Daniel Liu

Anastasiya Belyaeva, Joel Shor, Daniel E. Cook et al.

Accurate genome sequencing can improve our understanding of biology and the genetic basis of disease. The standard approach for generating DNA sequences from PacBio instruments relies on HMM-based models. Here, we introduce Distilled DeepConsensus - a distilled transformer-encoder model for sequence correction, which improves upon the HMM-based methods with runtime constraints in mind. Distilled DeepConsensus is 1.3x faster and 1.5x smaller than its larger counterpart while improving the yield of high quality reads (Q30) over the HMM-based method by 1.69x (vs. 1.73x for larger model). With improved accuracy of genomic sequences, Distilled DeepConsensus improves downstream applications of genomic sequence analysis such as reducing variant calling errors by 39% (34% for larger model) and improving genome assembly quality by 3.8% (4.2% for larger model). We show that the representations learned by Distilled DeepConsensus are similar between faster and slower models.

Nick Angelou, Ayoub Benaissa, Bogdan Cebere et al.

We present a multi-language, cross-platform, open-source library for asymmetric private set intersection (PSI) and PSI-Cardinality (PSI-C). Our protocol combines traditional DDH-based PSI and PSI-C protocols with compression based on Bloom filters that helps reduce communication in the asymmetric setting. Currently, our library supports C++, C, Go, WebAssembly, JavaScript, Python, and Rust, and runs on both traditional hardware (x86) and browser targets. We further apply our library to two use cases: (i) a privacy-preserving contact tracing protocol that is compatible with existing approaches, but improves their privacy guarantees, and (ii) privacy-preserving machine learning on vertically partitioned data.

Daniel Liu, Ronald Yu, Hao Su

The importance of training robust neural network grows as 3D data is increasingly utilized in deep learning for vision tasks in robotics, drone control, and autonomous driving. One commonly used 3D data type is 3D point clouds, which describe shape information. We examine the problem of creating robust models from the perspective of the attacker, which is necessary in understanding how 3D neural networks can be exploited. We explore two categories of attacks: distributional attacks that involve imperceptible perturbations to the distribution of points, and shape attacks that involve deforming the shape represented by a point cloud. We explore three possible shape attacks for attacking 3D point cloud classification and show that some of them are able to be effective even against preprocessing steps, like the previously proposed point-removal defenses.

Daniel Liu, Ronald Yu, Hao Su

3D object classification and segmentation using deep neural networks has been extremely successful. As the problem of identifying 3D objects has many safety-critical applications, the neural networks have to be robust against adversarial changes to the input data set. There is a growing body of research on generating human-imperceptible adversarial attacks and defenses against them in the 2D image classification domain. However, 3D objects have various differences with 2D images, and this specific domain has not been rigorously studied so far. We present a preliminary evaluation of adversarial attacks on deep 3D point cloud classifiers, namely PointNet and PointNet++, by evaluating both white-box and black-box adversarial attacks that were proposed for 2D images and extending those attacks to reduce the perceptibility of the perturbations in 3D space. We also show the high effectiveness of simple defenses against those attacks by proposing new defenses that exploit the unique structure of 3D point clouds. Finally, we attempt to explain the effectiveness of the defenses through the intrinsic structures of both the point clouds and the neural network architectures. Overall, we find that networks that process 3D point cloud data are weak to adversarial attacks, but they are also more easily defensible compared to 2D image classifiers. Our investigation will provide the groundwork for future studies on improving the robustness of deep neural networks that handle 3D data.

Saehan Jo, Immanuel Trummer, Weicheng Yu et al.

We present a novel natural language query interface, the AggChecker, aimed at text summaries of relational data sets. The tool focuses on natural language claims that translate into an SQL query and a claimed query result. Similar in spirit to a spell checker, the AggChecker marks up text passages that seem to be inconsistent with the actual data. At the heart of the system is a probabilistic model that reasons about the input document in a holistic fashion. Based on claim keywords and the document structure, it maps each text claim to a probability distribution over associated query translations. By efficiently executing tens to hundreds of thousands of candidate translations for a typical input document, the system maps text claims to correctness probabilities. This process becomes practical via a specialized processing backend, avoiding redundant work via query merging and result caching. Verification is an interactive process in which users are shown tentative results, enabling them to take corrective actions if necessary. Our system was tested on a set of 53 public articles containing 392 claims. Our test cases include articles from major newspapers, summaries of survey results, and Wikipedia articles. Our tool revealed erroneous claims in roughly a third of test cases. A detailed user study shows that users using our tool are in average six times faster at checking text summaries, compared to generic SQL interfaces. In fully automated verification, our tool achieves significantly higher recall and precision than baselines from the areas of natural language query interfaces and fact-checking.