Privacy in the Genomic Era

Genome sequencing technology has advanced at a rapid pace and it is now possible to generate highly-detailed genotypes inexpensively. The collection and analysis of such data has the potential to support various applications, including personalized medical services. While the benefits of the genomics revolution are trumpeted by the biomedical community, the increased availability of such data has major implications for personal privacy; notably because the genome has certain essential features, which include (but are not limited to) (i) an association with traits and certain diseases, (ii) identification capability (e.g., forensics), and (iii) revelation of family relationships. Moreover, direct-to-consumer DNA testing increases the likelihood that genome data will be made available in less regulated environments, such as the Internet and for-profit companies. The problem of genome data privacy thus resides at the crossroads of computer science, medicine, and public policy. While the computer scientists have addressed data privacy for various data types, there has been less attention dedicated to genomic data. Thus, the goal of this paper is to provide a systematization of knowledge for the computer science community. In doing so, we address some of the (sometimes erroneous) beliefs of this field and we report on a survey we conducted about genome data privacy with biomedical specialists. Then, after characterizing the genome privacy problem, we review the state-of-the-art regarding privacy attacks on genomic data and strategies for mitigating such attacks, as well as contextualizing these attacks from the perspective of medicine and public policy. This paper concludes with an enumeration of the challenges for genome data privacy and presents a framework to systematize the analysis of threats and the design of countermeasures as the field moves forward

Efficient Privacy-Preserving Variable-Length Substring Match for Genome Sequence

Finding a similar substring that commonly appears in query and database sequences is an essential task for genome data analysis. This study proposes a secure two-party variable-length string search protocol based on secret sharing. The unique feature of our protocol is that time, communication, and round complexities are not dependent on the database length N, after the query input. This property brings dramatic performance improvements in search time, since N is usually quite large in an actual genome database, and the same database is repeatedly used for many queries. Our concept hinges on a technique that efficiently applies the compressed full-text index (FOCS 2000) for a secret-sharing scheme. We conducted an experiment using a human genomic sequence with the length of 10 million as the database and a query with the length of 100 and found that the query response time of our protocol was at least three orders of magnitude faster than a well-designed baseline protocol under the realistic computation/network environment

Secure secondary utilization system of genomic data using quantum secure cloud

量子セキュアクラウドによる高速安全なゲノム解析システムの開発に成功 --従来不可能だった情報理論的安全で高速な処理を実現--. 京都大学プレスリリース. 2022-11-24.Secure storage and secondary use of individual human genome data is increasingly important for genome research and personalized medicine. Currently, it is necessary to store the whole genome sequencing information (FASTQ data), which enables detections of de novo mutations and structural variations in the analysis of hereditary diseases and cancer. Furthermore, bioinformatics tools to analyze FASTQ data are frequently updated to improve the precision and recall of detected variants. However, existing secure secondary use of data, such as multi-party computation or homomorphic encryption, can handle only a limited algorithms and usually requires huge computational resources. Here, we developed a high-performance one-stop system for large-scale genome data analysis with secure secondary use of the data by the data owner and multiple users with different levels of data access control. Our quantum secure cloud system is a distributed secure genomic data analysis system (DSGD) with a “trusted server” built on a quantum secure cloud, the information-theoretically secure Tokyo QKD Network. The trusted server will be capable of deploying and running a variety of sequencing analysis hardware, such as GPUs and FPGAs, as well as CPU-based software. We demonstrated that DSGD achieved comparable throughput with and without encryption on the trusted server Therefore, our system is ready to be installed at research institutes and hospitals that make diagnoses based on whole genome sequencing on a daily basis

