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This study investigates how user demographics influence the linguistic characteristics and readability of the reviews and the performance of sentiment classification methods. Two restaurant review datasets representing consumers of distinct demographics, such as English language fluency levels, socio-culture, and geographic locations, are compared. It is observed that demographic dissimilarities affect various linguistic attributes, such as sentence structure and vocabulary usage of reviews. The Mann–Whitney U test indicates significant differences in these two sets of reviews on various linguistic aspects. Regarding the readability of the two corpora, no noticeable difference is perceived by Flesch Reading Ease (FRE) test. The discrepancy in the results of lexicon-based and machine learning-based sentiment classification methods in two corpora suggests that demography has an influential role in the performance of sentiment classifiers.

Although cryo-electron microscopy (cryo-EM) has been successfully used to derive atomic structures for many proteins, it is still challenging to derive atomic structures when the resolution of cryo-EM density maps is in the medium resolution range, such as 5–10 Å. Detection of protein secondary structures, such as helices and β-sheets, from cryo-EM density maps provides constraints for deriving atomic structures from such maps. As more deep learning methodologies are being developed for solving various molecular problems, effective tools are needed for users to access them. We have developed an effective software bundle, DeepSSETracer, for the detection of protein secondary structure from cryo-EM component maps in medium resolution. The bundle contains the network architecture and a U-Net model trained with a curriculum and gradient of episodic memory (GEM). The bundle integrates the deep neural network with the visualization capacity provided in ChimeraX. Using a Linux server that is remotely accessed by Windows users, it takes about 6 s on one CPU and one GPU for the trained deep neural network to detect secondary structures in a cryo-EM component map containing 446 amino acids. A test using 28 chain components of cryo-EM maps shows overall residue-level F1 scores of 0.72 and 0.65 to detect helices and β-sheets, respectively. Although deep learning applications are built on software frameworks, such as PyTorch and Tensorflow, our pioneer work here shows that integration of deep learning applications with ChimeraX is a promising and effective approach. Our experiments show that the F1 score measured at the residue level is an effective evaluation of secondary structure detection for individual classes. The test using 28 cryo-EM component maps shows that DeepSSETracer detects β-sheets more accurately than Emap2sec+, with a weighted average residue-level F1 score of 0.65 and 0.42, respectively. It also shows that Emap2sec+ detects helices more accurately than DeepSSETracer with a weighted average residue-level F1 score of 0.77 and 0.72 respectively.

Bengali is a low-resource language that lacks tools and resources for various natural language processing (NLP) tasks, such as sentiment analysis or profanity identification. In Bengali, only the translated versions of English sentiment lexicons are available. Moreover, no dictionary exists for detecting profanity in Bengali social media text. This study introduces a Bengali sentiment lexicon, BengSentiLex, and a Bengali swear lexicon, BengSwearLex. For creating BengSentiLex, a cross-lingual methodology is proposed that utilizes a machine translation system, a review corpus, two English sentiment lexicons, pointwise mutual information (PMI), and supervised machine learning (ML) classifiers in various stages. A semi-automatic methodology is presented to develop BengSwearLex that leverages an obscene corpus, word embedding, and part-of-speech (POS) taggers. The performance of BengSentiLex compared with the translated English lexicons in three evaluation datasets. BengSentiLex achieves 5%–50% improvement over the translated lexicons. For identifying profanity, BengSwearLex achieves documentlevel coverage of around 85% in an document-level in the evaluation dataset. The experimental results imply that BengSentiLex and BengSwearLex are effective resources for classifying sentiment and identifying profanity in Bengali social media content, respectively.

The presence of abusive and vulgar language in social media has become an issue of increasing concern in recent years. However, research pertaining to the prevalence and identification of vulgar language has remained largely unexplored in low-resource languages such as Bengali. In this paper, we provide the first comprehensive analysis on the presence of vulgarity in Bengali social media content. We develop two benchmark corpora consisting of 7,245 reviews collected from YouTube and manually annotate them into vulgar and non-vulgar categories. The manual annotation reveals the ubiquity of vulgar and swear words in Bengali social media content (i.e., in two corpora), ranging from 20% to 34%. To automatically identify vulgarity, we employ various approaches, such as classical machine learning (CML) classifiers, Stochastic Gradient Descent (SGD) optimizer, a deep learning (DL) based architecture, and lexicon-based methods. Although small in size, we find that the swear/vulgar lexicon is effective at identifying the vulgar language due to the high presence of some swear terms in Bengali social media. We observe that the performances of machine leanings (ML) classifiers are affected by the class distribution of the dataset. The DL-based BiLSTM (Bidirectional Long Short Term Memory) model yields the highest recall scores for identifying vulgarity in both datasets (i.e., in both original and class-balanced settings). Besides, the analysis reveals that vulgarity is highly correlated with negative sentiment in social media comments.

