Engineering topics
Alexandrov, Boian
Publications and source records attributed to Alexandrov, Boian.
Enhancing Code Translation in Language Models with Few-Shot Learning via Retrieval-Augmented Generation
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Tensor Extraction of Latent Features (TELF)
Tensor ELF is a user-friendly parallel tensor decomposition Python toolbox that includes a suite of machine learning algorithms for CPU and GPU architectures for the analysis of sparse and dense data including utility tools for pre-processing and post-processing.
Defense of Supervised and Unsupervised Machine Learning Models
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Navier-Stokes: Tensorization of the Sod and Blow-off problems [Slides]
Abstract not provided.
Tensors Optimized for High-level Research (THOR): an efficient and easy-to-use library for tensor networks [Slides]
What is THOR library? The THOR Project (Tensors Optimized for High-level Research) aims to advance the state-of-the-art in tensor calculations, manipulation, and research. The library contains versions in Fortran, Matlab, and Python.
Configurational Integrals Solved by Tensorization [Slides]
Abstract not provided.
Conotoxin Prediction: New Features to Increase Prediction Accuracy
Conotoxins are toxic, disulfide-bond-rich peptides from cone snail venom that target a wide range of receptors and ion channels with multiple pathophysiological effects. Conotoxins have extraordinary potential for medical therapeutics that include cancer, microbial infections, epilepsy, autoimmune diseases, neurological conditions, and cardiovascular disorders. Despite the potential for these compounds in novel therapeutic treatment development, the process of identifying and characterizing the toxicities of conotoxins is difficult, costly, and time-consuming. This challenge requires a series of diverse, complex, and labor-intensive biological, toxicological, and analytical techniques for effective characterization. While recent attempts, using machine learning based solely on primary amino acid sequences to predict biological toxins (e.g., conotoxins and animal venoms), have improved toxin identification, these methods are limited due to peptide conformational flexibility and the high frequency of cysteines present in toxin sequences. This results in an enumerable set of disulfide-bridged foldamers with different conformations of the same primary amino acid sequence that affect function and toxicity levels. Consequently, a given peptide may be toxic when its cysteine residues form a particular disulfide-bond pattern, while alternative bonding patterns (isoforms) or its reduced form (free cysteines with no disulfide bridges) may have little or no toxicological effects. Similarly, the same disulfide-bond pattern may be possible for other peptide sequences and result in different conformations that all exhibit varying toxicities to the same receptor or to different receptors. We present here new features, when combined with primary sequence features to train machine learning algorithms to predict conotoxins, that significantly increase prediction accuracy.
AdversarialTensors
This library builds a framework for defending ML models against adversarial attacks. The library will be developed at various stages leading to publication and software release at each stage. We employ tensor decomposition strategies as preprocessing stages for the first stage to provide robustness against the prominent adversarial noise. In the second stage, we develop a latent noise generator capable of generating novel adversarial noise that threatens the existing state-of-the-art defense strategy. In the third stage, we develop a UNSUP-GAN model, where the generator is trained to denoise against latent noise and most adversarial noises. This generator can provide a robust adversarial attack against any unseen attack.
Distributed out-of-memory NMF on CPU/GPU architectures
We propose an efficient distributed out-of-memory implementation of the non-negative matrix factorization (NMF) algorithm for heterogeneous high-performance-computing systems. The proposed implementation is based on prior work on NMFk, which can perform automatic model selection and extract latent variables and patterns from data. In this work, we extend NMFk by adding support for dense and sparse matrix operation on multi-node, multi-GPU systems. The resulting algorithm is optimized for out-of-memory problems where the memory required to factorize a given matrix is greater than the available GPU memory. Memory complexity is reduced by batching/tiling strategies, and sparse and dense matrix operations are significantly accelerated with GPU cores (or tensor cores when available). Input/output latency associated with batch copies between host and device is hidden using CUDA streams to overlap data transfers and compute asynchronously, and latency associated with collective communications (both intra-node and inter-node) is reduced using optimized NVIDIA Collective Communication Library (NCCL) based communicators. Benchmark results show significant improvement, from 32X to 76x speedup, with the new implementation using GPUs over the CPU-based NMFk. Good weak scaling was demonstrated on up to 4096 multi-GPU cluster nodes with approximately 25,000 GPUs when decomposing a dense 340 Terabyte-size matrix and an 11 Exabyte-size sparse matrix of density 10 -6 .
