A query suggestion workflow for life science IR-systems

Summary Information Retrieval (IR) plays a central role in the exploration and interpretation of integrated biological datasets that represent the heterogeneous ecosystem of life sciences. Here, keyword based query systems are popular user interfaces. In turn, to a large extend, the used query phrases determine the quality of the search result and the effort a scientist has to invest for query refinement. In this context, computer aided query expansion and suggestion is one of the most challenging tasks for life science information systems. Existing query front-ends support aspects like spelling correction, query refinement or query expansion. However, the majority of the front-ends only make limited use of enhanced IR algorithms to implement comprehensive and computer aided query refinement workflows. In this work, we present the design of a multi-stage query suggestion workflow and its implementation in the life science IR system LAILAPS. The presented workflow includes enhanced tokenisation, word breaking, spelling correction, query expansion and query suggestion ranking. A spelling correction benchmark with 5,401 queries and manually selected use cases for query expansion demonstrate the performance of the implemented workflow and its advantages compared with state-of-the-art systems.</jats:p

A Query Suggestion Workflow for Life Science IR-Systems

Information Retrieval (IR) plays a central role in the exploration and interpretation of integrated biological datasets that represent the heterogeneous ecosystem of life sciences. Here, keyword based query systems are popular user interfaces. In turn, to a large extend, the used query phrases determine the quality of the search result and the effort a scientist has to invest for query refinement

KnetMiner - An integrated data platform for gene mining and biological knowledge discovery

Hassani-Pak K. KnetMiner - An integrated data platform for gene mining and biological knowledge discovery. Bielefeld: Universität Bielefeld; 2017.Discovery of novel genes that control important phenotypes and diseases is one of the key challenges in biological sciences. Now, in the post-genomics era, scientists have access to a vast range of genomes, genotypes, phenotypes and ‘omics data which - when used systematically - can help to gain new insights and make faster discoveries. However, the volume and diversity of such un-integrated data is often seen as a burden that only those with specialist bioinformatics skills, but often only minimal specialist biological knowledge, can penetrate. Therefore, new tools are required to allow researchers to connect, explore and compare large-scale datasets to identify the genes and pathways that control important phenotypes and diseases in plants, animals and humans. KnetMiner, with a silent "K" and standing for Knowledge Network Miner, is a suite of open-source software tools for integrating and visualising large biological datasets. The software mines the myriad databases that describe an organism’s biology to present links between relevant pieces of information, such as genes, biological pathways, phenotypes and publications with the aim to provide leads for scientists who are investigating the molecular basis for a particular trait. The KnetMiner approach is based on 1) integration of heterogeneous, complex and interconnected biological information into a knowledge graph; 2) text-mining to enrich the knowledge graph with novel relations extracted from literature; 3) graph queries of varying depths to find paths between genes and evidence nodes; 4) evidence-based gene rank algorithm that combines graph and information theory; 5) fast search and interactive knowledge visualisation techniques. Overall, [KnetMiner](http://knetminer.rothamsted.ac.uk) is a publicly available resource that helps scientists trawl diverse biological databases for clues to design better crop varieties and understand diseases. The key strength of KnetMiner is to include the end user into the “interactive” knowledge discovery process with the goal of supporting human intelligence with machine intelligence

Analyzing and Applying Cryptographic Mechanisms to Protect Privacy in Applications