Privacy and trustworthiness management in moving object environments

The use of location-based services (LBS) (e.g., Intel\u27s Thing Finder) is expanding. Besides the traditional centralized location-based services, distributed ones are also emerging due to the development of Vehicular Ad-hoc Networks (VANETs), a dynamic network which allows vehicles to communicate with one another. Due to the nature of the need of tracking users\u27 locations, LBS have raised increasing concerns on users\u27 location privacy. Although many research has been carried out for users to submit their locations anonymously, the collected anonymous location data may still be mapped to individuals when the adversary has related background knowledge. To improve location privacy, in this dissertation, the problem of anonymizing the collected location datasets is addressed so that they can be published for public use without violating any privacy concerns. Specifically, a privacy-preserving trajectory publishing algorithm is proposed that preserves high data utility rate. Moreover, the scalability issue is tackled in the case the location datasets grows gigantically due to continuous data collection as well as increase of LBS users by developing a distributed version of our trajectory publishing algorithm which leveraging the MapReduce technique. As a consequence of users being anonymous, it becomes more challenging to evaluate the trustworthiness of messages disseminated by anonymous users. Existing research efforts are mainly focused on privacy-preserving authentication of users which helps in tracing malicious vehicles only after the damage is done. However, it is still not sufficient to prevent malicious behavior from happening in the case where attackers do not care whether they are caught later on. Therefore, it would be more effective to also evaluate the content of the message. In this dissertation, a novel information-oriented trustworthiness evaluation is presented which enables each individual user to evaluate the message content and make informed decisions --Abstract, page iii

Efficient Change Management of XML Documents

XML-based documents play a major role in modern information architectures and their corresponding work-flows. In this context, the ability to identify and represent differences between two versions of a document is essential. A second important aspect is the merging of document versions, which becomes crucial in parallel editing processes. Many different approaches exist that meet these challenges. Most rely on operational transformation or document annotation. In both approaches, the operations leading to changes are tracked, which requires corresponding editing applications. In the context of software development, however, a state-based approach is common. Here, document versions are compared and merged using external tools, called diff and patch. This allows users for freely editing documents without being tightened to special tools. Approaches exist that are able to compare XML documents. A corresponding merge capability is still not available. In this thesis, I present a comprehensive framework that allows for comparing and merging of XML documents using a state-based approach. Its design is based on an analysis of XML documents and their modification patterns. The heart of the framework is a context-oriented delta model. I present a diff algorithm that appears to be highly efficient in terms of speed and delta quality. The patch algorithm is able to merge document versions efficiently and reliably. The efficiency and the reliability of my approach are verified using a competitive test scenario

