Privacy Disclosure of Similarity in Speech and Language Processing

Speaker, author, and other biometric identification applications often compare a sample's similarity to a database of templates to determine the identity. Given that data may be noisy and similarity measures can be inaccurate, such a comparison may not reliably identify the true identity as the most similar. Still, even the similarity rank based on an inaccurate similarity measure can disclose private information about the true identity. We propose a methodology for quantifying the privacy disclosure of such a similarity rank by estimating its probability distribution. It is based on determining the histogram of the similarity rank of the true speaker, or when data is scarce, modeling the histogram with the beta-binomial distribution. We express the disclosure in terms of entropy (bits), such that the disclosure from independent features are additive. Our experiments demonstrate that all tested speaker and author characterizations contain personally identifying information (PII) that can aid in identification, with embeddings from speaker recognition algorithms containing the most information, followed by phone embeddings, linguistic embeddings, and fundamental frequency. Our initial experiments show that the disclosure of PII increases with the length of test samples, but it is bounded by the length of database templates. The provided metric, similarity rank disclosure, provides a way to compare the disclosure of PII between biometric features and merge them to aid identification. It can thus aid in the holistic evaluation of threats to privacy in speech and other biometric technologies.

Machine and deep learning methods for predicting 3D genome organization

Three-Dimensional (3D) chromatin interactions, such as enhancer-promoter interactions (EPIs), loops, Topologically Associating Domains (TADs), and A/B compartments play critical roles in a wide range of cellular processes by regulating gene expression. Recent development of chromatin conformation capture technologies has enabled genome-wide profiling of various 3D structures, even with single cells. However, current catalogs of 3D structures remain incomplete and unreliable due to differences in technology, tools, and low data resolution. Machine learning methods have emerged as an alternative to obtain missing 3D interactions and/or improve resolution. Such methods frequently use genome annotation data (ChIP-seq, DNAse-seq, etc.), DNA sequencing information (k-mers, Transcription Factor Binding Site (TFBS) motifs), and other genomic properties to learn the associations between genomic features and chromatin interactions. In this review, we discuss computational tools for predicting three types of 3D interactions (EPIs, chromatin interactions, TAD boundaries) and analyze their pros and cons. We also point out obstacles of computational prediction of 3D interactions and suggest future research directions.