Distributed non-negative RESCAL with automatic model selection for exascale data
Not Available
Challenging the Curse of Dimensionality in Multidimensional Numerical Integration by Using a Low-Rank Tensor-Train Format
Numerical integration is a basic step in the implementation of more complex numerical algorithms suitable, for example, to solve ordinary and partial differential equations. The straightforward extension of a one-dimensional integration rule to a multidimensional grid by the tensor product of the spatial directions is deemed to be practically infeasible beyond a relatively small number of dimensions, e.g., three or four. In fact, the computational burden in terms of storage and floating point operations scales exponentially with the number of dimensions. This phenomenon is known as the curse of dimensionality and motivated the development of alternative methods such as the Monte Carlo method. The tensor product approach can be very effective for high-dimensional numerical integration if we can resort to an accurate low-rank tensor-train representation of the integrand function. In this work, we discuss this approach and present numerical evidence showing that it is very competitive with the Monte Carlo method in terms of accuracy and computational costs up to several hundredths of dimensions if the integrand function is regular enough and a sufficiently accurate low-rank approximation is available.
Distributed Out-of-Memory SVD on CPU/GPU Architectures
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Special Session on Cutting Edge Approaches in Data Analytics for Nonproliferation.
Abstract not provided.
Factorization of Binary Matrices: Rank Relations, Uniqueness and Model Selection of Boolean Decomposition
The application of binary matrices are numerous. Representing a matrix as a mixture of a small collection of latent vectors via low-rank decomposition is often seen as an advantageous method to interpret and analyze data. In this work, we examine the factorizations of binary matrices using standard arithmetic (real and nonnegative) and logical operations (Boolean and $\mathbb{Z}$ 2 ). We examine the relationships between the different ranks, and discuss when factorization is unique. In particular, we characterize when a Boolean factorization X = W$\land$H has a unique W, a unique H (for a fixed W), and when both W and H are unique, given a rank constraint. We introduce a method for robust Boolean model selection, called BMFk, and show on numerical examples that BMFk not only accurately determines the correct number of Boolean latent features but reconstruct the pre-determined factors accurately.
Nonnegative canonical tensor decomposition with linear constraints: nnCANDELINC
Abstract There is an emerging interest for tensor factorization applications in big‐data analytics and machine learning. To speed up the factorization of extra‐large datasets, organized in multidimensional arrays (also known as tensors), easy to compute compression‐based tensor representations, such as, Tucker and tensor train formats, are used to approximate the initial large‐tensor. Further, tensor factorization is used to extract latent features that can facilitate discoveries of new mechanisms and signatures hidden in the data, where the explainability of the latent features is of principal importance. Nonnegative tensor factorization extracts latent features that are naturally sparse and parts of the data, which makes them easily interpretable. However, to take into account available domain knowledge and subject matter expertise, often additional constraints need to be imposed, which lead us to canonical decomposition with linear constraints (CANDELINC), a canonical polyadic decomposition with rank deficient factors. In CANDELINC, Tucker compression is used as a preprocessing step, which lead to a larger residual error but to more explainable latent features. Here, we propose a nonnegative CANDELINC (nnCANDELINC) accomplished via a specific nonnegative Tucker decomposition; we refer to as minimal or canonical nonnegative Tucker. We derive several results required to understand the specificity of nnCANDELINC, focusing on the difficulties of preserving the nonnegative rank of a tensor to its Tucker core and comparing the real valued to nonnegative case. Finally, we demonstrate nnCANDELINC performance on synthetic and real‐world examples.
pyDRESCALk
Modern data scientists are tasked to analyze ever-growing data sets with increasingly complex relationships. Tensor decompositions have come to play a central role in identifying underlying latent structures in higher-order data. The problem of fitting tensor models to different distributions is complicated by the combinations of size, dimensionality, and sparsity present in real world data. The situation demands efficient algorithms designed for shared-memory and distributed systems. This work will present new research that tackles these challenges on several different fronts, leveraging optimizations in numerical algorithms and sparse tensor representations in heterogeneous high performance computing environments.