Privacy in rfid and mobile objects

Los sistemas RFID permiten la identificación rápida y automática de etiquetas RFID a través de un canal de comunicación inalámbrico. Dichas etiquetas son dispositivos con cierto poder de cómputo y capacidad de almacenamiento de información. Es por ello que los objetos que contienen una etiqueta RFID adherida permiten la lectura de una cantidad rica y variada de datos que los describen y caracterizan, por ejemplo, un código único de identificación, el nombre, el modelo o la fecha de expiración. Además, esta información puede ser leída sin la necesidad de un contacto visual entre el lector y la etiqueta, lo cual agiliza considerablemente los procesos de inventariado, identificación, o control automático. Para que el uso de la tecnología RFID se generalice con éxito, es conveniente cumplir con varios objetivos: eficiencia, seguridad y protección de la privacidad. Sin embargo, el diseño de protocolos de identificación seguros, privados, y escalables es un reto difícil de abordar dada las restricciones computacionales de las etiquetas RFID y su naturaleza inalámbrica. Es por ello que, en la presente tesis, partimos de protocolos de identificación seguros y privados, y mostramos cómo se puede lograr escalabilidad mediante una arquitectura distribuida y colaborativa. De este modo, la seguridad y la privacidad se alcanzan mediante el propio protocolo de identificación, mientras que la escalabilidad se logra por medio de novedosos métodos colaborativos que consideran la posición espacial y temporal de las etiquetas RFID. Independientemente de los avances en protocolos inalámbricos de identificación, existen ataques que pueden superar exitosamente cualquiera de estos protocolos sin necesidad de conocer o descubrir claves secretas válidas ni de encontrar vulnerabilidades en sus implementaciones criptográficas. La idea de estos ataques, conocidos como ataques de “relay”, consiste en crear inadvertidamente un puente de comunicación entre una etiqueta legítima y un lector legítimo. De este modo, el adversario usa los derechos de la etiqueta legítima para pasar el protocolo de autenticación usado por el lector. Nótese que, dada la naturaleza inalámbrica de los protocolos RFID, este tipo de ataques representa una amenaza importante a la seguridad en sistemas RFID. En esta tesis proponemos un nuevo protocolo que además de autenticación realiza un chequeo de la distancia a la cual se encuentran el lector y la etiqueta. Este tipo de protocolos se conocen como protocolos de acotación de distancia, los cuales no impiden este tipo de ataques, pero sí pueden frustrarlos con alta probabilidad. Por último, afrontamos los problemas de privacidad asociados con la publicación de información recogida a través de sistemas RFID. En particular, nos concentramos en datos de movilidad que también pueden ser proporcionados por otros sistemas ampliamente usados tales como el sistema de posicionamiento global (GPS) y el sistema global de comunicaciones móviles. Nuestra solución se basa en la conocida noción de k-anonimato, alcanzada mediante permutaciones y microagregación. Para este fin, definimos una novedosa función de distancia entre trayectorias con la cual desarrollamos dos métodos diferentes de anonimización de trayectorias.Els sistemes RFID permeten la identificació ràpida i automàtica d’etiquetes RFID a través d’un canal de comunicació sense fils. Aquestes etiquetes són dispositius amb cert poder de còmput i amb capacitat d’emmagatzematge de informació. Es per això que els objectes que porten una etiqueta RFID adherida permeten la lectura d’una quantitat rica i variada de dades que els descriuen i caracteritzen, com per exemple un codi únic d’identificació, el nom, el model o la data d’expiració. A més, aquesta informació pot ser llegida sense la necessitat d’un contacte visual entre el lector i l’etiqueta, la qual cosa agilitza considerablement els processos d’inventariat, identificació o control automàtic. Per a que l’ús de la tecnologia RFID es generalitzi amb èxit, es convenient complir amb diversos objectius: eficiència, seguretat i protecció de la privacitat. No obstant això, el disseny de protocols d’identificació segurs, privats i escalables, es un repte difícil d’abordar dades les restriccions computacionals de les etiquetes RFID i la seva naturalesa sense fils. Es per això que, en la present tesi, partim de protocols d’identificació segurs i privats, i mostrem com es pot aconseguir escalabilitat mitjançant una arquitectura distribuïda i col•laborativa. D’aquesta manera, la seguretat i la privacitat s’aconsegueixen mitjançant el propi protocol d’identificació, mentre que l’escalabilitat s’aconsegueix per mitjà de nous protocols col•laboratius que consideren la posició espacial i temporal de les etiquetes RFID. Independentment dels avenços en protocols d’identificació sense fils, existeixen atacs que poden passar exitosament qualsevol d’aquests protocols sense necessitat de conèixer o descobrir claus secretes vàlides, ni de trobar vulnerabilitats a les seves implantacions criptogràfiques. La idea d’aquestos atacs, coneguts com atacs de “relay”, consisteix en crear inadvertidament un pont de comunicació entre una etiqueta legítima i un lector legítim. D’aquesta manera, l’adversari utilitza els drets de l’etiqueta legítima per passar el protocol d’autentificació utilitzat pel lector. Es important tindre en compte que, dada la naturalesa sense fils dels protocols RFID, aquests tipus d’atacs representen una amenaça important a la seguretat en sistemes RFID. En aquesta dissertació proposem un nou protocol que, a més d’autentificació, realitza una revisió de la distància a la qual es troben el lector i l’etiqueta. Aquests tipus de protocols es coneixen com a “distance-boulding protocols”, els quals no prevenen aquests tipus d’atacs, però si que poden frustrar-los amb alta probabilitat. Per últim, afrontem els problemes de privacitat associats amb la publicació de informació recol•lectada a través de sistemes RFID. En concret, ens concentrem en dades de mobilitat, que també poden ser proveïdes per altres sistemes àmpliament utilitzats tals com el sistema de posicionament global (GPS) i el sistema global de comunicacions mòbils. La nostra solució es basa en la coneguda noció de privacitat “k-anonymity” i parcialment en micro-agregació. Per a aquesta finalitat, definim una nova funció de distància entre trajectòries amb la qual desenvolupen dos mètodes diferents d’anonimització de trajectòries.Radio Frequency Identification (RFID) is a technology aimed at efficiently identifying and tracking goods and assets. Such identification may be performed without requiring line-of-sight alignment or physical contact between the RFID tag and the RFID reader, whilst tracking is naturally achieved due to the short interrogation field of RFID readers. That is why the reduction in price of the RFID tags has been accompanied with an increasing attention paid to this technology. However, since tags are resource-constrained devices sending identification data wirelessly, designing secure and private RFID identification protocols is a challenging task. This scenario is even more complex when scalability must be met by those protocols. Assuming the existence of a lightweight, secure, private and scalable RFID identification protocol, there exist other concerns surrounding the RFID technology. Some of them arise from the technology itself, such as distance checking, but others are related to the potential of RFID systems to gather huge amount of tracking data. Publishing and mining such moving objects data is essential to improve efficiency of supervisory control, assets management and localisation, transportation, etc. However, obvious privacy threats arise if an individual can be linked with some of those published trajectories. The present dissertation contributes to the design of algorithms and protocols aimed at dealing with the issues explained above. First, we propose a set of protocols and heuristics based on a distributed architecture that improve the efficiency of the identification process without compromising privacy or security. Moreover, we present a novel distance-bounding protocol based on graphs that is extremely low-resource consuming. Finally, we present two trajectory anonymisation methods aimed at preserving the individuals' privacy when their trajectories are released

