Max-sum diversity via convex programming

Diversity maximization is an important concept in information retrieval, computational geometry and operations research. Usually, it is a variant of the following problem: Given a ground set, constraints, and a function $f(\cdot)$ that measures diversity of a subset, the task is to select a feasible subset $S$ such that $f(S)$ is maximized. The \emph{sum-dispersion} function $f(S) = \sum_{x,y \in S} d(x,y)$, which is the sum of the pairwise distances in $S$, is in this context a prominent diversification measure. The corresponding diversity maximization is the \emph{max-sum} or \emph{sum-sum diversification}. Many recent results deal with the design of constant-factor approximation algorithms of diversification problems involving sum-dispersion function under a matroid constraint. In this paper, we present a PTAS for the max-sum diversification problem under a matroid constraint for distances $d(\cdot,\cdot)$ of \emph{negative type}. Distances of negative type are, for example, metric distances stemming from the $\ell_2$ and $\ell_1$ norm, as well as the cosine or spherical, or Jaccard distance which are popular similarity metrics in web and image search

Provable randomized rounding for minimum-similarity diversification

When searching for information in a data collection, we are often interested not only in finding relevant items, but also in assembling a diverse set, so as to explore different concepts that are present in the data. This problem has been researched extensively. However, finding a set of items with minimal pairwise similarities can be computationally challenging, and most existing works striving for quality guarantees assume that item relatedness is measured by a distance function. Given the widespread use of similarity functions in many domains, we believe this to be an important gap in the literature. In this paper we study the problem of finding a diverse set of items, when item relatedness is measured by a similarity function. We formulate the diversification task using a flexible, broadly applicable minimization objective, consisting of the sum of pairwise similarities of the selected items and a relevance penalty term. To find good solutions we adopt a randomized rounding strategy, which is challenging to analyze because of the cardinality constraint present in our formulation. Even though this obstacle can be overcome using dependent rounding, we show that it is possible to obtain provably good solutions using an independent approach, which is faster, simpler to implement and completely parallelizable. Our analysis relies on a novel bound for the ratio of Poisson-Binomial densities, which is of independent interest and has potential implications for other combinatorial-optimization problems. We leverage this result to design an efficient randomized algorithm that provides a lower-order additive approximation guarantee. We validate our method using several benchmark datasets, and show that it consistently outperforms the greedy approaches that are commonly used in the literature.Peer reviewe

Diversity and Novelty: Measurement, Learning and Optimization

The primary objective of this dissertation is to investigate research methods to answer the question: ``How (and why) does one measure, learn and optimize novelty and diversity of a set of items?" The computational models we develop to answer this question also provide foundational mathematical techniques to throw light on the following three questions: 1. How does one reliably measure the creativity of ideas? 2. How does one form teams to evaluate design ideas? 3. How does one filter good ideas out of hundreds of submissions? Solutions to these questions are key to enable the effective processing of a large collection of design ideas generated in a design contest. In the first part of the dissertation, we discuss key qualities needed in design metrics and propose new diversity and novelty metrics for judging design products. We show that the proposed metrics have higher accuracy and sensitivity compared to existing alternatives in literature. To measure the novelty of a design item, we propose learning from human subjective responses to derive low dimensional triplet embeddings. To measure diversity, we propose an entropy-based diversity metric, which is more accurate and sensitive than benchmarks. In the second part of the dissertation, we introduce the bipartite b-matching problem and argue the need for incorporating diversity in the objective function for matching problems. We propose new submodular and supermodular objective functions to measure diversity and develop multiple matching algorithms for diverse team formation in offline and online cases. Finally, in the third part, we demonstrate filtering and ranking of ideas using diversity metrics based on Determinantal Point Processes as well as submodular functions. In real-world crowd experiments, we demonstrate that such ranking enables increased efficiency in filtering high-quality ideas compared to traditionally used methods

