Available data in machine learning applications is becoming increasingly complex, due to higher dimensionality and difficult classes. There exists a wide variety of approaches to measuring complexity of labeled data, according to class overlap, separability or boundary shapes, as well as group morphology. Many techniques can transform the data in order to find better features, but few focus on specifically reducing data complexity. Most data transformation methods mainly treat the dimensionality aspect, leaving aside the available information within class labels which can be useful when classes are somehow complex. This paper proposes an autoencoder-based approach to complexity reduction, using class labels in order to inform the loss function about the adequacy of the generated variables. This leads to three different new feature learners, Scorer, Skaler and Slicer. They are based on Fisher's discriminant ratio, the Kullback-Leibler divergence and least-squares support vector machines, respectively. They can be applied as a preprocessing stage for a binary classification problem. A thorough experimentation across a collection of 27 datasets and a range of complexity and classification metrics shows that class-informed autoencoders perform better than 4 other popular unsupervised feature extraction techniques, especially when the final objective is using the data for a classification task.
Identifying the targets of an antimicrobial peptide is a fundamental step in studying the innate immune response and combating antibiotic resistance, and more broadly, precision medicine and public health. There have been extensive studies on the statistical and computational approaches to identify (i) whether a peptide is an antimicrobial peptide (AMP) or a non-AMP and (ii) which targets are these sequences effective to (Gram-positive, Gram-negative, etc.). Despite the existing deep learning methods on this problem, most of them are unable to handle the small AMP classes (anti-insect, anti-parasite, etc.). And more importantly, some AMPs can have multiple targets, which the previous methods fail to consider. In this study, we build a diverse and comprehensive multi-label protein sequence database by collecting and cleaning amino acids from various AMP databases. To generate efficient representations and features for the small classes dataset, we take advantage of a protein language model trained on 250 million protein sequences. Based on that, we develop an end-to-end hierarchical multi-label deep forest framework, HMD-AMP, to annotate AMP comprehensively. After identifying an AMP, it further predicts what targets the AMP can effectively kill from eleven available classes. Extensive experiments suggest that our framework outperforms state-of-the-art models in both the binary classification task and the multi-label classification task, especially on the minor classes.The model is robust against reduced features and small perturbations and produces promising results. We believe HMD-AMP contributes to both the future wet-lab investigations of the innate structural properties of different antimicrobial peptides and build promising empirical underpinnings for precise medicine with antibiotics.
Interaction group detection has been previously addressed with bottom-up approaches which relied on the position and orientation information of individuals. These approaches were primarily based on pairwise affinity matrices and were limited to static, third-person views. This problem can greatly benefit from a holistic approach based on Graph Neural Networks (GNNs) beyond pairwise relationships, due to the inherent spatial configuration that exists between individuals who form interaction groups. Our proposed method, GROup detection With Link prediction (GROWL), demonstrates the effectiveness of a GNN based approach. GROWL predicts the link between two individuals by generating a feature embedding based on their neighbourhood in the graph and determines whether they are connected with a shallow binary classification method such as Multi-layer Perceptrons (MLPs). We test our method against other state-of-the-art group detection approaches on both a third-person view dataset and a robocentric (i.e., egocentric) dataset. In addition, we propose a multimodal approach based on RGB and depth data to calculate a representation GROWL can utilise as input. Our results show that a GNN based approach can significantly improve accuracy across different camera views, i.e., third-person and egocentric views.
In binary classification, imbalance refers to situations in which one class is heavily under-represented. This issue is due to either a data collection process or because one class is indeed rare in a population. Imbalanced classification frequently arises in applications such as biology, medicine, engineering, and social sciences. In this paper, for the first time, we theoretically study the impact of imbalance class sizes on the linear discriminant analysis (LDA) in high dimensions. We show that due to data scarcity in one class, referred to as the minority class, and high-dimensionality of the feature space, the LDA ignores the minority class yielding a maximum misclassification rate. We then propose a new construction of hard-thresholding rules based on a data splitting technique that reduces the large difference between the misclassification rates. We show that the proposed method is asymptotically optimal. We further study two well-known sparse versions of the LDA in imbalanced cases. We evaluate the finite-sample performance of different methods using simulations and by analyzing two real data sets. The results show that our method either outperforms its competitors or has comparable performance based on a much smaller subset of selected features, while being computationally more efficient.