A Garbled Circuit Accelerator for Arbitrary, Fast Privacy-Preserving Computation

Privacy and security have rapidly emerged as priorities in system design. One powerful solution for providing both is privacy-preserving computation, where functions are computed directly on encrypted data and control can be provided over how data is used. Garbled circuits (GCs) are a PPC technology that provide both confidential computing and control over how data is used. The challenge is that they incur significant performance overheads compared to plaintext. This paper proposes a novel garbled circuit accelerator and compiler, named HAAC, to mitigate performance overheads and make privacy-preserving computation more practical. HAAC is a hardware-software co-design. GCs are exemplars of co-design as programs are completely known at compile time, i.e., all dependence, memory accesses, and control flow are fixed. The design philosophy of HAAC is to keep hardware simple and efficient, maximizing area devoted to our proposed custom execution units and other circuits essential for high performance (e.g., on-chip storage). The compiler can leverage its program understanding to realize hardware's performance potential by generating effective instruction schedules, data layouts, and orchestrating off-chip events. In taking this approach we can achieve ASIC performance/efficiency without sacrificing generality. Insights of our approach include how co-design enables expressing arbitrary GC programs as streams, which simplifies hardware and enables complete memory-compute decoupling, and the development of a scratchpad that captures data reuse by tracking program execution, eliminating the need for costly hardware managed caches and tagging logic. We evaluate HAAC with VIP-Bench and achieve a speedup of 608$\times$ in 4.3mm$^2$ of area

