We introduce c-lasso, a Python package that enables sparse and robust linear regression and classification with linear equality constraints. The underlying statistical forward model is assumed to be of the following form: \[ y = X \beta + \sigma \epsilon \qquad \textrm{subject to} \qquad C\beta=0 \] Here, $X \in \mathbb{R}^{n\times d}$is a given design matrix and the vector $y \in \mathbb{R}^{n}$ is a continuous or binary response vector. The matrix $C$ is a general constraint matrix. The vector $\beta \in \mathbb{R}^{d}$ contains the unknown coefficients and $\sigma$ an unknown scale. Prominent use cases are (sparse) log-contrast regression with compositional data $X$, requiring the constraint $1_d^T \beta = 0$ (Aitchion and Bacon-Shone 1984) and the Generalized Lasso which is a special case of the described problem (see, e.g, (James, Paulson, and Rusmevichientong 2020), Example 3). The c-lasso package provides estimators for inferring unknown coefficients and scale (i.e., perspective M-estimators (Combettes and M\"uller 2020a)) of the form \[ \min_{\beta \in \mathbb{R}^d, \sigma \in \mathbb{R}_{0}} f\left(X\beta - y,{\sigma} \right) + \lambda \left\lVert \beta\right\rVert_1 \qquad \textrm{subject to} \qquad C\beta = 0 \] for several convex loss functions $f(\cdot,\cdot)$. This includes the constrained Lasso, the constrained scaled Lasso, and sparse Huber M-estimators with linear equality constraints.
The classification of DNA sequences is a key research area in bioinformatics as it enables researchers to conduct genomic analysis and detect possible diseases. In this paper, three state-of-the-art algorithms, namely Convolutional Neural Networks, Deep Neural Networks, and N-gram Probabilistic Models, are used for the task of DNA classification. Furthermore, we introduce a novel feature extraction method based on the Levenshtein distance and randomly generated DNA sub-sequences to compute information-rich features from the DNA sequences. We also use an existing feature extraction method based on 3-grams to represent amino acids and combine both feature extraction methods with a multitude of machine learning algorithms. Four different data sets, each concerning viral diseases such as Covid-19, AIDS, Influenza, and Hepatitis C, are used for evaluating the different approaches. The results of the experiments show that all methods obtain high accuracies on the different DNA datasets. Furthermore, the domain-specific 3-gram feature extraction method leads in general to the best results in the experiments, while the newly proposed technique outperforms all other methods on the smallest Covid-19 dataset
In this paper we revisit the classical problem of nonparametric regression, but impose local differential privacy constraints. Under such constraints, the raw data $(X_1,Y_1),\ldots,(X_n,Y_n)$, taking values in $\mathbb{R}^d \times \mathbb{R}$, cannot be directly observed, and all estimators are functions of the randomised output from a suitable privacy mechanism. The statistician is free to choose the form of the privacy mechanism, and here we add Laplace distributed noise to a discretisation of the location of a feature vector $X_i$ and to the value of its response variable $Y_i$. Based on this randomised data, we design a novel estimator of the regression function, which can be viewed as a privatised version of the well-studied partitioning regression estimator. The main result is that the estimator is strongly universally consistent. Our methods and analysis also give rise to a strongly universally consistent binary classification rule for locally differentially private data.
We propose a tree-based algorithm for classification and regression problems in the context of functional data analysis, which allows to leverage representation learning and multiple splitting rules at the node level, reducing generalization error while retaining the interpretability of a tree. This is achieved by learning a weighted functional $L^{2}$ space by means of constrained convex optimization, which is then used to extract multiple weighted integral features from the input functions, in order to determine the binary split for each internal node of the tree. The approach is designed to manage multiple functional inputs and/or outputs, by defining suitable splitting rules and loss functions that can depend on the specific problem and can also be combined with scalar and categorical data, as the tree is grown with the original greedy CART algorithm. We focus on the case of scalar-valued functional inputs defined on unidimensional domains and illustrate the effectiveness of our method in both classification and regression tasks, through a simulation study and four real world applications.
