Baker's yeast (Saccharomyces cerevisiae) is a model organism for studying the morphology that emerges at the scale of multi-cell colonies. To look at how morphology develops, we collect a dataset of time-lapse photographs of the growth of different strains of S. cerevisiae. We discuss the general statistical challenges that arise when using time-lapse photographs to extract time-dependent features. In particular, we show how texture-based feature engineering and representative clustering can be successfully applied to categorize the development of yeast colony morphology using our dataset. The local binary pattern (LBP) from image processing is used to score the surface texture of colonies. This texture score develops along a smooth trajectory during growth. The path taken depends on how the morphology emerges. A hierarchical clustering of the colonies is performed according to their texture development trajectories. The clustering method is designed for practical interpretability; it obtains the best representative colony image for any hierarchical sub-cluster.
A time series represents a set of observations collected over time. Typically, these observations are captured with a uniform sampling frequency (e.g. daily). When data points are observed in uneven time intervals the time series is referred to as irregular or intermittent. In such scenarios, the most common solution is to reconstruct the time series to make it regular, thus removing its intermittency. We hypothesise that, in irregular time series, the time at which each observation is collected may be helpful to summarise the dynamics of the data and improve forecasting performance. We study this idea by developing a novel automatic feature engineering framework, which focuses on extracting information from this point of view, i.e., when each instance is collected. We study how valuable this information is by integrating it in a time series forecasting workflow and investigate how it compares to or complements state-of-the-art methods for regular time series forecasting. In the end, we contribute by providing a novel framework that tackles feature engineering for time series from an angle previously vastly ignored. We show that our approach has the potential to further extract more information about time series that significantly improves forecasting performance.
Hashtag segmentation, also known as hashtag decomposition, is a common step in preprocessing pipelines for social media datasets. It usually precedes tasks such as sentiment analysis and hate speech detection. For sentiment analysis in medium to low-resourced languages, previous research has demonstrated that a multilingual approach that resorts to machine translation can be competitive or superior to previous approaches to the task. We develop a zero-shot hashtag segmentation framework and demonstrate how it can be used to improve the accuracy of multilingual sentiment analysis pipelines. Our zero-shot framework establishes a new state-of-the-art for hashtag segmentation datasets, surpassing even previous approaches that relied on feature engineering and language models trained on in-domain data.
Ontology alignment (a.k.a ontology matching (OM)) plays a critical role in knowledge integration. Owing to the success of machine learning in many domains, it has been applied in OM. However, the existing methods, which often adopt ad-hoc feature engineering or non-contextual word embeddings, have not yet outperformed rule-based systems especially in an unsupervised setting. In this paper, we propose a novel OM system named BERTMap which can support both unsupervised and semi-supervised settings. It first predicts mappings using a classifier based on fine-tuning the contextual embedding model BERT on text semantics corpora extracted from ontologies, and then refines the mappings through extension and repair by utilizing the ontology structure and logic. Our evaluation with three alignment tasks on biomedical ontologies demonstrates that BERTMap can often perform better than the leading OM systems LogMap and AML.
Precision medicine is a clinical approach for disease prevention, detection and treatment, which considers each individual's genetic background, environment and lifestyle. The development of this tailored avenue has been driven by the increased availability of omics methods, large cohorts of temporal samples, and their integration with clinical data. Despite the immense progression, existing computational methods for data analysis fail to provide appropriate solutions for this complex, high-dimensional and longitudinal data. In this work we have developed a new method termed TCAM, a dimensionality reduction technique for multi-way data, that overcomes major limitations when doing trajectory analysis of longitudinal omics data. Using real-world data, we show that TCAM outperforms traditional methods, as well as state-of-the-art tensor-based approaches for longitudinal microbiome data analysis. Moreover, we demonstrate the versatility of TCAM by applying it to several different omics datasets, and the applicability of it as a drop-in replacement within straightforward ML tasks.
