Understanding the morphological changes of primary neuronal cells induced by chemical compounds is essential for drug discovery. Using the data from a single high-throughput imaging assay, a classification model for predicting the biological activity of candidate compounds was introduced. The image recognition model which is based on deep convolutional neural network (CNN) architecture with residual connections achieved accuracy of 99.6$\%$ on a binary classification task of distinguishing untreated and treated rodent primary neuronal cells with Amyloid-$\beta_{(25-35)}$.
The most important part of model selection and hyperparameter tuning is the evaluation of model performance. The most popular measures, such as AUC, F1, ACC for binary classification, or RMSE, MAD for regression, or cross-entropy for multilabel classification share two common weaknesses. First is, that they are not on an interval scale. It means that the difference in performance for the two models has no direct interpretation. It makes no sense to compare such differences between datasets. Second is, that for k-fold cross-validation, the model performance is in most cases calculated as an average performance from particular folds, which neglects the information how stable is the performance for different folds. In this talk, we introduce a new EPP rating system for predictive models. We also demonstrate numerous advantages for this system, First, differences in EPP scores have probabilistic interpretation. Based on it we can assess the probability that one model will achieve better performance than another. Second, EPP scores can be directly compared between datasets. Third, they can be used for navigated hyperparameter tuning and model selection. Forth, we can create embeddings for datasets based on EPP scores.
The goal of lossy data compression is to reduce the storage cost of a data set $X$ while retaining as much information as possible about something ($Y$) that you care about. For example, what aspects of an image $X$ contain the most information about whether it depicts a cat? Mathematically, this corresponds to finding a mapping $X\to Z\equiv f(X)$ that maximizes the mutual information $I(Z,Y)$ while the entropy $H(Z)$ is kept below some fixed threshold. We present a method for mapping out the Pareto frontier for classification tasks, reflecting the tradeoff between retained entropy and class information. We first show how a random variable $X$ (an image, say) drawn from a class $Y\in\{1,...,n\}$ can be distilled into a vector $W=f(X)\in \mathbb{R}^{n-1}$ losslessly, so that $I(W,Y)=I(X,Y)$; for example, for a binary classification task of cats and dogs, each image $X$ is mapped into a single real number $W$ retaining all information that helps distinguish cats from dogs. For the $n=2$ case of binary classification, we then show how $W$ can be further compressed into a discrete variable $Z=g_\beta(W)\in\{1,...,m_\beta\}$ by binning $W$ into $m_\beta$ bins, in such a way that varying the parameter $\beta$ sweeps out the full Pareto frontier, solving a generalization of the Discrete Information Bottleneck (DIB) problem. We argue that the most interesting points on this frontier are "corners" maximizing $I(Z,Y)$ for a fixed number of bins $m=2,3...$ which can be conveniently be found without multiobjective optimization. We apply this method to the CIFAR-10, MNIST and Fashion-MNIST datasets, illustrating how it can be interpreted as an information-theoretically optimal image clustering algorithm.
We propose $\ell_1$ norm regularized quadratic surface support vector machine models for binary classification in supervised learning. We establish their desired theoretical properties, including the existence and uniqueness of the optimal solution, reduction to the standard SVMs over (almost) linearly separable data sets, and detection of true sparsity pattern over (almost) quadratically separable data sets if the penalty parameter of $\ell_1$ norm is large enough. We also demonstrate their promising practical efficiency by conducting various numerical experiments on both synthetic and publicly available benchmark data sets.
Automatic abnormality detection in abdominal CT scans can help doctors improve the accuracy and efficiency in diagnosis. In this paper we aim at detecting pancreatic ductal adenocarcinoma (PDAC), the most common pancreatic cancer. Taking the fact that the existence of tumor can affect both the shape and the texture of pancreas, we design a system to extract the shape and texture feature at the same time for detecting PDAC. In this paper we propose a two-stage method for this 3D classification task. First, we segment the pancreas into a binary mask. Second, a FusionNet is proposed to take both the binary mask and CT image as input and perform a binary classification. The optimal architecture of the FusionNet is obtained by searching a pre-defined functional space. We show that the classification results using either shape or texture information are complementary, and by fusing them with the optimized architecture, the performance improves by a large margin. Our method achieves a specificity of 97% and a sensitivity of 92% on 200 normal scans and 136 scans with PDAC.