Producing or sharing Child Sexual Exploitation Material (CSEM) is a serious crime fought vigorously by Law Enforcement Agencies (LEAs). When an LEA seizes a computer from a potential producer or consumer of CSEM, they need to analyze the suspect's hard disk's files looking for pieces of evidence. However, a manual inspection of the file content looking for CSEM is a time-consuming task. In most cases, it is unfeasible in the amount of time available for the Spanish police using a search warrant. Instead of analyzing its content, another approach that can be used to speed up the process is to identify CSEM by analyzing the file names and their absolute paths. The main challenge for this task lies behind dealing with short text distorted deliberately by the owners of this material using obfuscated words and user-defined naming patterns. This paper presents and compares two approaches based on short text classification to identify CSEM files. The first one employs two independent supervised classifiers, one for the file name and the other for the path, and their outputs are later on fused into a single score. Conversely, the second approach uses only the file name classifier to iterate over the file's absolute path. Both approaches operate at the character n-grams level, while binary and orthographic features enrich the file name representation, and a binary Logistic Regression model is used for classification. The presented file classifier achieved an average class recall of 0.98. This solution could be integrated into forensic tools and services to support Law Enforcement Agencies to identify CSEM without tackling every file's visual content, which is computationally much more highly demanding.
This work examines how to train fair classifiers in settings where training labels are corrupted with random noise, and where the error rates of corruption depend both on the label class and on the membership function for a protected subgroup. Heterogeneous label noise models systematic biases towards particular groups when generating annotations. We begin by presenting analytical results which show that naively imposing parity constraints on demographic disparity measures, without accounting for heterogeneous and group-dependent error rates, can decrease both the accuracy and the fairness of the resulting classifier. Our experiments demonstrate these issues arise in practice as well. We address these problems by performing empirical risk minimization with carefully defined surrogate loss functions and surrogate constraints that help avoid the pitfalls introduced by heterogeneous label noise. We provide both theoretical and empirical justifications for the efficacy of our methods. We view our results as an important example of how imposing fairness on biased data sets without proper care can do at least as much harm as it does good.
Machine learning systems are often used in settings where individuals adapt their features to obtain a desired outcome. In such settings, strategic behavior leads to a sharp loss in model performance in deployment. In this work, we aim to address this problem by learning classifiers that encourage decision subjects to change their features in a way that leads to improvement in both predicted \emph{and} true outcome. We frame the dynamics of prediction and adaptation as a two-stage game, and characterize optimal strategies for the model designer and its decision subjects. In benchmarks on simulated and real-world datasets, we find that classifiers trained using our method maintain the accuracy of existing approaches while inducing higher levels of improvement and less manipulation.
So far, multi-label classification algorithms have been evaluated using statistical methods that do not consider the semantics of the considered classes and that fully depend on abstract computations such as Bayesian Reasoning. Currently, there are several attempts to develop ontology-based methods for a better assessment of supervised classification algorithms. In this research paper, we define a novel approach that aligns expected labels with predicted labels in multi-label classification using ontology-driven feature-based semantic similarity measures and we use it to develop a method for creating precise confusion matrices for a more effective evaluation of multi-label classification algorithms.
We introduce the AVECL-UMons dataset for audio-visual event classification and localization in the context of office environments. The audio-visual dataset is composed of 11 event classes recorded at several realistic positions in two different rooms. Two types of sequences are recorded according to the number of events in the sequence. The dataset comprises 2662 unilabel sequences and 2724 multilabel sequences corresponding to a total of 5.24 hours. The dataset is publicly accessible online : https://zenodo.org/record/3965492#.X09wsobgrCI.
Social media has become an important tool to share information about crisis events such as natural disasters and mass attacks. Detecting actionable posts that contain useful information requires rapid analysis of huge volume of data in real-time. This poses a complex problem due to the large amount of posts that do not contain any actionable information. Furthermore, the classification of information in real-time systems requires training on out-of-domain data, as we do not have any data from a new emerging crisis. Prior work focuses on models pre-trained on similar event types. However, those models capture unnecessary event-specific biases, like the location of the event, which affect the generalizability and performance of the classifiers on new unseen data from an emerging new event. In our work, we train an adversarial neural model to remove latent event-specific biases and improve the performance on tweet importance classification.
