Spin: An Efficient Secure Computation Framework with GPU Acceleration

Accuracy and efficiency remain challenges for multi-party computation (MPC) frameworks. Spin is a GPU-accelerated MPC framework that supports multiple computation parties and a dishonest majority adversarial setup. We propose optimized protocols for non-linear functions that are critical for machine learning, as well as several novel optimizations specific to attention that is the fundamental unit of Transformer models, allowing Spin to perform non-trivial CNNs training and Transformer inference without sacrificing security. At the backend level, Spin leverages GPU, CPU, and RDMA-enabled smart network cards for acceleration. Comprehensive evaluations demonstrate that Spin can be up to $2\times$ faster than the state-of-the-art for deep neural network training. For inference on a Transformer model with 18.9 million parameters, our attention-specific optimizations enable Spin to achieve better efficiency, less communication, and better accuracy

Secure Poisson Regression

We introduce the first construction for secure two-party computation of Poisson regression, which enables two parties who hold shares of the input samples to learn only the resulting Poisson model while protecting the privacy of the inputs. Our construction relies on new protocols for secure fixed-point exponentiation and correlated matrix multiplications. Our secure exponentiation construction avoids expensive bit decomposition and achieves orders of magnitude improvement in both online and offline costs over state of the art works. As a result, the dominant cost for our secure Poisson regression are matrix multiplications with one fixed matrix. We introduce a new technique, called correlated Beaver triples, which enables many such multiplications at the cost of roughly one matrix multiplication. This further brings down the cost of secure Poisson regression. We implement our constructions and show their extreme efficiency. In a LAN setting, our secure exponentiation for 20-bit fractional precision takes less than 0.07ms with a batch-size of 100,000. One iteration of secure Poisson regression on a dataset with 10,000 samples with 1000 binary features needs about 65.82s in the offline phase, 55.14s in the online phase and 17MB total communication. For several real datasets this translates into training that takes seconds and only a couple of MB communication

PyEvolve: a toolkit for statistical modelling of molecular evolution

BACKGROUND: Examining the distribution of variation has proven an extremely profitable technique in the effort to identify sequences of biological significance. Most approaches in the field, however, evaluate only the conserved portions of sequences – ignoring the biological significance of sequence differences. A suite of sophisticated likelihood based statistical models from the field of molecular evolution provides the basis for extracting the information from the full distribution of sequence variation. The number of different problems to which phylogeny-based maximum likelihood calculations can be applied is extensive. Available software packages that can perform likelihood calculations suffer from a lack of flexibility and scalability, or employ error-prone approaches to model parameterisation. RESULTS: Here we describe the implementation of PyEvolve, a toolkit for the application of existing, and development of new, statistical methods for molecular evolution. We present the object architecture and design schema of PyEvolve, which includes an adaptable multi-level parallelisation schema. The approach for defining new methods is illustrated by implementing a novel dinucleotide model of substitution that includes a parameter for mutation of methylated CpG's, which required 8 lines of standard Python code to define. Benchmarking was performed using either a dinucleotide or codon substitution model applied to an alignment of BRCA1 sequences from 20 mammals, or a 10 species subset. Up to five-fold parallel performance gains over serial were recorded. Compared to leading alternative software, PyEvolve exhibited significantly better real world performance for parameter rich models with a large data set, reducing the time required for optimisation from ~10 days to ~6 hours. CONCLUSION: PyEvolve provides flexible functionality that can be used either for statistical modelling of molecular evolution, or the development of new methods in the field. The toolkit can be used interactively or by writing and executing scripts. The toolkit uses efficient processes for specifying the parameterisation of statistical models, and implements numerous optimisations that make highly parameter rich likelihood functions solvable within hours on multi-cpu hardware. PyEvolve can be readily adapted in response to changing computational demands and hardware configurations to maximise performance. PyEvolve is released under the GPL and can be downloaded from http://cbis.anu.edu.au/software webcite