Deep learning has recently gained popularity in digital pathology due to its high prediction quality. However, the medical domain requires explanation and insight for a better understanding beyond standard quantitative performance evaluation. Recently, explanation methods have emerged, which are so far still rarely used in medicine. This work shows their application to generate heatmaps that allow to resolve common challenges encountered in deep learning-based digital histopathology analyses. These challenges comprise biases typically inherent to histopathology data. We study binary classification tasks of tumor tissue discrimination in publicly available haematoxylin and eosin slides of various tumor entities and investigate three types of biases: (1) biases which affect the entire dataset, (2) biases which are by chance correlated with class labels and (3) sampling biases. While standard analyses focus on patch-level evaluation, we advocate pixel-wise heatmaps, which offer a more precise and versatile diagnostic instrument and furthermore help to reveal biases in the data. This insight is shown to not only detect but also to be helpful to remove the effects of common hidden biases, which improves generalization within and across datasets. For example, we could see a trend of improved area under the receiver operating characteristic curve by 5% when reducing a labeling bias. Explanation techniques are thus demonstrated to be a helpful and highly relevant tool for the development and the deployment phases within the life cycle of real-world applications in digital pathology.
This paper is about a machine learning approach based on the multilinear projection of an unknown function (or probability distribution) to be estimated towards a linear (or multilinear) dimensional space E'. The proposal transforms the problem of predicting the target of an observation x into a problem of determining a consensus among the k nearest neighbors of x's image within the dimensional space E'. The algorithms that concretize it allow both regression and binary classification. Implementations carried out using Scala/Spark and assessed on a dozen LIBSVM datasets have demonstrated improvements in prediction accuracies in comparison with other prediction algorithms implemented within Spark MLLib such as multilayer perceptrons, logistic regression classifiers and random forests.
Among interpretable machine learning methods, the class of Generalised Additive Neural Networks (GANNs) is referred to as Self-Explaining Neural Networks (SENN) because of the linear dependence on explicit functions of the inputs. In binary classification this shows the precise weight that each input contributes towards the logit. The nomogram is a graphical representation of these weights. We show that functions of individual and pairs of variables can be derived from a functional Analysis of Variance (ANOVA) representation, enabling an efficient feature selection to be carried by application of the logistic Lasso. This process infers the structure of GANNs which otherwise needs to be predefined. As this method is particularly suited for tabular data, it starts by fitting a generic flexible model, in this case a Multi-layer Perceptron (MLP) to which the ANOVA decomposition is applied. This has the further advantage that the resulting GANN can be replicated as a SENN, enabling further refinement of the univariate and bivariate component functions to take place. The component functions are partial responses hence the SENN is a partial response network. The Partial Response Network (PRN) is equally as transparent as a traditional logistic regression model, but capable of non-linear classification with comparable or superior performance to the original MLP. In other words, the PRN is a fully interpretable representation of the MLP, at the level of univariate and bivariate effects. The performance of the PRN is shown to be competitive for benchmark data, against state-of-the-art machine learning methods including GBM, SVM and Random Forests. It is also compared with spline-based Sparse Additive Models (SAM) showing that a semi-parametric representation of the GAM as a neural network can be as effective as the SAM though less constrained by the need to set spline nodes.
Multimodal signals are more powerful than unimodal data for emotion recognition since they can represent emotions more comprehensively. In this paper, we introduce deep canonical correlation analysis (DCCA) to multimodal emotion recognition. The basic idea behind DCCA is to transform each modality separately and coordinate different modalities into a hyperspace by using specified canonical correlation analysis constraints. We evaluate the performance of DCCA on five multimodal datasets: the SEED, SEED-IV, SEED-V, DEAP, and DREAMER datasets. Our experimental results demonstrate that DCCA achieves state-of-the-art recognition accuracy rates on all five datasets: 94.58% on the SEED dataset, 87.45% on the SEED-IV dataset, 84.33% and 85.62% for two binary classification tasks and 88.51% for a four-category classification task on the DEAP dataset, 83.08% on the SEED-V dataset, and 88.99%, 90.57%, and 90.67% for three binary classification tasks on the DREAMER dataset. We also compare the noise robustness of DCCA with that of existing methods when adding various amounts of noise to the SEED-V dataset. The experimental results indicate that DCCA has greater robustness. By visualizing feature distributions with t-SNE and calculating the mutual information between different modalities before and after using DCCA, we find that the features transformed by DCCA from different modalities are more homogeneous and discriminative across emotions.