Graph set data mining

Graphs are among the most versatile abstract data types in computer science. With the variety comes great adoption in various application fields, such as chemistry, biology, social analysis, logistics, and computer science itself. With the growing capacities of digital storage, the collection of large amounts of data has become the norm in many application fields. Data mining, i.e., the automated extraction of non-trivial patterns from data, is a key step to extract knowledge from these datasets and generate value. This thesis is dedicated to concurrent scalable data mining algorithms beyond traditional notions of efficiency for large-scale datasets of small labeled graphs; more precisely, structural clustering and representative subgraph pattern mining. It is motivated by, but not limited to, the need to analyze molecular libraries of ever-increasing size in the drug discovery process. Structural clustering makes use of graph theoretical concepts, such as (common) subgraph isomorphisms and frequent subgraphs, to model cluster commonalities directly in the application domain. It is considered computationally demanding for non-restricted graph classes and with very few exceptions prior algorithms are only suitable for very small datasets. This thesis discusses the first truly scalable structural clustering algorithm StruClus with linear worst-case complexity. At the same time, StruClus embraces the inherent values of structural clustering algorithms, i.e., interpretable, consistent, and high-quality results. A novel two-fold sampling strategy with stochastic error bounds for frequent subgraph mining is presented. It enables fast extraction of cluster commonalities in the form of common subgraph representative sets. StruClus is the first structural clustering algorithm with a directed selection of structural cluster-representative patterns regarding homogeneity and separation aspects in the high-dimensional subgraph pattern space. Furthermore, a novel concept of cluster homogeneity balancing using dynamically-sized representatives is discussed. The second part of this thesis discusses the representative subgraph pattern mining problem in more general terms. A novel objective function maximizes the number of represented graphs for a cardinality-constrained representative set. It is shown that the problem is a special case of the maximum coverage problem and is NP-hard. Based on the greedy approximation of Nemhauser, Wolsey, and Fisher for submodular set function maximization a novel sampling approach is presented. It mines candidate sets that contain an optimal greedy solution with a probabilistic maximum error. This leads to a constant-time algorithm to generate the candidate sets given a fixed-size sample of the dataset. In combination with a cheap single-pass streaming evaluation of the candidate sets, this enables scalability to datasets with billions of molecules on a single machine. Ultimately, the sampling approach leads to the first distributed subgraph pattern mining algorithm that distributes the pattern space and the dataset graphs at the same time

Probabilistic Protein Engineering

Machine learning-guided protein engineering is a new paradigm that enables the optimization of complex protein functions. Machine-learning methods use data to predict protein function without requiring a detailed model of the underlying physics or biological pathways. They accelerate protein engineering by learning from information contained in all measured variants and using it to select variants that are likely to be improved. We begin with a review of the basics of machine learning with a focus on applications to protein engineering and protein sequence-function datasets (Chapter 1). We used the entire machine-learning guided engineering paradigm to engineer the algal-derived light-gated channel channelrhodopsin (ChR), which can be used to modulate neuronal activity with light. We build models that discover ChRs with strong plasma membrane localization in mammalian cells (Chapter 2) and unprecedented light sensitivity and photocurrents for optogenetic applications (Chapter 3). Machine learning-guided evolution requires a machine-learning model that learns the relationship between sequence and function. For machine-learning models to learn about protein sequences, protein sequences must be represented as vectors or matrices of numbers. How each protein sequence is represented determines what can be learned. We learn continuous vector encodings of sequences from patterns in unlabeled sequences (Chapter 4). Learned encodings are low-dimensional, do not require alignments, and may improve performance by transferring information in unlabeled sequences to specific prediction tasks. Alternately, we demonstrate an interpretable Gaussian process kernel tailored to biological sequences (Chapter 6). In addition to a model to predict function from sequence, engineering requires a method to use the model to choose sequences for the next round of evolution. Most machine-learning guided engineering strategies assume that selected sequences can be queried directly. However, in directed evolution it is common to design a library of sequences and then sample stochastic batches from that library. We propose a batched stochastic Bayesian optimization algorithm for iteratively designing and screening site-saturation mutagenesis libraries (Chapter 5).</p