Secure and Efficient Comparisons between Untrusted Parties

A vast number of online services is based on users contributing their personal information. Examples are manifold, including social networks, electronic commerce, sharing websites, lodging platforms, and genealogy. In all cases user privacy depends on a collective trust upon all involved intermediaries, like service providers, operators, administrators or even help desk staff. A single adversarial party in the whole chain of trust voids user privacy. Even more, the number of intermediaries is ever growing. Thus, user privacy must be preserved at every time and stage, independent of the intrinsic goals any involved party. Furthermore, next to these new services, traditional offline analytic systems are replaced by online services run in large data centers. Centralized processing of electronic medical records, genomic data or other health-related information is anticipated due to advances in medical research, better analytic results based on large amounts of medical information and lowered costs. In these scenarios privacy is of utmost concern due to the large amount of personal information contained within the centralized data. We focus on the challenge of privacy-preserving processing on genomic data, specifically comparing genomic sequences. The problem that arises is how to efficiently compare private sequences of two parties while preserving confidentiality of the compared data. It follows that the privacy of the data owner must be preserved, which means that as little information as possible must be leaked to any party participating in the comparison. Leakage can happen at several points during a comparison. The secured inputs for the comparing party might leak some information about the original input, or the output might leak information about the inputs. In the latter case, results of several comparisons can be combined to infer information about the confidential input of the party under observation. Genomic sequences serve as a use-case, but the proposed solutions are more general and can be applied to the generic field of privacy-preserving comparison of sequences. The solution should be efficient such that performing a comparison yields runtimes linear in the length of the input sequences and thus producing acceptable costs for a typical use-case. To tackle the problem of efficient, privacy-preserving sequence comparisons, we propose a framework consisting of three main parts. a) The basic protocol presents an efficient sequence comparison algorithm, which transforms a sequence into a set representation, allowing to approximate distance measures over input sequences using distance measures over sets. The sets are then represented by an efficient data structure - the Bloom filter -, which allows evaluation of certain set operations without storing the actual elements of the possibly large set. This representation yields low distortion for comparing similar sequences. Operations upon the set representation are carried out using efficient, partially homomorphic cryptographic systems for data confidentiality of the inputs. The output can be adjusted to either return the actual approximated distance or the result of an in-range check of the approximated distance. b) Building upon this efficient basic protocol we introduce the first mechanism to reduce the success of inference attacks by detecting and rejecting similar queries in a privacy-preserving way. This is achieved by generating generalized commitments for inputs. This generalization is done by treating inputs as messages received from a noise channel, upon which error-correction from coding theory is applied. This way similar inputs are defined as inputs having a hamming distance of their generalized inputs below a certain predefined threshold. We present a protocol to perform a zero-knowledge proof to assess if the generalized input is indeed a generalization of the actual input. Furthermore, we generalize a very efficient inference attack on privacy-preserving sequence comparison protocols and use it to evaluate our inference-control mechanism. c) The third part of the framework lightens the computational load of the client taking part in the comparison protocol by presenting a compression mechanism for partially homomorphic cryptographic schemes. It reduces the transmission and storage overhead induced by the semantically secure homomorphic encryption schemes, as well as encryption latency. The compression is achieved by constructing an asymmetric stream cipher such that the generated ciphertext can be converted into a ciphertext of an associated homomorphic encryption scheme without revealing any information about the plaintext. This is the first compression scheme available for partially homomorphic encryption schemes. Compression of ciphertexts of fully homomorphic encryption schemes are several orders of magnitude slower at the conversion from the transmission ciphertext to the homomorphically encrypted ciphertext. Indeed our compression scheme achieves optimal conversion performance. It further allows to generate keystreams offline and thus supports offloading to trusted devices. This way transmission-, storage- and power-efficiency is improved. We give security proofs for all relevant parts of the proposed protocols and algorithms to evaluate their security. A performance evaluation of the core components demonstrates the practicability of our proposed solutions including a theoretical analysis and practical experiments to show the accuracy as well as efficiency of approximations and probabilistic algorithms. Several variations and configurations to detect similar inputs are studied during an in-depth discussion of the inference-control mechanism. A human mitochondrial genome database is used for the practical evaluation to compare genomic sequences and detect similar inputs as described by the use-case. In summary we show that it is indeed possible to construct an efficient and privacy-preserving (genomic) sequences comparison, while being able to control the amount of information that leaves the comparison. To the best of our knowledge we also contribute to the field by proposing the first efficient privacy-preserving inference detection and control mechanism, as well as the first ciphertext compression system for partially homomorphic cryptographic systems