Hashing for Similarity Search: A Survey

Similarity search (nearest neighbor search) is a problem of pursuing the data items whose distances to a query item are the smallest from a large database. Various methods have been developed to address this problem, and recently a lot of efforts have been devoted to approximate search. In this paper, we present a survey on one of the main solutions, hashing, which has been widely studied since the pioneering work locality sensitive hashing. We divide the hashing algorithms two main categories: locality sensitive hashing, which designs hash functions without exploring the data distribution and learning to hash, which learns hash functions according the data distribution, and review them from various aspects, including hash function design and distance measure and search scheme in the hash coding space

Analysis and application of hash-based similarity estimation techniques for biological sequence analysis

In Bioinformatics, a large group of problems requires the computation or estimation of sequence similarity. However, the analysis of biological sequence data has, among many others, three capital challenges: a large amount generated data which contains technology-specific errors (that can be mistaken for biological signals), and that might need to be analyzed without access to a reference genome. Through the use of locality sensitive hashing methods, both the efficient estimation of sequence similarity and tolerance against the errors specific to biological data can be achieved. We developed a variant of the winnowing algorithm for local minimizer computation, which is specifically geared to deal with repetitive regions within biological sequences. Through compressing redundant information, we can both reduce the size of the hash tables required to save minimizer sketches, as well as reduce the amount of redundant low quality alignment candidates. Analyzing the distribution of segment lengths generated by this approach, we can better judge the size of required data structures, as well as identify hash functions feasible for this technique. Our evaluation could verify that simple and fast hash functions, even when using small hash value spaces (hash functions with small codomain), are sufficient to compute compressed minimizers and perform comparable to uniformly randomly chosen hash values. We also outlined an index for a taxonomic protein database using multiple compressed winnowings to identify alignment candidates. To store MinHash values, we present a cache-optimized implementation of a hash table using Hopscotch hashing to resolve collisions. As a biological application of similarity based analysis, we describe the analysis of double digest restriction site associated DNA sequencing (ddRADseq). We implemented a simulation software able to model the biological and technological influences of this technology to allow better development and testing of ddRADseq analysis software. Using datasets generated by our software, as well as data obtained from population genetic experiments, we developed an analysis workflow for ddRADseq data, based on the Stacks software. Since the quality of results generated by Stacks strongly depends on how well the used parameters are adapted to the specific dataset, we developed a Snakemake workflow that automates preprocessing tasks while also allowing the automatic exploration of different parameter sets. As part of this workflow, we developed a PCR deduplication approach able to generate consensus reads incorporating the base quality values (as reported by the sequencing device), without performing an alignment first. As an outlook, we outline a MinHashing approach that can be used for a faster and more robust clustering, while addressing incomplete digestion and null alleles, two effects specific for ddRADseq that current analysis tools cannot reliably detect

Fast Data Analytics by Learning

Today, we collect a large amount of data, and the volume of the data we collect is projected to grow faster than the growth of the computational power. This rapid growth of data inevitably increases query latencies, and horizontal scaling alone is not sufficient for real-time data analytics of big data. Approximate query processing (AQP) speeds up data analytics at the cost of small quality losses in query answers. AQP produces query answers based on synopses of the original data. The sizes of the synopses are smaller than the original data; thus, AQP requires less computational efforts for producing query answers, thus can produce answers more quickly. In AQP, there is a general tradeoff between query latencies and the quality of query answers; obtaining higher-quality answers requires longer query latencies. In this dissertation, we show we can speed up the approximate query processing without reducing the quality of the query answers by optimizing the synopses using two approaches. The two approaches we employ for optimizing the synopses are as follows: 1. Exploiting past computations: We exploit the answers to the past queries. This approach relies on the fact that, if two aggregation involve common or correlated values, the aggregated results must also be correlated. We formally capture this idea using a probabilistic distribution function, which is then used to refine the answers to new queries. 2. Building task-aware synopses: By optimizing synopses for a few common types of data analytics, we can produce higher quality answers (or more quickly for certain target quality) to those data analytics tasks. We use this approach for constructing synopses optimized for searching and visualizations. For exploiting past computations and building task-aware synopses, our work incorporates statistical inference and optimization techniques. The contributions in this dissertation resulted in up to 20x speedups for real-world data analytics workloads.PHDComputer Science & EngineeringUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttps://deepblue.lib.umich.edu/bitstream/2027.42/138598/1/pyongjoo_1.pd