Privacy-Enhancing Technologies (PETs) emerged as a technology-based response to the increased collection and storage of data as well as the associated threats to individuals' privacy in modern applications. They rely on a variety of cryptographic mechanisms that allow to perform some computation without directly obtaining knowledge of plaintext information. However, many challenges have so far prevented effective real-world usage in many existing applications. For one, some mechanisms leak some information or have been proposed outside of security models established within the cryptographic community, leaving open how effective they are at protecting privacy in various applications. Additionally, a major challenge causing PETs to remain largely academic is their practicality-in both efficiency and usability. Cryptographic mechanisms introduce a lot of overhead, which is mostly prohibitive, and due to a lack of high-level tools are very hard to integrate for outsiders. In this thesis, we move towards making PETs more effective and practical in protecting privacy in numerous applications. We take a two-sided approach of first analyzing the effective security (cryptanalysis) of candidate mechanisms and then building constructions and tools (cryptographic engineering) for practical use in specified emerging applications in the domain of machine learning crucial to modern use cases. In the process, we incorporate an interdisciplinary perspective for analyzing mechanisms and by collaboratively building privacy-preserving architectures with requirements from the application domains' experts. Cryptanalysis. While mechanisms like Homomorphic Encryption (HE) or Secure Multi-Party Computation (SMPC) provably leak no additional information, Encrypted Search Algorithms (ESAs) and Randomization-only Two-Party Computation (RoTPC) possess additional properties that require cryptanalysis to determine effective privacy protection. ESAs allow for search on encrypted data, an important functionality in many applications. Most efficient ESAs possess some form of well-defined information leakage, which is cryptanalyzed via a breadth of so-called leakage attacks proposed in the literature. However, it is difficult to assess their practical effectiveness given that previous evaluations were closed-source, used restricted data, and made assumptions about (among others) the query distribution because real-world query data is very hard to find. For these reasons, we re-implement known leakage attacks in an open-source framework and perform a systematic empirical re-evaluation of them using a variety of new data sources that, for the first time, contain real-world query data. We obtain many more complete and novel results where attacks work much better or much worse than what was expected based on previous evaluations. RoTPC mechanisms require cryptanalysis as they do not rely on established techniques and security models, instead obfuscating messages using only randomizations. A prominent protocol is a privacy-preserving scalar product protocol by Lu et al. (IEEE TPDS'13). We show that this protocol is formally insecure and that this translates to practical insecurity by presenting attacks that even allow to test for certain inputs, making the case for more scrutiny of RoTPC protocols used as PETs. This part of the thesis is based on the following two publications: [KKM+22] S. KAMARA, A. KATI, T. MOATAZ, T. SCHNEIDER, A. TREIBER, M. YONLI. “SoK: Cryptanalysis of Encrypted Search with LEAKER - A framework for LEakage AttacK Evaluation on Real-world data”. In: 7th IEEE European Symposium on Security and Privacy (EuroS&P’22). Full version: https://ia.cr/2021/1035. Code: https://encrypto.de/code/LEAKER. IEEE, 2022, pp. 90–108. Appendix A. [ST20] T. SCHNEIDER , A. TREIBER. “A Comment on Privacy-Preserving Scalar Product Protocols as proposed in “SPOC””. In: IEEE Transactions on Parallel and Distributed Systems (TPDS) 31.3 (2020). Full version: https://arxiv.org/abs/1906.04862. Code: https://encrypto.de/code/SPOCattack, pp. 543–546. CORE Rank A*. Appendix B. Cryptographic Engineering. Given the above results about cryptanalysis, we investigate using the leakage-free and provably-secure cryptographic mechanisms of HE and SMPC to protect privacy in machine learning applications. As much of the cryptographic community has focused on PETs for neural network applications, we focus on two other important applications and models: Speaker recognition and sum product networks. We particularly show the efficiency of our solutions in possible real-world scenarios and provide tools usable for non-domain experts. In speaker recognition, a user's voice data is matched with reference data stored at the service provider. Using HE and SMPC, we build the first privacy-preserving speaker recognition system that includes the state-of-the-art technique of cohort score normalization using cohort pruning via SMPC. Then, we build a privacy-preserving speaker recognition system relying solely on SMPC, which we show outperforms previous solutions based on HE by a factor of up to 4000x. We show that both our solutions comply with specific standards for biometric information protection and, thus, are effective and practical PETs for speaker recognition. Sum Product Networks (SPNs) are noteworthy probabilistic graphical models that-like neural networks-also need efficient methods for privacy-preserving inference as a PET. We present CryptoSPN, which uses SMPC for privacy-preserving inference of SPNs that (due to a combination of machine learning and cryptographic techniques and contrary to most works on neural networks) even hides the network structure. Our implementation is integrated into the prominent SPN framework SPFlow and evaluates medium-sized SPNs within seconds. This part of the thesis is based on the following three publications: [NPT+19] A. NAUTSCH, J. PATINO, A. TREIBER, T. STAFYLAKIS, P. MIZERA, M. TODISCO, T. SCHNEIDER, N. EVANS. Privacy-Preserving Speaker Recognition with Cohort Score Normalisation”. In: 20th Conference of the International Speech Communication Association (INTERSPEECH’19). Online: https://arxiv.org/abs/1907.03454. International Speech Communication Association (ISCA), 2019, pp. 2868–2872. CORE Rank A. Appendix C. [TNK+19] A. TREIBER, A. NAUTSCH , J. KOLBERG , T. SCHNEIDER , C. BUSCH. “Privacy-Preserving PLDA Speaker Verification using Outsourced Secure Computation”. In: Speech Communication 114 (2019). Online: https://encrypto.de/papers/TNKSB19.pdf. Code: https://encrypto.de/code/PrivateASV, pp. 60–71. CORE Rank B. Appendix D. [TMW+20] A. TREIBER , A. MOLINA , C. WEINERT , T. SCHNEIDER , K. KERSTING. “CryptoSPN: Privacy-preserving Sum-Product Network Inference”. In: 24th European Conference on Artificial Intelligence (ECAI’20). Full version: https://arxiv.org/abs/2002.00801. Code: https://encrypto.de/code/CryptoSPN. IOS Press, 2020, pp. 1946–1953. CORE Rank A. Appendix E. Overall, this thesis contributes to a broader security analysis of cryptographic mechanisms and new systems and tools to effectively protect privacy in various sought-after applications