An ensuing challenge in Artificial Intelligence (AI) is the perceived difficulty in interpreting sophisticated machine learning models, whose ever-increasing complexity makes it hard for such models to be understood, trusted and thus accepted by human beings. The lack, if not complete absence, of interpretability for these so-called black-box models can lead to serious economic and ethical consequences, thereby hindering the development and deployment of AI in wider fields, particularly in those involving critical and regulatory applications. Yet, the building services industry is a highly-regulated domain requiring transparency and decision-making processes that can be understood and trusted by humans. To this end, the design and implementation of autonomous Heating, Ventilation and Air Conditioning systems for the automatic but concurrently interpretable optimisation of energy efficiency and room thermal comfort is of topical interest. This work therefore presents an interpretable machine learning model aimed at predicting room temperature in non-domestic buildings, for the purpose of optimising the use of the installed HVAC system. We demonstrate experimentally that the proposed model can accurately forecast room temperatures eight hours ahead in real-time by taking into account historical RT information, as well as additional environmental and time-series features. In this paper, an enhanced feature engineering process is conducted based on the Exploratory Data Analysis results. Furthermore, beyond the commonly used Interpretable Machine Learning techniques, we propose a Permutation Feature-based Frequency Response Analysis (PF-FRA) method for quantifying the contributions of the different predictors in the frequency domain. Based on the generated reason codes, we find that the historical RT feature is the dominant factor that has most impact on the model prediction.
There are good arguments to support the claim that deep neural networks (DNNs) capture better feature representations than the previous hand-crafted feature engineering, which leads to a significant performance improvement. In this paper, we move a tiny step towards understanding the dynamics of feature representations over layers. Specifically, we model the process of class separation of intermediate representations in pre-trained DNNs as the evolution of communities in dynamic graphs. Then, we introduce modularity, a generic metric in graph theory, to quantify the evolution of communities. In the preliminary experiment, we find that modularity roughly tends to increase as the layer goes deeper and the degradation and plateau arise when the model complexity is great relative to the dataset. Through an asymptotic analysis, we prove that modularity can be broadly used for different applications. For example, modularity provides new insights to quantify the difference between feature representations. More crucially, we demonstrate that the degradation and plateau in modularity curves represent redundant layers in DNNs and can be pruned with minimal impact on performance, which provides theoretical guidance for layer pruning. Our code is available at https://github.com/yaolu-zjut/Dynamic-Graphs-Construction.
Atrial fibrillation (AF) is the most prevalent cardiac arrhythmia worldwide, with 2% of the population affected. It is associated with an increased risk of strokes, heart failure and other heart-related complications. Monitoring at-risk individuals and detecting asymptomatic AF could result in considerable public health benefits, as individuals with asymptomatic AF could take preventive measures with lifestyle changes. With increasing affordability to wearables, personalized health care is becoming more accessible. These personalized healthcare solutions require accurate classification of bio-signals while being computationally inexpensive. By making inferences on-device, we avoid issues inherent to cloud-based systems such as latency and network connection dependency. We propose an efficient pipeline for real-time Atrial Fibrillation Detection with high accuracy that can be deployed in ultra-edge devices. The feature engineering employed in this research catered to optimizing the resource-efficient classifier used in the proposed pipeline, which was able to outperform the best performing standard ML model by $10^5\times$ in terms of memory footprint with a mere trade-off of 2% classification accuracy. We also obtain higher accuracy of approximately 6% while consuming 403$\times$ lesser memory and being 5.2$\times$ faster compared to the previous state-of-the-art (SoA) embedded implementation.
The increase in people's use of mobile messaging services has led to the spread of social engineering attacks like phishing, considering that spam text is one of the main factors in the dissemination of phishing attacks to steal sensitive data such as credit cards and passwords. In addition, rumors and incorrect medical information regarding the COVID-19 pandemic are widely shared on social media leading to people's fear and confusion. Thus, filtering spam content is vital to reduce risks and threats. Previous studies relied on machine learning and deep learning approaches for spam classification, but these approaches have two limitations. Machine learning models require manual feature engineering, whereas deep neural networks require a high computational cost. This paper introduces a dynamic deep ensemble model for spam detection that adjusts its complexity and extracts features automatically. The proposed model utilizes convolutional and pooling layers for feature extraction along with base classifiers such as random forests and extremely randomized trees for classifying texts into spam or legitimate ones. Moreover, the model employs ensemble learning procedures like boosting and bagging. As a result, the model achieved high precision, recall, f1-score and accuracy of 98.38\%.
Generative models trained in an unsupervised manner may set high likelihood and low reconstruction loss to Out-of-Distribution (OoD) samples. This increases Type II errors and leads to missed anomalies, overall decreasing Anomaly Detection (AD) performance. In addition, AD models underperform due to the rarity of anomalies. To address these limitations, we propose the OoD Minimum Anomaly Score GAN (OMASGAN). OMASGAN generates, in a negative data augmentation manner, anomalous samples on the estimated distribution boundary. These samples are then used to refine an AD model, leading to more accurate estimation of the underlying data distribution including multimodal supports with disconnected modes. OMASGAN performs retraining by including the abnormal minimum-anomaly-score OoD samples generated on the distribution boundary in a self-supervised learning manner. For inference, for AD, we devise a discriminator which is trained with negative and positive samples either generated (negative or positive) or real (only positive). OMASGAN addresses the rarity of anomalies by generating strong and adversarial OoD samples on the distribution boundary using only normal class data, effectively addressing mode collapse. A key characteristic of our model is that it uses any f-divergence distribution metric in its variational representation, not requiring invertibility. OMASGAN does not use feature engineering and makes no assumptions about the data distribution. The evaluation of OMASGAN on image data using the leave-one-out methodology shows that it achieves an improvement of at least 0.24 and 0.07 points in AUROC on average on the MNIST and CIFAR-10 datasets, respectively, over other benchmark and state-of-the-art models for AD.