Timely diagnosis is important for saving the life of epileptic patients. In past few years, a lot of treatments are available for epilepsy. These treatments require use of anti-seizure drugs but are not effective in controlling frequency of seizure. There is need of removal of an affected region using surgery. Electroencephalogram (EEG) is a widely used technique for monitoring the brain activity and widely popular for seizure region detection. It is used before surgery for locating affected region. This manual process, using EEG graphs, is time consuming and requires deep expertise. In the present paper, a model has been proposed that preserves the true nature of an EEG signal in form of textual one-dimensional vector. The proposed model achieves a state of art performance for Bonn University dataset giving an average sensitivity, specificity of 81% and 81.4% respectively for classification of EEG data among all five classes. Also for binary classification achieving 99.9%, 99.5% score value for specificity and sensitivity instead of 2D models used by other researchers. Thus, developed system will significantly help neurosurgeons in the increase of their performance.
We consider the use of automated supervised learning systems for data tables that not only contain numeric/categorical columns, but one or more text fields as well. Here we assemble 18 multimodal data tables that each contain some text fields and stem from a real business application. Our publicly-available benchmark enables researchers to comprehensively evaluate their own methods for supervised learning with numeric, categorical, and text features. To ensure that any single modeling strategy which performs well over all 18 datasets will serve as a practical foundation for multimodal text/tabular AutoML, the diverse datasets in our benchmark vary greatly in: sample size, problem types (a mix of classification and regression tasks), number of features (with the number of text columns ranging from 1 to 28 between datasets), as well as how the predictive signal is decomposed between text vs. numeric/categorical features (and predictive interactions thereof). Over this benchmark, we evaluate various straightforward pipelines to model such data, including standard two-stage approaches where NLP is used to featurize the text such that AutoML for tabular data can then be applied. Compared with human data science teams, the fully automated methodology that performed best on our benchmark (stack ensembling a multimodal Transformer with various tree models) also manages to rank 1st place when fit to the raw text/tabular data in two MachineHack prediction competitions and 2nd place (out of 2380 teams) in Kaggle's Mercari Price Suggestion Challenge.
Automatic spoken instruction understanding (SIU) of the controller-pilot conversations in the air traffic control (ATC) requires not only recognizing the words and semantics of the speech but also determining the role of the speaker. However, few of the published works on the automatic understanding systems in air traffic communication focus on speaker role identification (SRI). In this paper, we formulate the SRI task of controller-pilot communication as a binary classification problem. Furthermore, the text-based, speech-based, and speech and text based multi-modal methods are proposed to achieve a comprehensive comparison of the SRI task. To ablate the impacts of the comparative approaches, various advanced neural network architectures are applied to optimize the implementation of text-based and speech-based methods. Most importantly, a multi-modal speaker role identification network (MMSRINet) is designed to achieve the SRI task by considering both the speech and textual modality features. To aggregate modality features, the modal fusion module is proposed to fuse and squeeze acoustic and textual representations by modal attention mechanism and self-attention pooling layer, respectively. Finally, the comparative approaches are validated on the ATCSpeech corpus collected from a real-world ATC environment. The experimental results demonstrate that all the comparative approaches are worked for the SRI task, and the proposed MMSRINet shows the competitive performance and robustness than the other methods on both seen and unseen data, achieving 98.56%, and 98.08% accuracy, respectively.
In this work we set out to find a method to classify protein structures using a Deep Learning methodology. Our Artificial Intelligence has been trained to recognize complex biomolecule structures extrapolated from the Protein Data Bank (PDB) database and reprocessed as images; for this purpose various tests have been conducted with pre-trained Convolutional Neural Networks, such as InceptionResNetV2 or InceptionV3, in order to extract significant features from these images and correctly classify the molecule. A comparative analysis of the performances of the various networks will therefore be produced.
