Pulasthi Wickramasinghe

Pulasthi Wickramasinghe, Geoffrey Fox

Multidimensional scaling of gene sequence data has long played a vital role in analysing gene sequence data to identify clusters and patterns. However the computation complexities and memory requirements of state-of-the-art dimensional scaling algorithms make it infeasible to scale to large datasets. In this paper we present an autoencoder-based dimensional reduction model which can easily scale to datasets containing millions of gene sequences, while attaining results comparable to state-of-the-art MDS algorithms with minimal resource requirements. The model also supports out-of-sample data points with a 99.5%+ accuracy based on our experiments. The proposed model is evaluated against DAMDS with a real world fungi gene sequence dataset. The presented results showcase the effectiveness of the autoencoder-based dimension reduction model and its advantages.

Niranda Perera, Vibhatha Abeykoon, Chathura Widanage et al.

In the current era of Big Data, data engineering has transformed into an essential field of study across many branches of science. Advancements in Artificial Intelligence (AI) have broadened the scope of data engineering and opened up new applications in both enterprise and research communities. Aggregations (also termed reduce in functional programming) are an integral functionality in these applications. They are traditionally aimed at generating meaningful information on large data-sets, and today, they are being used for engineering more effective features for complex AI models. Aggregations are usually carried out on top of data abstractions such as tables/ arrays and are combined with other operations such as grouping of values. There are frameworks that excel in the said domains individually. But, we believe that there is an essential requirement for a data analytics tool that can universally integrate with existing frameworks, and thereby increase the productivity and efficiency of the entire data analytics pipeline. Cylon endeavors to fulfill this void. In this paper, we present Cylon's fast and scalable aggregation operations implemented on top of a distributed in-memory table structure that universally integrates with existing frameworks.

Vibhatha Abeykoon, Niranda Perera, Chathura Widanage et al.

Data engineering is becoming an increasingly important part of scientific discoveries with the adoption of deep learning and machine learning. Data engineering deals with a variety of data formats, storage, data extraction, transformation, and data movements. One goal of data engineering is to transform data from original data to vector/matrix/tensor formats accepted by deep learning and machine learning applications. There are many structures such as tables, graphs, and trees to represent data in these data engineering phases. Among them, tables are a versatile and commonly used format to load and process data. In this paper, we present a distributed Python API based on table abstraction for representing and processing data. Unlike existing state-of-the-art data engineering tools written purely in Python, our solution adopts high performance compute kernels in C++, with an in-memory table representation with Cython-based Python bindings. In the core system, we use MPI for distributed memory computations with a data-parallel approach for processing large datasets in HPC clusters.