Similarity learning for person re-identification and semantic video retrieval

Many computer vision problems boil down to the learning of a good visual similarity function that calculates a score of how likely two instances share the same semantic concept. In this thesis, we focus on two problems related to similarity learning: Person Re-Identification, and Semantic Video Retrieval. Person Re-Identification aims to maintain the identity of an individual in diverse locations through different non-overlapping camera views. Starting with two cameras, we propose a novel visual word co-occurrence based appearance model to measure the similarities between pedestrian images. This model naturally accounts for spatial similarities and variations caused by pose, illumination and configuration changes across camera views. As a generalization to multiple camera views, we introduce the Group Membership Prediction (GMP) problem. The GMP problem involves predicting whether a collection of instances shares the same semantic property. In this context, we propose a novel probability model and introduce latent view-specific and view-shared random variables to jointly account for the view-specific appearance and cross-view similarities among data instances. Our method is tested on various benchmarks demonstrating superior accuracy over state-of-art. Semantic Video Retrieval seeks to match complex activities in a surveillance video to user described queries. In surveillance scenarios with noise and clutter usually present, visual uncertainties introduced by error-prone low-level detectors, classifiers and trackers compose a significant part of the semantic gap between user defined queries and the archive video. To bridge the gap, we propose a novel probabilistic activity localization formulation that incorporates learning of object attributes, between-object relationships, and object re-identification without activity-level training data. Our experiments demonstrate that the introduction of similarity learning components effectively compensate for noise and error in previous stages, and result in preferable performance on both aerial and ground surveillance videos. Considering the computational complexity of our similarity learning models, we attempt to develop a way of training complicated models efficiently while remaining good performance. As a proof-of-concept, we propose training deep neural networks for supervised learning of hash codes. With slight changes in the optimization formulation, we could explore the possibilities of incorporating the training framework for Person Re-Identification and related problems.2019-07-09T00:00:00