In this work we present a system based on a Deep Learning approach, by using a Convolutional Neural Network, capable of classifying protein chains of amino acids based on the protein description contained in the Protein Data Bank. Each protein is fully described in its chemical-physical-geometric properties in a file in XML format. The aim of the work is to design a prototypical Deep Learning machinery for the collection and management of a huge amount of data and to validate it through its application to the classification of a sequences of amino acids. We envisage applying the described approach to more general classification problems in biomolecules, related to structural properties and similarities.
The enormous amount of data being generated on the web and social media has increased the demand for detecting online hate speech. Detecting hate speech will reduce their negative impact and influence on others. A lot of effort in the Natural Language Processing (NLP) domain aimed to detect hate speech in general or detect specific hate speech such as religion, race, gender, or sexual orientation. Hate communities tend to use abbreviations, intentional spelling mistakes, and coded words in their communication to evade detection, adding more challenges to hate speech detection tasks. Thus, word representation will play an increasingly pivotal role in detecting hate speech. This paper investigates the feasibility of leveraging domain-specific word embedding in Bidirectional LSTM based deep model to automatically detect/classify hate speech. Furthermore, we investigate the use of the transfer learning language model (BERT) on hate speech problem as a binary classification task. The experiments showed that domainspecific word embedding with the Bidirectional LSTM based deep model achieved a 93% f1-score while BERT achieved up to 96% f1-score on a combined balanced dataset from available hate speech datasets.
Realistically -- and equitably -- modeling the dynamics of group-level disparities in machine learning remains an open problem. In particular, we desire models that do not suppose inherent differences between artificial groups of people -- but rather endogenize disparities by appeal to unequal initial conditions of insular subpopulations. In this paper, agents each have a real-valued feature $X$ (e.g., credit score) informed by a "true" binary label $Y$ representing qualification (e.g., for a loan). Each agent alternately (1) receives a binary classification label $\hat{Y}$ (e.g., loan approval) from a Bayes-optimal machine learning classifier observing $X$ and (2) may update their qualification $Y$ by imitating successful strategies (e.g., seek a raise) within an isolated group $G$ of agents to which they belong. We consider the disparity of qualification rates $\Pr(Y=1)$ between different groups and how this disparity changes subject to a sequence of Bayes-optimal classifiers repeatedly retrained on the global population. We model the evolving qualification rates of each subpopulation (group) using the replicator equation, which derives from a class of imitation processes. We show that differences in qualification rates between subpopulations can persist indefinitely for a set of non-trivial equilibrium states due to uniformed classifier deployments, even when groups are identical in all aspects except initial qualification densities. We next simulate the effects of commonly proposed fairness interventions on this dynamical system along with a new feedback control mechanism capable of permanently eliminating group-level qualification rate disparities. We conclude by discussing the limitations of our model and findings and by outlining potential future work.
This document presents in detail the work done for the sexism detection task at EXIST2021 workshop. Our methodology is built on ensembles of Transformer-based models which are trained on different background and corpora and fine-tuned on the provided dataset from the EXIST2021 workshop. We report accuracy of 0.767 for the binary classification task (task1), and f1 score 0.766, and for the multi-class task (task2) accuracy 0.623 and f1-score 0.535.
Uncertainty sampling in active learning is heavily used in practice to reduce the annotation cost. However, there has been no wide consensus on the function to be used for uncertainty estimation in binary classification tasks and convergence guarantees of the corresponding active learning algorithms are not well understood. The situation is even more challenging for multi-category classification. In this work, we propose an efficient uncertainty estimator for binary classification which we also extend to multiple classes, and provide a non-asymptotic rate of convergence for our uncertainty sampling-based active learning algorithm in both cases under no-noise conditions (i.e., linearly separable data). We also extend our analysis to the noisy case and provide theoretical guarantees for our algorithm under the influence of noise in the task of binary and multi-class classification.