This paper introduces a two-phase deep feature engineering framework for efficient learning of semantics enhanced joint embedding, which clearly separates the deep feature engineering in data preprocessing from training the text-image joint embedding model. We use the Recipe1M dataset for the technical description and empirical validation. In preprocessing, we perform deep feature engineering by combining deep feature engineering with semantic context features derived from raw text-image input data. We leverage LSTM to identify key terms, deep NLP models from the BERT family, TextRank, or TF-IDF to produce ranking scores for key terms before generating the vector representation for each key term by using word2vec. We leverage wideResNet50 and word2vec to extract and encode the image category semantics of food images to help semantic alignment of the learned recipe and image embeddings in the joint latent space. In joint embedding learning, we perform deep feature engineering by optimizing the batch-hard triplet loss function with soft-margin and double negative sampling, taking into account also the category-based alignment loss and discriminator-based alignment loss. Extensive experiments demonstrate that our SEJE approach with deep feature engineering significantly outperforms the state-of-the-art approaches.
Tangled multi-party dialogue contexts lead to challenges for dialogue reading comprehension, where multiple dialogue threads flow simultaneously within a common dialogue record, increasing difficulties in understanding the dialogue history for both human and machine. Previous studies mainly focus on utterance encoding methods with carefully designed features but pay inadequate attention to characteristic features of the structure of dialogues. We specially take structure factors into account and design a novel model for dialogue disentangling. Based on the fact that dialogues are constructed on successive participation and interactions between speakers, we model structural information of dialogues in two aspects: 1)speaker property that indicates whom a message is from, and 2) reference dependency that shows whom a message may refer to. The proposed method achieves new state-of-the-art on the Ubuntu IRC benchmark dataset and contributes to dialogue-related comprehension.
Activity recognition systems that are capable of estimating human activities from wearable inertial sensors have come a long way in the past decades. Not only have state-of-the-art methods moved away from feature engineering and have fully adopted end-to-end deep learning approaches, best practices for setting up experiments, preparing datasets, and validating activity recognition approaches have similarly evolved. This tutorial was first held at the 2021 ACM International Symposium on Wearable Computers (ISWC'21) and International Joint Conference on Pervasive and Ubiquitous Computing (UbiComp'21). The tutorial, after a short introduction in the research field of activity recognition, provides a hands-on and interactive walk-through of the most important steps in the data pipeline for the deep learning of human activities. All presentation slides shown during the tutorial, which also contain links to all code exercises, as well as the link of the GitHub page of the tutorial can be found on: https://mariusbock.github.io/dl-for-har
In this paper we present our 2nd place solution to ACM RecSys 2021 Challenge organized by Twitter. The challenge aims to predict user engagement for a set of tweets, offering an exceptionally large data set of 1 billion data points sampled from over four weeks of real Twitter interactions. Each data point contains multiple sources of information, such as tweet text along with engagement features, user features, and tweet features. The challenge brings the problem close to a real production environment by introducing strict latency constraints in the model evaluation phase: the average inference time for single tweet engagement prediction is limited to 6ms on a single CPU core with 64GB memory. Our proposed model relies on extensive feature engineering performed with methods such as the Efficient Manifold Density Estimator (EMDE) - our previously introduced algorithm based on Locality Sensitive Hashing method, and novel Fourier Feature Encoding, among others. In total, we create numerous features describing a user's Twitter account status and the content of a tweet. In order to adhere to the strict latency constraints, the underlying model is a simple residual feed-forward neural network. The system is a variation of our previous methods which proved successful in KDD Cup 2021, WSDM Challenge 2021, and SIGIR eCom Challenge 2020. We release the source code at: https://github.com/Synerise/recsys-challenge-2021
Temporal relational data, perhaps the most commonly used data type in industrial machine learning applications, needs labor-intensive feature engineering and data analyzing for giving precise model predictions. An automatic machine learning framework is needed to ease the manual efforts in fine-tuning the models so that the experts can focus more on other problems that really need humans' engagement such as problem definition, deployment, and business services. However, there are three main challenges for building automatic solutions for temporal relational data: 1) how to effectively and automatically mining useful information from the multiple tables and the relations from them? 2) how to be self-adjustable to control the time and memory consumption within a certain budget? and 3) how to give generic solutions to a wide range of tasks? In this work, we propose our solution that successfully addresses the above issues in an end-to-end automatic way. The proposed framework, AutoSmart, is the winning solution to the KDD Cup 2019 of the AutoML Track, which is one of the largest AutoML competition to date (860 teams with around 4,955 submissions). The framework includes automatic data processing, table merging, feature engineering, and model tuning, with a time\&memory controller for efficiently and automatically formulating the models. The proposed framework outperforms the baseline solution significantly on several datasets in various domains.
