Human Papillomavirus (HPV) is the causal agent of 5% of cancers worldwide and the main cause of cervical cancer and it is also associated with a significant percentage of oropharyngeal and anogenital cancers. More than 60% of cervical cancers are caused by HPV16 genotype, which has been classified into lineages (A, B, C, and D). Lineages are related to the progression of cervical cancer and the current method to assess lineages is by building a Maximum Likelihood Tree (MLT); which is slow, it cannot assess poor sequenced samples, and annotation is done manually. In this study, we have developed a new model to assess HPV16 lineage using machine learning tools. A total of 645 HPV16 genomes were analyzed using Genome-Wide Association Study (GWAS), which identified 56 lineage-specific Single Nucleotide Polymorphisms (SNPs). From the SNPs found, training-test models were constructed using different algorithms such as Random Forest (RF), Support Vector Machine (SVM), and K-nearest neighbor (KNN). A distinct set of HPV16 sequences (n = 1,028), whose lineage was previously determined by MLT, was used for validation. The RF-based model allowed a precise assignment of HPV16 lineage, showing an accuracy of 99.5% in the known lineage samples. Moreover, the RF model could assess lineage to 273 samples that MLT could not determine. In terms of computer consuming time, the RF-based model was almost 40 times faster than MLT. Having a fast and efficient method for assigning HPV16 lineages,...

ABSTRACT Coronal mass ejections (CMEs) are the most geoeffective space weather phenomena, being associated with large geomagnetic storms, having the potential to cause disturbances to telecommunication, satellite network disruptions, power grid damages and failures. Thus, considering these storms' potential effects on human activities, accurate forecasts of the geoeffectiveness of CMEs are paramount. This work focuses on experimenting with different machine learning methods trained on white-light coronagraph datasets of close to sun CMEs, to estimate whether such a newly erupting ejection has the potential to induce geomagnetic activity. We developed binary classification models using logistic regression, K-Nearest Neighbors, Support Vector Machines, feed forward artificial neural networks, as well as ensemble models. At this time, we limited our forecast to exclusively use solar onset parameters, to ensure extended warning times. We discuss the main challenges of this task, namely the extreme imbalance between the number of geoeffective and ineffective events in our dataset, along with their numerous similarities and the limited number of available variables. We show that even in such conditions, adequate hit rates can be achieved with these models. INTRODUCTION The purpose of this work is to develop a machine learning (ML) based model that can predict whether a coronal mass ejection (CME) will be geoeffective, using only numerical solar parameters as input. Coronal mass ejections are solar eruptive events whose magnetically charged particles can, directly or indirectly, under certain circumstances, reach Earth and cause geomagnetic storms (GSs), i.e., be geoeffective. These storms represent perturbations in the Earth's magnetic field, which have the potential to lead to electrical systems and grids failure and/or damage, power outages, navigation errors, radio signal perturbations, significant exposure to dangerous radiations for astronauts during space missions, etc. Given the potential negative impacts of such storms, predicting their occurrence is paramount for enabling safeguarding of human technology (Schwenn 2006; Pulkkinen 2007; Council 2013; Vourlidas et al. 2019; Temmer 2021). The intensity of the storms can be measured by various geomagnetic indices such as Ap, Kp, AE, PC or Dst (see Lockwood 2013, and references therein). Herein, we have chosen to use the values of the Dst index (Sugiura 1964) to establish whether the magnetic field perturbations do, in fact, manifest as storms. This is an index that is calculated using four geomagnetic stations situated at low latitudes. Depending on the value of this index, it can be established whether these perturbations are associated with geomagnetic storms or not. In terms of storm intensity, one of the most popular classifications that takes into consideration the minimum value of the Dst index is that of Gonzalez et al. (1994).

Stuttering is a varied speech disorder that harms an individual's communication ability. Persons who stutter (PWS) often use speech therapy to cope with their condition. Improving speech recognition systems for people with such non-typical speech or tracking the effectiveness of speech therapy would require systems that can detect dysfluencies while at the same time being able to detect speech techniques acquired in therapy. This paper shows that fine-tuning wav2vec 2.0 [1] for the classification of stuttering on a sizeable English corpus containing stuttered speech, in conjunction with multi-task learning, boosts the effectiveness of the general-purpose wav2vec 2.0 features for detecting stuttering in speech; both within and across languages. We evaluate our method on FluencyBank , [2] and the German therapy-centric Kassel State of Fluency (KSoF) [3] dataset by training Support Vector Machine classifiers using features extracted from the finetuned models for six different stuttering-related event types: blocks, prolongations, sound repetitions, word repetitions, interjections, and - specific to therapy - speech modifications. Using embeddings from the fine-tuned models leads to relative classification performance gains up to 27% w.r.t. F1-score.

Online discussions, panels, talk page edits, etc., often contain harmful conversational content i.e., hate speech, death threats and offensive language, especially towards certain demographic groups. For example, individuals who identify as members of the LGBTQIA+ community and/or BIPOC (Black, Indigenous, People of Color) are at higher risk for abuse and harassment online. In this work, we first introduce a real-world dataset that will enable us to study and understand harmful online conversational content. Then, we conduct several exploratory data analysis experiments to gain deeper insights from the dataset. We later describe our approach for detecting harmful online Anti-LGBTQIA+ conversational content, and finally, we implement two baseline machine learning models (i.e., Support Vector Machine and Logistic Regression), and fine-tune 3 pre-trained large language models (BERT, RoBERTa, and HateBERT). Our findings verify that large language models can achieve very promising performance on detecting online Anti-LGBTQIA+ conversational content detection tasks.