In recent years, supervised machine learning (ML) methods have realized remarkable performance gains for sentiment classification utilizing labeled data. However, labeled data are usually expensive to obtain, thus, not always achievable. When annotated data are unavailable, the unsupervised tools are exercised, which still lag behind the performance of supervised ML methods by a large margin. Therefore, in this work, we focus on improving the performance of sentiment classification from unlabeled data. We present a self-supervised hybrid methodology SSentiA (Self-supervised Sentiment Analyzer) that couples an ML classifier with a lexicon-based method for sentiment classification from unlabeled data. We first introduce LRSentiA (Lexical Rule-based Sentiment Analyzer), a lexicon-based method to predict the semantic orientation of a review along with the confidence score of prediction. Utilizing the confidence scores of LRSentiA, we generate highly accurate pseudo-labels for SSentiA that incorporates a supervised ML algorithm to improve the performance of sentiment classification for less polarized and complex reviews. We compare the performances of LRSentiA and SSSentA with the existing unsupervised, lexicon-based and self-supervised methods in multiple datasets. The LRSentiA performs similarly to the existing lexicon-based methods in both binary and 3-class sentiment analysis. By combining LRSentiA with an ML classifier, the hybrid approach SSentiA attains 10%–30% improvements in macro F1 score for both binary and 3-class sentiment analysis. The results suggest that in domains where annotated data are unavailable, SSentiA can significantly improve the performance of sentiment classification. Moreover, we demonstrate that using 30%–60% annotated training data, SSentiA delivers similar performances of the fully labeled training dataset.

Within cells, cytoskeletal filaments are often arranged into loosely aligned bundles. These fibrous bundles are dense enough to exhibit a certain regularity and mean direction, however, their packing is not sufficient to impose a symmetry between—or specific shape on—individual filaments. This intermediate regularity is computationally difficult to handle because individual filaments have a certain directional freedom, however, the filament densities are not well segmented from each other (especially in the presence of noise, such as in cryo-electron tomography). In this paper, we develop a dynamic programming-based framework, Spaghetti Tracer, to characterizing the structural arrangement of filaments in the challenging 3D maps of subcellular components. Assuming that the tomogram can be rotated such that the filaments are oriented in a mean direction, the proposed framework first identifies local seed points for candidate filament segments, which are then grown from the seeds using a dynamic programming algorithm. We validate various algorithmic variations of our framework on simulated tomograms that closely mimic the noise and appearance of experimental maps. As we know the ground truth in the simulated tomograms, the statistical analysis consisting of precision, recall, and F1 scores allows us to optimize the performance of this new approach. We find that a bipyramidal accumulation scheme for path density is superior to straight-line accumulation. In addition, the multiplication of forward and backward path densities provides for an efficient filter that lifts the filament density above the noise level. Resulting from our tests is a robust method that can be expected to perform well (F1 scores 0.86–0.95) under experimental noise conditions.

The scientometric indices, such as the journal Impact Factor (IF) or SCImago Journal Rank (SJR), often play a determining role while choosing a journal for possible publication. The Editor-in-Chief (EiC), also known as a lead editor or chief editor, usually decides the outcomes (e.g., accept, reject) of the submitted manuscripts taking the reviewer’s feedback into account. This study investigates the associations between the EiC’s scholarly reputation (i.e., citation-level metrics) and the rankings of top Bioinformatics and Computational Biology (BCB) and Medical Informatics (MI) journals. I consider three scholarly indices (i.e., citation, h-index, and i-10 index) of the EiC and four scientometric indices (i.e., h5-index, h5-median, impact factor, and SJR) of various journals. To study the correlation between scientometric indices of the EiC and journal, I apply Spearman (ρ) and Kendall (τ) correlation coefficients. Moreover, I employ machine learning (ML) models for the journal’s SJR and IF predictions leveraging the EiC’s scholarly reputation indices. The analysis reveals no correlation between the EiC’s scholarly achievement and the journal’s quantitative metrics. ML models yield high prediction errors for SJR and IF estimations, which suggests that the EiC’s scholarly indices are not good representations of the journal rankings.

Cryo-electron tomography (cryo-ET) is a powerful method of visualizing the three-dimensional organization of supramolecular complexes, such as the cytoskeleton, in their native cell and tissue contexts. Due to its minimal electron dose and reconstruction artifacts arising from the missing wedge during data collection, cryo-ET typically results in noisy density maps that display anisotropic XY versus Z resolution. Molecular crowding further exacerbates the challenge of automatically detecting supramolecular complexes, such as the actin bundle in hair cell stereocilia. Stereocilia are pivotal to the mechanoelectrical transduction process in inner ear sensory epithelial hair cells. Given the complexity and dense arrangement of actin bundles, traditional approaches to filament detection and tracing have failed in these cases. In this study, we introduce BundleTrac, an effective method to trace hundreds of filaments in a bundle. A comparison between BundleTrac and manually tracing the actin filaments in a stereocilium showed that BundleTrac accurately built 326 of 330 filaments (98.8%), with an overall cross-distance of 1.3 voxels for the 330 filaments. BundleTrac is an effective semi-automatic modeling approach in which a seed point is provided for each filament and the rest of the filament is computationally identified. We also demonstrate the potential of a denoising method that uses a polynomial regression to address the resolution and high-noise anisotropic environment of the density map.

Cryo-electron microscopy (cryo-EM) is a structure determination method for large molecular complexes. As more and more atomic structures are determined using this technique, it is becoming possible to perform statistical characterization of side-chain conformations. Two data sets were involved to characterize block lengths for each of the 18 types of amino acids. One set contains 9131 structures resolved using X-ray crystallography from density maps with better than or equal to 1.5 Å resolutions, and the other contains 237 protein structures derived from cryo-EM density maps with 2–4 Å resolutions. The results show that the normalized probability density function of block lengths is similar between the X-ray data set and the cryo-EM data set for most of the residue types, but differences were observed for ARG, GLU, ILE, LYS, PHE, TRP, and TYR for which conformations with certain shorter block lengths are more likely to be observed in the cryo-EM set with 2–4 Å resolutions.