Recognition and analysis of Diabetic Foot Ulcers (DFU) using computerized methods is an emerging research area with the evolution of image-based machine learning algorithms. Existing research using visual computerized methods mainly focuses on recognition, detection, and segmentation of the visual appearance of the DFU as well as tissue classification. According to DFU medical classification systems, the presence of infection (bacteria in the wound) and ischaemia (inadequate blood supply) has important clinical implications for DFU assessment, which are used to predict the risk of amputation. In this work, we propose a new dataset and computer vision techniques to identify the presence of infection and ischaemia in DFU. This is the first time a DFU dataset with ground truth labels of ischaemia and infection cases is introduced for research purposes. For the handcrafted machine learning approach, we propose a new feature descriptor, namely the Superpixel Color Descriptor. Then we use the Ensemble Convolutional Neural Network (CNN) model for more effective recognition of ischaemia and infection. We propose to use a natural data-augmentation method, which identifies the region of interest on foot images and focuses on finding the salient features existing in this area. Finally, we evaluate the performance of our proposed techniques on binary classification, i.e. ischaemia versus non-ischaemia and infection versus non-infection. Overall, our method performed better in the classification of ischaemia than infection. We found that our proposed Ensemble CNN deep learning algorithms performed better for both classification tasks as compared to handcrafted machine learning algorithms, with 90% accuracy in ischaemia classification and 73% in infection classification.
The use of deep neural networks to make high risk decisions creates a need for global and local explanations so that users and experts have confidence in the modeling algorithms. We introduce a novel technique to find global and local explanations for time series data used in binary classification machine learning systems. We identify the most salient of the original features used by a black box model to distinguish between classes. The explanation can be made on categorical, continuous, and time series data and can be generalized to any binary classification model. The analysis is conducted on time series data to train a long short-term memory deep neural network and uses the time dependent structure of the underlying features in the explanation. The proposed technique attributes weights to features to explain an observations risk of belonging to a class as a multiplicative factor of a base hazard rate. We use a variation of the Cox Proportional Hazards regression, a Generalized Additive Model, to explain the effect of variables upon the probability of an in-class response for a score output from the black box model. The covariates incorporate time dependence structure in the features so the explanation is inclusive of the underlying time series data structure.
This paper studies binary classification problem associated with a family of loss functions called large-margin unified machines (LUM), which offers a natural bridge between distribution-based likelihood approaches and margin-based approaches. It also can overcome the so-called data piling issue of support vector machine in the high-dimension and low-sample size setting. In this paper we establish some new comparison theorems for all LUM loss functions which play a key role in the further error analysis of large-margin learning algorithms.
User independent emotion recognition with large scale physiological signals is a tough problem. There exist many advanced methods but they are conducted under relatively small datasets with dozens of subjects. Here, we propose Res-SIN, a novel end-to-end framework using Electrodermal Activity(EDA) signal images to classify human emotion. We first apply convex optimization-based EDA (cvxEDA) to decompose signals and mine the static and dynamic emotion changes. Then, we transform decomposed signals to images so that they can be effectively processed by CNN frameworks. The Res-SIN combines individual emotion features and external emotion benchmarks to accelerate convergence. We evaluate our approach on the PMEmo dataset, the currently largest emotional dataset containing music and EDA signals. To the best of author's knowledge, our method is the first attempt to classify large scale subject-independent emotion with 7962 pieces of EDA signals from 457 subjects. Experimental results demonstrate the reliability of our model and the binary classification accuracy of 73.65% and 73.43% on arousal and valence dimension can be used as a baseline.
In this work we propose a novel technique to quantify how distracting watermarks are on an image. We begin with watermark detection using a two-tower CNN model composed of a binary classification task and a semantic segmentation prediction. With this model, we demonstrate significant improvement in image precision while maintaining per-pixel accuracy, especially for our real-world dataset with sparse positive examples. We fit a nonlinear function to represent detected watermarks by a single score correlated with human perception based on their size, location, and visual obstructiveness. Finally, we validate our method in an image ranking setup, which is the main application of our watermark scoring algorithm.
A major challenge in matching images and text is that they have intrinsically different data distributions and feature representations. Most existing approaches are based either on embedding or classification, the first one mapping image and text instances into a common embedding space for distance measuring, and the second one regarding image-text matching as a binary classification problem. Neither of these approaches can, however, balance the matching accuracy and model complexity well. We propose a novel framework that achieves remarkable matching performance with acceptable model complexity. Specifically, in the training stage, we propose a novel Multi-modal Tensor Fusion Network (MTFN) to explicitly learn an accurate image-text similarity function with rank-based tensor fusion rather than seeking a common embedding space for each image-text instance. Then, during testing, we deploy a generic Cross-modal Re-ranking (RR) scheme for refinement without requiring additional training procedure. Extensive experiments on two datasets demonstrate that our MTFN-RR consistently achieves the state-of-the-art matching performance with much less time complexity. The implementation code is available at https://github.com/Wangt-CN/MTFN-RR-PyTorch-Code.