This work considers the problem of selective-sampling for best-arm identification. Given a set of potential options $\mathcal{Z}\subset\mathbb{R}^d$, a learner aims to compute with probability greater than $1-\delta$, $\arg\max_{z\in \mathcal{Z}} z^{\top}\theta_{\ast}$ where $\theta_{\ast}$ is unknown. At each time step, a potential measurement $x_t\in \mathcal{X}\subset\mathbb{R}^d$ is drawn IID and the learner can either choose to take the measurement, in which case they observe a noisy measurement of $x^{\top}\theta_{\ast}$, or to abstain from taking the measurement and wait for a potentially more informative point to arrive in the stream. Hence the learner faces a fundamental trade-off between the number of labeled samples they take and when they have collected enough evidence to declare the best arm and stop sampling. The main results of this work precisely characterize this trade-off between labeled samples and stopping time and provide an algorithm that nearly-optimally achieves the minimal label complexity given a desired stopping time. In addition, we show that the optimal decision rule has a simple geometric form based on deciding whether a point is in an ellipse or not. Finally, our framework is general enough to capture binary classification improving upon previous works.
Data-driven decision making is rapidly gaining popularity, fueled by the ever-increasing amounts of available data and encouraged by the development of models that can identify beyond linear input-output relationships. Simultaneously the need for interpretable prediction- and classification methods is increasing, as this improves both our trust in these models and the amount of information we can abstract from data. An important aspect of this interpretability is to obtain insight in the sensitivity-specificity trade-off constituted by multiple plausible input-output relationships. These are often shown in a receiver operating characteristic (ROC) curve. These developments combined lead to the need for a method that can abstract complex yet interpretable input-output relationships from large data, i.e. data containing large numbers of samples and sample features. Boolean phrases in disjunctive normal form (DNF) are highly suitable for explaining non-linear input-output relationships in a comprehensible way. Mixed integer linear programming (MILP) can be used to abstract these Boolean phrases from binary data, though its computational complexity prohibits the analysis of large datasets. This work presents IRELAND, an algorithm that allows for abstracting Boolean phrases in DNF from data with up to 10,000 samples and sample characteristics. The results show that for large datasets IRELAND outperforms the current state-of-the-art and can find solutions for datasets where current models run out of memory or need excessive runtimes. Additionally, by construction IRELAND allows for an efficient computation of the sensitivity-specificity trade-off curve, allowing for further understanding of the underlying input-output relationship.
Self-supervised learning has gradually emerged as a powerful technique for graph representation learning. However, transferable, generalizable, and robust representation learning on graph data still remains a challenge for pre-training graph neural networks. In this paper, we propose a simple and effective self-supervised pre-training strategy, named Pairwise Half-graph Discrimination (PHD), that explicitly pre-trains a graph neural network at graph-level. PHD is designed as a simple binary classification task to discriminate whether two half-graphs come from the same source. Experiments demonstrate that the PHD is an effective pre-training strategy that offers comparable or superior performance on 13 graph classification tasks compared with state-of-the-art strategies, and achieves notable improvements when combined with node-level strategies. Moreover, the visualization of learned representation revealed that PHD strategy indeed empowers the model to learn graph-level knowledge like the molecular scaffold. These results have established PHD as a powerful and effective self-supervised learning strategy in graph-level representation learning.