Complex queries and complex data

With the widespread availability of wearable computers, equipped with sensors such as GPS or cameras, and with the ubiquitous presence of micro-blogging platforms, social media sites and digital marketplaces, data can be collected and shared on a massive scale. A necessary building block for taking advantage from this vast amount of information are efficient and effective similarity search algorithms that are able to find objects in a database which are similar to a query object. Due to the general applicability of similarity search over different data types and applications, the formalization of this concept and the development of strategies for evaluating similarity queries has evolved to an important field of research in the database community, spatio-temporal database community, and others, such as information retrieval and computer vision. This thesis concentrates on a special instance of similarity queries, namely k-Nearest Neighbor (kNN) Queries and their close relative, Reverse k-Nearest Neighbor (RkNN) Queries. As a first contribution we provide an in-depth analysis of the RkNN join. While the problem of reverse nearest neighbor queries has received a vast amount of research interest, the problem of performing such queries in a bulk has not seen an in-depth analysis so far. We first formalize the RkNN join, identifying its monochromatic and bichromatic versions and their self-join variants. After pinpointing the monochromatic RkNN join as an important and interesting instance, we develop solutions for this class, including a self-pruning and a mutual pruning algorithm. We then evaluate these algorithms extensively on a variety of synthetic and real datasets. From this starting point of similarity queries on certain data we shift our focus to uncertain data, addressing nearest neighbor queries in uncertain spatio-temporal databases. Starting from the traditional definition of nearest neighbor queries and a data model for uncertain spatio-temporal data, we develop efficient query mechanisms that consider temporal dependencies during query evaluation. We define intuitive query semantics, aiming not only at returning the objects closest to the query but also their probability of being a nearest neighbor. After theoretically evaluating these query predicates we develop efficient querying algorithms for the proposed query predicates. Given the findings of this research on nearest neighbor queries, we extend these results to reverse nearest neighbor queries. Finally we address the problem of querying large datasets containing set-based objects, namely image databases, where images are represented by (multi-)sets of vectors and additional metadata describing the position of features in the image. We aim at reducing the number of kNN queries performed during query processing and evaluate a modified pipeline that aims at optimizing the query accuracy at a small number of kNN queries. Additionally, as feature representations in object recognition are moving more and more from the real-valued domain to the binary domain, we evaluate efficient indexing techniques for binary feature vectors.Nicht nur durch die Verbreitung von tragbaren Computern, die mit einer Vielzahl von Sensoren wie GPS oder Kameras ausgestattet sind, sondern auch durch die breite Nutzung von Microblogging-Plattformen, Social-Media Websites und digitale Marktplätze wie Amazon und Ebay wird durch die User eine gigantische Menge an Daten veröffentlicht. Um aus diesen Daten einen Mehrwert erzeugen zu können bedarf es effizienter und effektiver Algorithmen zur Ähnlichkeitssuche, die zu einem gegebenen Anfrageobjekt ähnliche Objekte in einer Datenbank identifiziert. Durch die Allgemeinheit dieses Konzeptes der Ähnlichkeit über unterschiedliche Datentypen und Anwendungen hinweg hat sich die Ähnlichkeitssuche zu einem wichtigen Forschungsfeld, nicht nur im Datenbankumfeld oder im Bereich raum-zeitlicher Datenbanken, sondern auch in anderen Forschungsgebieten wie dem Information Retrieval oder dem Maschinellen Sehen entwickelt. In der vorliegenden Arbeit beschäftigen wir uns mit einem speziellen Anfrageprädikat im Bereich der Ähnlichkeitsanfragen, mit k-nächste Nachbarn (kNN) Anfragen und ihrem Verwandten, den Revers k-nächsten Nachbarn (RkNN) Anfragen. In einem ersten Beitrag analysieren wir den RkNN Join. Obwohl das Problem von reverse nächsten Nachbar Anfragen in den letzten Jahren eine breite Aufmerksamkeit in der Forschungsgemeinschaft erfahren hat, wurde das Problem eine Menge von RkNN Anfragen gleichzeitig auszuführen nicht ausreichend analysiert. Aus diesem Grund formalisieren wir das Problem des RkNN Joins mit seinen monochromatischen und bichromatischen Varianten. Wir identifizieren den monochromatischen RkNN Join als einen wichtigen und interessanten Fall und entwickeln entsprechende Anfragealgorithmen. In einer detaillierten Evaluation vergleichen wir die ausgearbeiteten Verfahren auf einer Vielzahl von synthetischen und realen Datensätzen. Nach diesem Kapitel über Ähnlichkeitssuche auf sicheren Daten konzentrieren wir uns auf unsichere Daten, speziell im Bereich raum-zeitlicher Datenbanken. Ausgehend von der traditionellen Definition von Nachbarschaftsanfragen und einem Datenmodell für unsichere raum-zeitliche Daten entwickeln wir effiziente Anfrageverfahren, die zeitliche Abhängigkeiten bei der Anfragebearbeitung beachten. Zu diesem Zweck definieren wir Anfrageprädikate die nicht nur die Objekte zurückzugeben, die dem Anfrageobjekt am nächsten sind, sondern auch die Wahrscheinlichkeit mit der sie ein nächster Nachbar sind. Wir evaluieren die definierten Anfrageprädikate theoretisch und entwickeln effiziente Anfragestrategien, die eine Anfragebearbeitung zu vertretbaren Laufzeiten gewährleisten. Ausgehend von den Ergebnissen für Nachbarschaftsanfragen erweitern wir unsere Ergebnisse auf Reverse Nachbarschaftsanfragen. Zuletzt behandeln wir das Problem der Anfragebearbeitung bei Mengen-basierten Objekten, die zum Beispiel in Bilddatenbanken Verwendung finden: Oft werden Bilder durch eine Menge von Merkmalsvektoren und zusätzliche Metadaten (zum Beispiel die Position der Merkmale im Bild) dargestellt. Wir evaluieren eine modifizierte Pipeline, die darauf abzielt, die Anfragegenauigkeit bei einer kleinen Anzahl an kNN-Anfragen zu maximieren. Da reellwertige Merkmalsvektoren im Bereich der Objekterkennung immer öfter durch Bitvektoren ersetzt werden, die sich durch einen geringeren Speicherplatzbedarf und höhere Laufzeiteffizienz auszeichnen, evaluieren wir außerdem Indexierungsverfahren für Binärvektoren