Standardized tests play a crucial role in the detection of cognitive impairment. Previous work demonstrated that automatic detection of cognitive impairment is possible using audio data from a standardized picture description task. The presented study goes beyond that, evaluating our methods on data taken from two standardized neuropsychological tests, namely the German SKT and a German version of the CERAD-NB, and a semi-structured clinical interview between a patient and a psychologist. For the tests, we focus on speech recordings of three sub-tests: reading numbers (SKT 3), interference (SKT 7), and verbal fluency (CERAD-NB 1). We show that acoustic features from standardized tests can be used to reliably discriminate cognitively impaired individuals from non-impaired ones. Furthermore, we provide evidence that even features extracted from random speech samples of the interview can be a discriminator of cognitive impairment. In our baseline experiments, we use OpenSMILE features and Support Vector Machine classifiers. In an improved setup, we show that using wav2vec 2.0 features instead, we can achieve an accuracy of up to 85%.

The theoretical analysis of multi-class classification has proved that the existing multi-class classification methods can train a classifier with high classification accuracy on the test set, when the instances are precise in the training and test sets with same distribution and enough instances can be collected in the training set. However, one limitation with multi-class classification has not been solved: how to improve the classification accuracy of multi-class classification problems when only imprecise observations are available. Hence, in this paper, we propose a novel framework to address a new realistic problem called multi-class classification with imprecise observations (MCIMO), where we need to train a classifier with fuzzy-feature observations. Firstly, we give the theoretical analysis of the MCIMO problem based on fuzzy Rademacher complexity. Then, two practical algorithms based on support vector machine and neural networks are constructed to solve the proposed new problem. Experiments on both synthetic and real-world datasets verify the rationality of our theoretical analysis and the efficacy of the proposed algorithms.

Kernel matrices are crucial in many learning tasks such as support vector machines or kernel ridge regression. The kernel matrix is typically dense and large-scale. Depending on the dimension of the feature space even the computation of all of its entries in reasonable time becomes a challenging task. For such dense matrices the cost of a matrix-vector product scales quadratically with the dimensionality N , if no customized methods are applied. We propose the use of an ANOVA kernel, where we construct several kernels based on lower-dimensional feature spaces for which we provide fast algorithms realizing the matrix-vector products. We employ the non-equispaced fast Fourier transform (NFFT), which is of linear complexity for fixed accuracy. Based on a feature grouping approach, we then show how the fast matrix-vector products can be embedded into a learning method choosing kernel ridge regression and the conjugate gradient solver. We illustrate the performance of our approach on several data sets.

This paper empirically investigates the influence of different data splits and splitting strategies on the performance of dysfluency detection systems. For this, we perform experiments using wav2vec 2.0 models with a classification head as well as support vector machines (SVM) in conjunction with the features extracted from the wav2vec 2.0 model to detect dysfluencies. We train and evaluate the systems with different non-speaker-exclusive and speaker-exclusive splits of the Stuttering Events in Podcasts (SEP-28k) dataset to shed some light on the variability of results w.r.t. to the partition method used. Furthermore, we show that the SEP-28k dataset is dominated by only a few speakers, making it difficult to evaluate. To remedy this problem, we created SEP-28k-Extended (SEP-28k-E), containing semi-automatically generated speaker and gender information for the SEP-28k corpus, and suggest different data splits, each useful for evaluating other aspects of methods for dysfluency detection.

Recently, the use of machine learning in meteorology has increased greatly. While many machine learning methods are not new, university classes on machine learning are largely unavailable to meteorology students and are not required to become a meteorologist. The lack of formal instruction has contributed to perception that machine learning methods are 'black boxes' and thus end-users are hesitant to apply the machine learning methods in their every day workflow. To reduce the opaqueness of machine learning methods and lower hesitancy towards machine learning in meteorology, this paper provides a survey of some of the most common machine learning methods. A familiar meteorological example is used to contextualize the machine learning methods while also discussing machine learning topics using plain language. The following machine learning methods are demonstrated: linear regression; logistic regression; decision trees; random forest; gradient boosted decision trees; naive Bayes; and support vector machines. Beyond discussing the different methods, the paper also contains discussions on the general machine learning process as well as best practices to enable readers to apply machine learning to their own datasets. Furthermore, all code (in the form of Jupyter notebooks and Google Colaboratory notebooks) used to make the examples in the paper is provided in an effort to catalyse the use of machine learning in meteorology.

Atmospheric Extreme Events (EEs) cause severe damages to human societies and ecosystems. The frequency and intensity of EEs and other associated events are increasing in the current climate change and global warming risk. The accurate prediction, characterization, and attribution of atmospheric EEs is therefore a key research field, in which many groups are currently working by applying different methodologies and computational tools. Machine Learning (ML) methods have arisen in the last years as powerful techniques to tackle many of the problems related to atmospheric EEs. This paper reviews the ML algorithms applied to the analysis, characterization, prediction, and attribution of the most important atmospheric EEs. A summary of the most used ML techniques in this area, and a comprehensive critical review of literature related to ML in EEs, are provided. A number of examples is discussed and perspectives and outlooks on the field are drawn.