Alzheimer's disease (AD) is a neurodegenerative disease that affects nearly 50 million individuals across the globe and is one of the leading causes of deaths globally. It is projected that by 2050, the number of people affected by the disease would more than double. Consequently, the growing advancements in technology beg the question, can technology be used to predict Alzheimer's for a better and early diagnosis? In this paper, we focus on this very problem. Specifically, we have trained both ML models and neural networks to predict and classify participants based on their speech patterns. We computed a number of linguistic variables using DementiaBank's Pitt Corpus, a database consisting of transcripts of interviews with subjects suffering from multiple neurodegenerative diseases. We then trained both binary classifiers, as well as multiclass classifiers to distinguish AD from normal aging and other neurodegenerative diseases. We also worked on establishing the link between specific speech factors that can help determine the onset of AD. Confusion matrices and feature importance graphs have been plotted model-wise to compare the performances of our models. In both multiclass and binary classification, neural networks were found to outperform the other models with a testing accuracy of 76.44% and 92.05% respectively. For the feature importance, it was concluded that '%_PRESP' (present participle), '%_3S' (3rd person present tense markers) were two of the most important speech features for our classifiers in predicting AD.
Over the past few years, several adversarial training methods have been proposed to improve the robustness of machine learning models against adversarial perturbations in the input. Despite remarkable progress in this regard, adversarial training is often observed to drop the standard test accuracy. This phenomenon has intrigued the research community to investigate the potential tradeoff between standard accuracy (a.k.a generalization) and robust accuracy (a.k.a robust generalization) as two performance measures. In this paper, we revisit this tradeoff for latent models and argue that this tradeoff is mitigated when the data enjoys a low-dimensional structure. In particular, we consider binary classification under two data generative models, namely Gaussian mixture model and generalized linear model, where the features data lie on a low-dimensional manifold. We develop a theory to show that the low-dimensional manifold structure allows one to obtain models that are nearly optimal with respect to both, the standard accuracy and the robust accuracy measures. We further corroborate our theory with several numerical experiments, including Mixture of Factor Analyzers (MFA) model trained on the MNIST dataset.
Genetic Programming (GP), an evolutionary learning technique, has multiple applications in machine learning such as curve fitting, data modelling, feature selection, classification etc. GP has several inherent parallel steps, making it an ideal candidate for GPU based parallelization. This paper describes a GPU accelerated stack-based variant of the generational GP algorithm which can be used for symbolic regression and binary classification. The selection and evaluation steps of the generational GP algorithm are parallelized using CUDA. We introduce representing candidate solution expressions as prefix lists, which enables evaluation using a fixed-length stack in GPU memory. CUDA based matrix vector operations are also used for computation of the fitness of population programs. We evaluate our algorithm on synthetic datasets for the Pagie Polynomial (ranging in size from $4096$ to $16$ million points), profiling training times of our algorithm with other standard symbolic regression libraries viz. gplearn, TensorGP and KarooGP. In addition, using $6$ large-scale regression and classification datasets usually used for comparing gradient boosting algorithms, we run performance benchmarks on our algorithm and gplearn, profiling the training time, test accuracy, and loss. On an NVIDIA DGX-A100 GPU, our algorithm outperforms all the previously listed frameworks, and in particular, achieves average speedups of $119\times$ and $40\times$ against gplearn on the synthetic and large scale datasets respectively.
Elbow fractures are one of the most common fracture types. Diagnoses on elbow fractures often need the help of radiographic imaging to be read and analyzed by a specialized radiologist with years of training. Thanks to the recent advances of deep learning, a model that can classify and detect different types of bone fractures needs only hours of training and has shown promising results. However, most existing deep learning models are purely data-driven, lacking incorporation of known domain knowledge from human experts. In this work, we propose a novel deep learning method to diagnose elbow fracture from elbow X-ray images by integrating domain-specific medical knowledge into a curriculum learning framework. In our method, the training data are permutated by sampling without replacement at the beginning of each training epoch. The sampling probability of each training sample is guided by a scoring criterion constructed based on clinically known knowledge from human experts, where the scoring indicates the diagnosis difficultness of different elbow fracture subtypes. We also propose an algorithm that updates the sampling probabilities at each epoch, which is applicable to other sampling-based curriculum learning frameworks. We design an experiment with 1865 elbow X-ray images for a fracture/normal binary classification task and compare our proposed method to a baseline method and a previous method using multiple metrics. Our results show that the proposed method achieves the highest classification performance. Also, our proposed probability update algorithm boosts the performance of the previous method.