Large-scale Content-based Visual Information Retrieval

Rather than restricting search to the use of metadata, content-based information retrieval methods attempt to index, search and browse digital objects by means of signatures or features describing their actual content. Such methods have been intensively studied in the multimedia community to allow managing the massive amount of raw multimedia documents created every day (e.g. video will account to 84% of U.S. internet traffic by 2018). Recent years have consequently witnessed a consistent growth of content-aware and multi-modal search engines deployed on massive multimedia data. Popular multimedia search applications such as Google images, Youtube, Shazam, Tineye or MusicID clearly demonstrated that the first generation of large-scale audio-visual search technologies is now mature enough to be deployed on real-world big data. All these successful applications did greatly benefit from 15 years of research on multimedia analysis and efficient content-based indexing techniques. Yet the maturity reached by the first generation of content-based search engines does not preclude an intensive research activity in the field. There is actually still a lot of hard problems to be solved before we can retrieve any information in images or sounds as easily as we do in text documents. Content-based search methods actually have to reach a finer understanding of the contents as well as a higher semantic level. This requires modeling the raw signals by more and more complex and numerous features, so that the algorithms for analyzing, indexing and searching such features have to evolve accordingly. This thesis describes several of my works related to large-scale content-based information retrieval. The different contributions are presented in a bottom-up fashion reflecting a typical three-tier software architecture of an end-to-end multimedia information retrieval system. The lowest layer is only concerned with managing, indexing and searching large sets of high-dimensional feature vectors, whatever their origin or role in the upper levels (visual or audio features, global or part-based descriptions, low or high semantic level, etc. ). The middle layer rather works at the document level and is in charge of analyzing, indexing and searching collections of documents. It typically extracts and embeds the low-level features, implements the querying mechanisms and post-processes the results returned by the lower layer. The upper layer works at the applicative level and is in charge of providing useful and interactive functionalities to the end-user. It typically implements the front-end of the search application, the crawler and the orchestration of the different indexing and search services

Spiking Neural Networks Through the Lens of Streaming Algorithms

We initiate the study of biological neural networks from the perspective of streaming algorithms. Like computers, human brains suffer from memory limitations which pose a significant obstacle when processing large scale and dynamically changing data. In computer science, these challenges are captured by the well-known streaming model, which can be traced back to Munro and Paterson `78 and has had significant impact in theory and beyond. In the classical streaming setting, one must compute some function $f$ of a stream of updates $\mathcal{S} = \{u_1,\ldots,u_m\}$, given restricted single-pass access to the stream. The primary complexity measure is the space used by the algorithm. We take the first steps towards understanding the connection between streaming and neural algorithms. On the upper bound side, we design neural algorithms based on known streaming algorithms for fundamental tasks, including distinct elements, approximate median, heavy hitters, and more. The number of neurons in our neural solutions almost matches the space bounds of the corresponding streaming algorithms. As a general algorithmic primitive, we show how to implement the important streaming technique of linear sketching efficient in spiking neural networks. On the lower bound side, we give a generic reduction, showing that any space-efficient spiking neural network can be simulated by a space-efficiently streaming algorithm. This reduction lets us translate streaming-space lower bounds into nearly matching neural-space lower bounds, establishing a close connection between these two models.Comment: To appear in DISC'20, shorten abstrac

Similarity learning for person re-identification and semantic video retrieval

Many computer vision problems boil down to the learning of a good visual similarity function that calculates a score of how likely two instances share the same semantic concept. In this thesis, we focus on two problems related to similarity learning: Person Re-Identification, and Semantic Video Retrieval. Person Re-Identification aims to maintain the identity of an individual in diverse locations through different non-overlapping camera views. Starting with two cameras, we propose a novel visual word co-occurrence based appearance model to measure the similarities between pedestrian images. This model naturally accounts for spatial similarities and variations caused by pose, illumination and configuration changes across camera views. As a generalization to multiple camera views, we introduce the Group Membership Prediction (GMP) problem. The GMP problem involves predicting whether a collection of instances shares the same semantic property. In this context, we propose a novel probability model and introduce latent view-specific and view-shared random variables to jointly account for the view-specific appearance and cross-view similarities among data instances. Our method is tested on various benchmarks demonstrating superior accuracy over state-of-art. Semantic Video Retrieval seeks to match complex activities in a surveillance video to user described queries. In surveillance scenarios with noise and clutter usually present, visual uncertainties introduced by error-prone low-level detectors, classifiers and trackers compose a significant part of the semantic gap between user defined queries and the archive video. To bridge the gap, we propose a novel probabilistic activity localization formulation that incorporates learning of object attributes, between-object relationships, and object re-identification without activity-level training data. Our experiments demonstrate that the introduction of similarity learning components effectively compensate for noise and error in previous stages, and result in preferable performance on both aerial and ground surveillance videos. Considering the computational complexity of our similarity learning models, we attempt to develop a way of training complicated models efficiently while remaining good performance. As a proof-of-concept, we propose training deep neural networks for supervised learning of hash codes. With slight changes in the optimization formulation, we could explore the possibilities of incorporating the training framework for Person Re-Identification and related problems.2019-07-09T00:00:00