Interactive Distillation of Large Single-Topic Corpora of Scientific Papers

Highly specific datasets of scientific literature are important for both research and education. However, it is difficult to build such datasets at scale. A common approach is to build these datasets reductively by applying topic modeling on an established corpus and selecting specific topics. A more robust but time-consuming approach is to build the dataset constructively in which a subject matter expert (SME) handpicks documents. This method does not scale and is prone to error as the dataset grows. Here we showcase a new tool, based on machine learning, for constructively generating targeted datasets of scientific literature. Given a small initial "core" corpus of papers, we build a citation network of documents. At each step of the citation network, we generate text embeddings and visualize the embeddings through dimensionality reduction. Papers are kept in the dataset if they are "similar" to the core or are otherwise pruned through human-in-the-loop selection. Additional insight into the papers is gained through sub-topic modeling using SeNMFk. We demonstrate our new tool for literature review by applying it to two different fields in machine learning.

MalwareDNA: Simultaneous Classification of Malware, Malware Families, and Novel Malware

Malware is one of the most dangerous and costly cyber threats to national security and a crucial factor in modern cyber-space. However, the adoption of machine learning (ML) based solutions against malware threats has been relatively slow. Shortcomings in the existing ML approaches are likely contributing to this problem. The majority of current ML approaches ignore real-world challenges such as the detection of novel malware. In addition, proposed ML approaches are often designed either for malware/benign-ware classification or malware family classification. Here we introduce and showcase preliminary capabilities of a new method that can perform precise identification of novel malware families, while also unifying the capability for malware/benign-ware classification and malware family classification into a single framework.

SeNMFk-SPLIT: Large Corpora Topic Modeling by Semantic Non-negative Matrix Factorization with Automatic Model Selection

As the amount of text data continues to grow, topic modeling is serving an important role in understanding the content hidden by the overwhelming quantity of documents. One popular topic modeling approach is non-negative matrix factorization (NMF), an unsupervised machine learning (ML) method. Recently, Semantic NMF with automatic model selection (SeNMFk) has been proposed as a modification to NMF. In addition to heuristically estimating the number of topics, SeNMFk also incorporates the semantic structure of the text. This is performed by jointly factorizing the term frequency-inverse document frequency (TF-IDF) matrix with the co-occurrence/word-context matrix, the values of which represent the number of times two words co-occur in a predetermined window of the text. In this paper, we introduce a novel distributed method, SeNMFk-SPLIT, for semantic topic extraction suitable for large corpora. Contrary to SeNMFk, our method enables the joint factorization of large documents by decomposing the word-context and term-document matrices separately. We demonstrate the capability of SeNMFk-SPLIT by applying it to the entire artificial intelligence (AI) and ML scientific literature uploaded on arXiv.

FedSPLIT: One-Shot Federated Recommendation System Based on Non-negative Joint Matrix Factorization and Knowledge Distillation

Non-negative matrix factorization (NMF) with missing-value completion is a well-known effective Collaborative Filtering (CF) method used to provide personalized user recommendations. However, traditional CF relies on the privacy-invasive collection of users' explicit and implicit feedback to build a central recommender model. One-shot federated learning has recently emerged as a method to mitigate the privacy problem while addressing the traditional communication bottleneck of federated learning. In this paper, we present the first unsupervised one-shot federated CF implementation, named FedSPLIT, based on NMF joint factorization. In our solution, the clients first apply local CF in-parallel to build distinct client-specific recommenders. Then, the privacy-preserving local item patterns and biases from each client are shared with the processor to perform joint factorization in order to extract the global item patterns. Extracted patterns are then aggregated to each client to build the local models via knowledge distillation. In our experiments, we demonstrate the feasibility of our approach with standard recommendation datasets. FedSPLIT can obtain similar results than the state of the art (and even outperform it in certain situations) with a substantial decrease in the number of communications.

Topic Analysis of Superconductivity Literature by Semantic Non-negative Matrix Factorization

We utilize a recently developed topic modeling method called SeNMFk, extending the standard Non-negative Matrix Factorization (NMF) methods by incorporating the semantic structure of the text, and adding a robust system for determining the number of topics. With SeNMFk, we were able to extract coherent topics validated by human experts. From these topics, a few are relatively general and cover broad concepts, while the majority can be precisely mapped to specific scientific effects or measurement techniques. The topics also differ by ubiquity, with only three topics prevalent in almost 40 percent of the abstract, while each specific topic tends to dominate a small subset of the abstracts. These results demonstrate the ability of SeNMFk to produce a layered and nuanced analysis of large scientific corpora.