This paper presents the contribution of the Data Science Kitchen at GermEval 2021 shared task on the identification of toxic, engaging, and fact-claiming comments. The task aims at extending the identification of offensive language, by including additional subtasks that identify comments which should be prioritized for fact-checking by moderators and community managers. Our contribution focuses on a feature-engineering approach with a conventional classification backend. We combine semantic and writing style embeddings derived from pre-trained deep neural networks with additional numerical features, specifically designed for this task. Classifier ensembles are used to derive predictions for each subtask via a majority voting scheme. Our best submission achieved macro-averaged F1-scores of 66.8\%,\,69.9\% and 72.5\% for the identification of toxic, engaging, and fact-claiming comments.
Sequence-to-sequence learning with neural networks has become the de facto standard for sequence prediction tasks. This approach typically models the local distribution over the next word with a powerful neural network that can condition on arbitrary context. While flexible and performant, these models often require large datasets for training and can fail spectacularly on benchmarks designed to test for compositional generalization. This work explores an alternative, hierarchical approach to sequence-to-sequence learning with quasi-synchronous grammars, where each node in the target tree is transduced by a node in the source tree. Both the source and target trees are treated as latent and induced during training. We develop a neural parameterization of the grammar which enables parameter sharing over the combinatorial space of derivation rules without the need for manual feature engineering. We apply this latent neural grammar to various domains -- a diagnostic language navigation task designed to test for compositional generalization (SCAN), style transfer, and small-scale machine translation -- and find that it performs respectably compared to standard baselines.
Trajectory data represent a trace of an object that changes its position in space over time. This kind of data is complex to handle and analyze, since it is generally produced in huge quantities, often prone to errors generated by the geolocation device, human mishandling, or area coverage limitation. Therefore, there is a need for software specifically tailored to preprocess trajectory data. In this work we propose PTRAIL, a python package offering several trajectory preprocessing steps, including filtering, feature extraction, and interpolation. PTRAIL uses parallel computation and vectorization, being suitable for large datasets and fast compared to other python libraries.
Graph-based anomaly detection has been widely used for detecting malicious activities in real-world applications. Existing attempts to address this problem have thus far focused on structural feature engineering or learning in the binary classification regime. In this work, we propose to leverage graph contrastive coding and present the supervised GraphCAD model for contrasting abnormal nodes with normal ones in terms of their distances to the global context (e.g., the average of all nodes). To handle scenarios with scarce labels, we further enable GraphCAD as a self-supervised framework by designing a graph corrupting strategy for generating synthetic node labels. To achieve the contrastive objective, we design a graph neural network encoder that can infer and further remove suspicious links during message passing, as well as learn the global context of the input graph. We conduct extensive experiments on four public datasets, demonstrating that 1) GraphCAD significantly and consistently outperforms various advanced baselines and 2) its self-supervised version without fine-tuning can achieve comparable performance with its fully supervised version.
We investigate the use of models from the theory of regularity structures as features in machine learning tasks. A model is a polynomial function of a space-time signal designed to well-approximate solutions to partial differential equations (PDEs), even in low regularity regimes. Models can be seen as natural multi-dimensional generalisations of signatures of paths; our work therefore aims to extend the recent use of signatures in data science beyond the context of time-ordered data. We provide a flexible definition of a model feature vector associated to a space-time signal, along with two algorithms which illustrate ways in which these features can be combined with linear regression. We apply these algorithms in several numerical experiments designed to learn solutions to PDEs with a given forcing and boundary data. Our experiments include semi-linear parabolic and wave equations with forcing, and Burgers' equation with no forcing. We find an advantage in favour of our algorithms when compared to several alternative methods. Additionally, in the experiment with Burgers' equation, we find non-trivial predictive power when noise is added to the observations.