A primary concern of excessive reuse of test datasets in machine learning is that it can lead to overfitting. Multiclass classification was recently shown to be more resistant to overfitting than binary classification. In an open problem of COLT 2019, Feldman, Frostig, and Hardt ask to characterize the dependence of the amount of overfitting bias with the number of classes $m$, the number of accuracy queries $k$, and the number of examples in the dataset $n$. We resolve this problem and determine the amount of overfitting possible in multi-class classification. We provide computationally efficient algorithms that achieve overfitting bias of $\tilde{\Theta}(\max\{\sqrt{{k}/{(mn)}}, k/n\})$, matching the known upper bounds.
Anti-money laundering (AML) regulations play a critical role in safeguarding financial systems, but bear high costs for institutions and drive financial exclusion for those on the socioeconomic and international margins. The advent of cryptocurrency has introduced an intriguing paradox: pseudonymity allows criminals to hide in plain sight, but open data gives more power to investigators and enables the crowdsourcing of forensic analysis. Meanwhile advances in learning algorithms show great promise for the AML toolkit. In this workshop tutorial, we motivate the opportunity to reconcile the cause of safety with that of financial inclusion. We contribute the Elliptic Data Set, a time series graph of over 200K Bitcoin transactions (nodes), 234K directed payment flows (edges), and 166 node features, including ones based on non-public data; to our knowledge, this is the largest labelled transaction data set publicly available in any cryptocurrency. We share results from a binary classification task predicting illicit transactions using variations of Logistic Regression (LR), Random Forest (RF), Multilayer Perceptrons (MLP), and Graph Convolutional Networks (GCN), with GCN being of special interest as an emergent new method for capturing relational information. The results show the superiority of Random Forest (RF), but also invite algorithmic work to combine the respective powers of RF and graph methods. Lastly, we consider visualization for analysis and explainability, which is difficult given the size and dynamism of real-world transaction graphs, and we offer a simple prototype capable of navigating the graph and observing model performance on illicit activity over time. With this tutorial and data set, we hope to a) invite feedback in support of our ongoing inquiry, and b) inspire others to work on this societally important challenge.
The Philippines is a common ground to natural calamities like typhoons, floods, volcanic eruptions and earthquakes. With Twitter as one of the most used social media platform in the Philippines, a total of 39,867 preprocessed tweets were obtained given a time frame starting from November 1, 2013 to January 31, 2014. Sentiment analysis determines the underlying emotion given a series of words. The main purpose of this study is to identify the sentiments expressed in the tweets sent by the Filipino people before, during, and after Typhoon Yolanda using two variations of Recurrent Neural Networks; standard and bidirectional. The best generated models after training with various hyperparameters achieved a high accuracy of 81.79% for fine-grained classification using standard RNN and 87.69% for binary classification using bidirectional RNN. Findings revealed that 51.1% of the tweets sent were positive expressing support, love, and words of courage to the victims; 19.8% were negative stating sadness and despair for the loss of lives and hate for corrupt officials; while the other 29% were neutral tweets from local news stations, announcements of relief operations, donation drives, and observations by citizens.
The paper presents Imbalance-XGBoost, a Python package that combines the powerful XGBoost software with weighted and focal losses to tackle binary label-imbalanced classification tasks. Though a small-scale program in terms of size, the package is, to the best of the authors' knowledge, the first of its kind which provides an integrated implementation for the two losses on XGBoost and brings a general-purpose extension on XGBoost for label-imbalanced scenarios. In this paper, the design and usage of the package are described with exemplar code listings, and its convenience to be integrated into Python-driven Machine Learning projects is illustrated. Furthermore, as the first- and second-order derivatives of the loss functions are essential for the implementations, the algebraic derivation is discussed and it can be deemed as a separate algorithmic contribution. The performances of the algorithms implemented in the package are empirically evaluated on Parkinson's disease classification data set, and multiple state-of-the-art performances have been observed. Given the scalable nature of XGBoost, the package has great potentials to be applied to real-life binary classification tasks, which are usually of large-scale and label-imbalanced.
Most speech recognition tasks pertain to mapping words across two modalities: acoustic and orthographic. In this work, we suggest learning encoders that map variable-length, acoustic or phonetic, sequences that represent words into fixed-dimensional vectors in a shared latent space; such that the distance between two word vectors represents how closely the two words sound. Instead of directly learning the distances between word vectors, we employ weak supervision and model a binary classification task to predict whether two inputs, one of each modality, represent the same word given a distance threshold. We explore various deep-learning models, bimodal contrastive losses, and techniques for mining hard negative examples such as the semi-supervised technique of self-labeling. Our best model achieves an $F_1$ score of 0.95 for the binary classification task.