COVID-19 Multidimensional Kaggle Literature Organization

The unprecedented outbreak of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), or COVID-19, continues to be a significant worldwide problem. As a result, a surge of new COVID-19 related research has followed suit. The growing number of publications requires document organization methods to identify relevant information. In this paper, we expand upon our previous work with clustering the CORD-19 dataset by applying multi-dimensional analysis methods. Tensor factorization is a powerful unsupervised learning method capable of discovering hidden patterns in a document corpus. We show that a higher-order representation of the corpus allows for the simultaneous grouping of similar articles, relevant journals, authors with similar research interests, and topic keywords. These groupings are identified within and among the latent components extracted via tensor decomposition. We further demonstrate the application of this method with a publicly available interactive visualization of the dataset.

Identification of Anomalous Diffusion Sources by Unsupervised Learning

Fractional Brownian motion (fBm) is a ubiquitous diffusion process in which the memory effects of the stochastic transport result in the mean squared particle displacement following a power law, $\langle {\Delta r}^2 \rangle \sim t^{\alpha}$, where the diffusion exponent $\alpha$ characterizes whether the transport is subdiffusive, ($\alpha<1$), diffusive ($\alpha = 1$), or superdiffusive, ($\alpha >1$). Due to the abundance of fBm processes in nature, significant efforts have been devoted to the identification and characterization of fBm sources in various phenomena. In practice, the identification of the fBm sources often relies on solving a complex and ill-posed inverse problem based on limited observed data. In the general case, the detected signals are formed by an unknown number of release sources, located at different locations and with different strengths, that act simultaneously. This means that the observed data is composed of mixtures of releases from an unknown number of sources, which makes the traditional inverse modeling approaches unreliable. Here, we report an unsupervised learning method, based on Nonnegative Matrix Factorization, that enables the identification of the unknown number of release sources as well the anomalous diffusion characteristics based on limited observed data and the general form of the corresponding fBm Green's function. We show that our method performs accurately for different types of sources and configurations with a predetermined number of sources with specific characteristics and introduced noise.

A Neural Network for Determination of Latent Dimensionality in Nonnegative Matrix Factorization

Non-negative Matrix Factorization (NMF) has proven to be a powerful unsupervised learning method for uncovering hidden features in complex and noisy data sets with applications in data mining, text recognition, dimension reduction, face recognition, anomaly detection, blind source separation, and many other fields. An important input for NMF is the latent dimensionality of the data, that is, the number of hidden features, K, present in the explored data set. Unfortunately, this quantity is rarely known a priori. We utilize a supervised machine learning approach in combination with a recent method for model determination, called NMFk, to determine the number of hidden features automatically. NMFk performs a set of NMF simulations on an ensemble of matrices, obtained by bootstrapping the initial data set, and determines which K produces stable groups of latent features that reconstruct the initial data set well. We then train a Multi-Layer Perceptron (MLP) classifier network to determine the correct number of latent features utilizing the statistics and characteristics of the NMF solutions, obtained from NMFk. In order to train the MLP classifier, a training set of 58,660 matrices with predetermined latent features were factorized with NMFk. The MLP classifier in conjunction with NMFk maintains a greater than 95% success rate when applied to a held out test set. Additionally, when applied to two well-known benchmark data sets, the swimmer and MIT face data, NMFk/MLP correctly recovered the established number of hidden features. Finally, we compared the accuracy of our method to the ARD, AIC and Stability-based methods.

Determination of Latent Dimensionality in International Trade Flow

Currently, high-dimensional data is ubiquitous in data science, which necessitates the development of techniques to decompose and interpret such multidimensional (aka tensor) datasets. Finding a low dimensional representation of the data, that is, its inherent structure, is one of the approaches that can serve to understand the dynamics of low dimensional latent features hidden in the data. Nonnegative RESCAL is one such technique, particularly well suited to analyze self-relational data, such as dynamic networks found in international trade flows. Nonnegative RESCAL computes a low dimensional tensor representation by finding the latent space containing multiple modalities. Estimating the dimensionality of this latent space is crucial for extracting meaningful latent features. Here, to determine the dimensionality of the latent space with nonnegative RESCAL, we propose a latent dimension determination method which is based on clustering of the solutions of multiple realizations of nonnegative RESCAL decompositions. We demonstrate the performance of our model selection method on synthetic data and then we apply our method to decompose a network of international trade flows data from International Monetary Fund and validate the resulting features against empirical facts from economic literature.