Topological Feature Vectors for Chatter Detection in Turning Processes

Machining processes are most accurately described using complex dynamical systems that include nonlinearities, time delays, and stochastic effects. Due to the nature of these models as well as the practical challenges which include time-varying parameters, the transition from numerical/analytical modeling of machining to the analysis of real cutting signals remains challenging. Some studies have focused on studying the time series of cutting processes using machine learning algorithms with the goal of identifying and predicting undesirable vibrations during machining referred to as chatter. These tools typically decompose the signal using Wavelet Packet Transforms (WPT) or Ensemble Empirical Mode Decomposition (EEMD). However, these methods require a significant overhead in identifying the feature vectors before a classifier can be trained. In this study, we present an alternative approach based on featurizing the time series of the cutting process using its topological features. We first embed the time series as a point cloud using Takens embedding. We then utilize Support Vector Machine, Logistic Regression, Random Forest and Gradient Boosting classifier combined with feature vectors derived from persistence diagrams, a tool from persistent homology, to encode chatter's distinguishing characteristics. We present the results for several choices of the topological feature vectors, and we compare our results to the WPT and EEMD methods using experimental turning data. Our results show that in two out of four cutting configurations the TDA-based features yield accuracies as high as 97%. We also show that combining Bezier curve approximation method and parallel computing can reduce runtime for persistence diagram computation of a single time series to less than a second thus making our approach suitable for online chatter detection.Comment: Implementations of parallel computing and Bezier curve approximation for persistence diagram computation are added into the manuscript. Abstract and results section are updated with respect to the results obtained from persistence diagrams computed with Bezier approximatio

Knowledge gaps in the early growth of semantic networks

Understanding the features of and mechanisms behind language learning can provide insights into the general process of knowledge acquisition. Recent methods from network science applied to language learning have advanced the field, particularly by noting associations between densely connected words and acquisition. However, the importance of sparse areas of the network, or knowledge gaps, remains unexplored. Here we create a semantic feature network in which words correspond to nodes and in which connections correspond to semantic similarity. We develop a new analytical approach built on principles of applied topology to query the prevalence of knowledge gaps, which we propose manifest as cavities within the network. We detect topological cavities of multiple dimensions in the growing semantic feature network of children ages 16 to 30 months. The pattern of cavity appearance matches that of a constrained null model, created by predefining the affinity of each node for connections. Furthermore, when word acquisition time is computed from children of mothers with differing levels of education, we find that despite variation at the word level, the global organization as measured by persistent homology remains comparable. We show that topological properties of a node correlate with filling in cavities better than simple lexical properties such as the length and frequency of the corresponding word. Finally, we show that the large-scale architecture of the semantic feature network is topologically accommodating to many node orders. We discuss the importance of topology in language learning, and we speculate that the formation and filling of knowledge gaps may be a robust feature of knowledge acquisition.Comment: 17 pages, 6 figure

Mutations strengthened SARS-CoV-2 infectivity

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infectivity is a major concern in coronavirus disease 2019 (COVID-19) prevention and economic reopening. However, rigorous determination of SARS-COV-2 infectivity is essentially impossible owing to its continuous evolution with over 13752 single nucleotide polymorphisms (SNP) variants in six different subtypes. We develop an advanced machine learning algorithm based on the algebraic topology to quantitatively evaluate the binding affinity changes of SARS-CoV-2 spike glycoprotein (S protein) and host angiotensin-converting enzyme 2 (ACE2) receptor following the mutations. Based on mutation-induced binding affinity changes, we reveal that five out of six SARS-CoV-2 subtypes have become either moderately or slightly more infectious, while one subtype has weakened its infectivity. We find that SARS-CoV-2 is slightly more infectious than SARS-CoV according to computed S protein-ACE2 binding affinity changes. Based on a systematic evaluation of all possible 3686 future mutations on the S protein receptor-binding domain (RBD), we show that most likely future mutations will make SARS-CoV-2 more infectious. Combining sequence alignment, probability analysis, and binding affinity calculation, we predict that a few residues on the receptor-binding motif (RBM), i.e., 452, 489, 500, 501, and 505, have very high chances to mutate into significantly more infectious COVID-19 strains.Comment: 24 pages, 2 tables and 19 figure

(Quasi)Periodicity Quantification in Video Data, Using Topology

This work introduces a novel framework for quantifying the presence and strength of recurrent dynamics in video data. Specifically, we provide continuous measures of periodicity (perfect repetition) and quasiperiodicity (superposition of periodic modes with non-commensurate periods), in a way which does not require segmentation, training, object tracking or 1-dimensional surrogate signals. Our methodology operates directly on video data. The approach combines ideas from nonlinear time series analysis (delay embeddings) and computational topology (persistent homology), by translating the problem of finding recurrent dynamics in video data, into the problem of determining the circularity or toroidality of an associated geometric space. Through extensive testing, we show the robustness of our scores with respect to several noise models/levels, we show that our periodicity score is superior to other methods when compared to human-generated periodicity rankings, and furthermore, we show that our quasiperiodicity score clearly indicates the presence of biphonation in videos of vibrating vocal folds, which has never before been accomplished end to end quantitatively.Comment: 27 pages, 1 column, 23 figures, SIAM Journal on Imaging Sciences, 201

