rapid prototyping of complex statistical models by means of "chance rules". The underlying PRISM system can then be used for several probabilistic inference tasks, including probability computation and parameter learning. We define the CHRiSM language in terms of syntax and operational semantics, and illustrate it with examples. We define the notion of ambiguous programs and define a distribution semantics for unambiguous programs. Next, we describe an implementation of CHRiSM, based on CHR(PRISM). We discuss the relation between CHRiSM and other probabilistic logic programming languages, in particular PCHR. Finally we identify potential application domains

VBPR: Visual Bayesian Personalized Ranking from Implicit Feedback

Modern recommender systems model people and items by discovering or `teasing apart' the underlying dimensions that encode the properties of items and users' preferences toward them. Critically, such dimensions are uncovered based on user feedback, often in implicit form (such as purchase histories, browsing logs, etc.); in addition, some recommender systems make use of side information, such as product attributes, temporal information, or review text. However one important feature that is typically ignored by existing personalized recommendation and ranking methods is the visual appearance of the items being considered. In this paper we propose a scalable factorization model to incorporate visual signals into predictors of people's opinions, which we apply to a selection of large, real-world datasets. We make use of visual features extracted from product images using (pre-trained) deep networks, on top of which we learn an additional layer that uncovers the visual dimensions that best explain the variation in people's feedback. This not only leads to significantly more accurate personalized ranking methods, but also helps to alleviate cold start issues, and qualitatively to analyze the visual dimensions that influence people's opinions.Comment: AAAI'1