According to the World Health Organization (WHO), cancer is the second leading cause of death worldwide, responsible for over 9.5 million deaths in 2018 alone. Brain tumors count for one out of every four cancer deaths. Therefore, accurate and timely diagnosis of brain tumors will lead to more effective treatments. Physicians classify brain tumors only with biopsy operation by brain surgery, and after diagnosing the type of tumor, a treatment plan is considered for the patient. Automatic systems based on machine learning algorithms can allow physicians to diagnose brain tumors with noninvasive measures. To date, several image classification approaches have been proposed to aid diagnosis and treatment. For brain tumor classification in this work, we offer a system based on deep learning, containing encoder blocks. These blocks are fed with post-max-pooling features as residual learning. Our approach shows promising results by improving the tumor classification accuracy in Magnetic resonance imaging (MRI) images using a limited medical image dataset. Experimental evaluations of this model on a dataset consisting of 3064 MR images show 95.98% accuracy, which is better than previous studies on this database.
Aspect-level sentiment classification (ALSC) and aspect oriented opinion words extraction (AOWE) are two highly relevant aspect-based sentiment analysis (ABSA) subtasks. They respectively aim to detect the sentiment polarity and extract the corresponding opinion words toward a given aspect in a sentence. Previous works separate them and focus on one of them by training neural models on small-scale labeled data, while neglecting the connections between them. In this paper, we propose a novel joint model, Opinion Transmission Network (OTN), to exploit the potential bridge between ALSC and AOWE to achieve the goal of facilitating them simultaneously. Specifically, we design two tailor-made opinion transmission mechanisms to control opinion clues flow bidirectionally, respectively from ALSC to AOWE and AOWE to ALSC. Experiment results on two benchmark datasets show that our joint model outperforms strong baselines on the two tasks. Further analysis also validates the effectiveness of opinion transmission mechanisms.
Text classification is a critical research topic with broad applications in natural language processing. Recently, graph neural networks (GNNs) have received increasing attention in the research community and demonstrated their promising results on this canonical task. Despite the success, their performance could be largely jeopardized in practice since they are: (1) unable to capture high-order interaction between words; (2) inefficient to handle large datasets and new documents. To address those issues, in this paper, we propose a principled model -- hypergraph attention networks (HyperGAT), which can obtain more expressive power with less computational consumption for text representation learning. Extensive experiments on various benchmark datasets demonstrate the efficacy of the proposed approach on the text classification task.
The goal of few-shot classification is to learn a model that can classify novel classes using only a few training examples. Despite the promising results shown by existing meta-learning algorithms in solving the few-shot classification problem, there still remains an important challenge: how to generalize to unseen domains while meta-learning on multiple seen domains? In this paper, we propose an optimization-based meta-learning method, called Combining Domain-Specific Meta-Learners (CosML), that addresses the cross-domain few-shot classification problem. CosML first trains a set of meta-learners, one for each training domain, to learn prior knowledge (i.e., meta-parameters) specific to each domain. The domain-specific meta-learners are then combined in the \emph{parameter space}, by taking a weighted average of their meta-parameters, which is used as the initialization parameters of a task network that is quickly adapted to novel few-shot classification tasks in an unseen domain. Our experiments show that CosML outperforms a range of state-of-the-art methods and achieves strong cross-domain generalization ability.
Error-Correcting Output Codes (ECOCs) offer a principled approach for combining simple binary classifiers into multiclass classifiers. In this paper, we investigate the problem of designing optimal ECOCs to achieve both nominal and adversarial accuracy using Support Vector Machines (SVMs) and binary deep learning models. In contrast to previous literature, we present an Integer Programming (IP) formulation to design minimal codebooks with desirable error correcting properties. Our work leverages the advances in IP solvers to generate codebooks with optimality guarantees. To achieve tractability, we exploit the underlying graph-theoretic structure of the constraint set in our IP formulation. This enables us to use edge clique covers to substantially reduce the constraint set. Our codebooks achieve a high nominal accuracy relative to standard codebooks (e.g., one-vs-all, one-vs-one, and dense/sparse codes). We also estimate the adversarial accuracy of our ECOC-based classifiers in a white-box setting. Our IP-generated codebooks provide non-trivial robustness to adversarial perturbations even without any adversarial training.