Semantic spaces

Any natural language can be considered as a tool for producing large databases (consisting of texts, written, or discursive). This tool for its description in turn requires other large databases (dictionaries, grammars etc.). Nowadays, the notion of database is associated with computer processing and computer memory. However, a natural language resides also in human brains and functions in human communication, from interpersonal to intergenerational one. We discuss in this survey/research paper mathematical, in particular geometric, constructions, which help to bridge these two worlds. In particular, in this paper we consider the Vector Space Model of semantics based on frequency matrices, as used in Natural Language Processing. We investigate underlying geometries, formulated in terms of Grassmannians, projective spaces, and flag varieties. We formulate the relation between vector space models and semantic spaces based on semic axes in terms of projectability of subvarieties in Grassmannians and projective spaces. We interpret Latent Semantics as a geometric flow on Grassmannians. We also discuss how to formulate G\"ardenfors' notion of "meeting of minds" in our geometric setting.Comment: 32 pages, TeX, 1 eps figur

Real Image Denoising with Feature Attention

Deep convolutional neural networks perform better on images containing spatially invariant noise (synthetic noise); however, their performance is limited on real-noisy photographs and requires multiple stage network modeling. To advance the practicability of denoising algorithms, this paper proposes a novel single-stage blind real image denoising network (RIDNet) by employing a modular architecture. We use a residual on the residual structure to ease the flow of low-frequency information and apply feature attention to exploit the channel dependencies. Furthermore, the evaluation in terms of quantitative metrics and visual quality on three synthetic and four real noisy datasets against 19 state-of-the-art algorithms demonstrate the superiority of our RIDNet.Comment: Accepted in ICCV (Oral), 201

A topological approach for protein classification

Protein function and dynamics are closely related to its sequence and structure. However prediction of protein function and dynamics from its sequence and structure is still a fundamental challenge in molecular biology. Protein classification, which is typically done through measuring the similarity be- tween proteins based on protein sequence or physical information, serves as a crucial step toward the understanding of protein function and dynamics. Persistent homology is a new branch of algebraic topology that has found its success in the topological data analysis in a variety of disciplines, including molecular biology. The present work explores the potential of using persistent homology as an indepen- dent tool for protein classification. To this end, we propose a molecular topological fingerprint based support vector machine (MTF-SVM) classifier. Specifically, we construct machine learning feature vectors solely from protein topological fingerprints, which are topological invariants generated during the filtration process. To validate the present MTF-SVM approach, we consider four types of problems. First, we study protein-drug binding by using the M2 channel protein of influenza A virus. We achieve 96% accuracy in discriminating drug bound and unbound M2 channels. Additionally, we examine the use of MTF-SVM for the classification of hemoglobin molecules in their relaxed and taut forms and obtain about 80% accuracy. The identification of all alpha, all beta, and alpha-beta protein domains is carried out in our next study using 900 proteins. We have found a 85% success in this identifica- tion. Finally, we apply the present technique to 55 classification tasks of protein superfamilies over 1357 samples. An average accuracy of 82% is attained. The present study establishes computational topology as an independent and effective alternative for protein classification

Effective Connectivity-Based Neural Decoding: A Causal Interaction-Driven Approach

We propose a geometric model-free causality measurebased on multivariate delay embedding that can efficiently detect linear and nonlinear causal interactions between time series with no prior information. We then exploit the proposed causal interaction measure in real MEG data analysis. The results are used to construct effective connectivity maps of brain activity to decode different categories of visual stimuli. Moreover, we discovered that the MEG-based effective connectivity maps as a response to structured images exhibit more geometric patterns, as disclosed by analyzing the evolution of toplogical structures of the underlying networks using persistent homology. Extensive simulation and experimental result have been carried out to substantiate the capabilities of the proposed approach.Comment: 16 pages, 13 figures, 2 table

Time Series Featurization via Topological Data Analysis

We develop a novel algorithm for feature extraction in time series data by leveraging tools from topological data analysis. Our algorithm provides a simple, efficient way to successfully harness topological features of the attractor of the underlying dynamical system for an observed time series. The proposed methodology relies on the persistent landscapes and silhouette of the Rips complex obtained after a de-noising step based on principal components applied to a time-delayed embedding of a noisy, discrete time series sample. We analyze the stability properties of the proposed approach and show that the resulting TDA-based features are robust to sampling noise. Experiments on synthetic and real-world data demonstrate the effectiveness of our approach. We expect our method to provide new insights on feature extraction from granular, noisy time series data.Comment: 28 page

Machine Learning pipeline for discovering neuroimaging-based biomarkers in neurology and psychiatry

We consider a problem of diagnostic pattern recognition/classification from neuroimaging data. We propose a common data analysis pipeline for neuroimaging-based diagnostic classification problems using various ML algorithms and processing toolboxes for brain imaging. We illustrate the pipeline application by discovering new biomarkers for diagnostics of epilepsy and depression based on clinical and MRI/fMRI data for patients and healthy volunteers.Comment: 20 pages, 2 figure