Cancers are the leading cause of death in many countries. Early diagnosis plays a crucial role in having proper treatment for this debilitating disease. The automated classification of the type of cancer is a challenging task since pathologists must examine a huge number of histopathological images to detect infinitesimal abnormalities. In this study, we propose a novel convolutional neural network (CNN) architecture composed of a Concatenation of multiple Networks, called C-Net, to classify biomedical images. The model incorporates multiple CNNs including Outer, Middle, and Inner. The first two parts of the architecture contain six networks that serve as feature extractors to feed into the Inner network to classify the images in terms of malignancy and benignancy. The C-Net is applied for histopathological image classification on two public datasets, including BreakHis and Osteosarcoma. To evaluate the performance, the model is tested using several evaluation metrics for its reliability. The C-Net model outperforms all other models on the individual metrics for both datasets and achieves zero misclassification. This approach has the potential to be extended to additional classification tasks, as experimental results demonstrate utilizing extensive evaluation metrics.
Representation learning from 3D point clouds is challenging due to their inherent nature of permutation invariance and irregular distribution in space. Existing deep learning methods follow a hierarchical feature extraction paradigm in which high-level abstract features are derived from low-level features. However, they fail to exploit different granularity of information due to the limited interaction between these features. To this end, we propose Multi-Abstraction Refinement Network (MARNet) that ensures an effective exchange of information between multi-level features to gain local and global contextual cues while effectively preserving them till the final layer. We empirically show the effectiveness of MARNet in terms of state-of-the-art results on two challenging tasks: Shape classification and Coarse-to-fine grained semantic segmentation. MARNet significantly improves the classification performance by 2% over the baseline and outperforms the state-of-the-art methods on semantic segmentation task.
Due to the difficulty in acquiring massive task-specific occluded images, the classification of occluded images with deep convolutional neural networks (CNNs) remains highly challenging. To alleviate the dependency on large-scale occluded image datasets, we propose a novel approach to improve the classification accuracy of occluded images by fine-tuning the pre-trained models with a set of augmented deep feature vectors (DFVs). The set of augmented DFVs is composed of original DFVs and pseudo-DFVs. The pseudo-DFVs are generated by randomly adding difference vectors (DVs), extracted from a small set of clean and occluded image pairs, to the real DFVs. In the fine-tuning, the back-propagation is conducted on the DFV data flow to update the network parameters. The experiments on various datasets and network structures show that the deep feature augmentation significantly improves the classification accuracy of occluded images without a noticeable influence on the performance of clean images. Specifically, on the ILSVRC2012 dataset with synthetic occluded images, the proposed approach achieves 11.21% and 9.14% average increases in classification accuracy for the ResNet50 networks fine-tuned on the occlusion-exclusive and occlusion-inclusive training sets, respectively.
Weakly supervised disease classification of CT imaging suffers from poor localization owing to case-level annotations, where even a positive scan can hold hundreds to thousands of negative slices along multiple planes. Furthermore, although deep learning segmentation and classification models extract distinctly unique combinations of anatomical features from the same target class(es), they are typically seen as two independent processes in a computer-aided diagnosis (CAD) pipeline, with little to no feature reuse. In this research, we propose a medical classifier that leverages the semantic structural concepts learned via multi-resolution segmentation feature maps, to guide weakly supervised 3D classification of chest CT volumes. Additionally, a comparative analysis is drawn across two different types of feature aggregation to explore the vast possibilities surrounding feature fusion. Using a dataset of 1593 scans labeled on a case-level basis via rule-based model, we train a dual-stage convolutional neural network (CNN) to perform organ segmentation and binary classification of four representative diseases (emphysema, pneumonia/atelectasis, mass and nodules) in lungs. The baseline model, with separate stages for segmentation and classification, results in AUC of 0.791. Using identical hyperparameters, the connected architecture using static and dynamic feature aggregation improves performance to AUC of 0.832 and 0.851, respectively. This study advances the field in two key ways. First, case-level report data is used to weakly supervise a 3D CT classifier of multiple, simultaneous diseases for an organ. Second, segmentation and classification models are connected with two different feature aggregation strategies to enhance the classification performance.
Prior research notes that BERT's computational cost grows quadratically with sequence length thus leading to longer training times, higher GPU memory constraints and carbon emissions. While recent work seeks to address these scalability issues at pre-training, these issues are also prominent in fine-tuning especially for long sequence tasks like document classification. Our work thus focuses on optimizing the computational cost of fine-tuning for document classification. We achieve this by complementary learning of both topic and language models in a unified framework, named TopicBERT. This significantly reduces the number of self-attention operations - a main performance bottleneck. Consequently, our model achieves a 1.4x ($\sim40\%$) speedup with $\sim40\%$ reduction in $CO_2$ emission while retaining $99.9\%$ performance over 5 datasets.