Recent technological advancements in data acquisition tools allowed life scientists to acquire multimodal data from different biological application domains. Broadly categorized in three types (i.e., sequences, images, and signals), these data are huge in amount and complex in nature. Mining such an enormous amount of data for pattern recognition is a big challenge and requires sophisticated data-intensive machine learning techniques. Artificial neural network-based learning systems are well known for their pattern recognition capabilities and lately their deep architectures - known as deep learning (DL) - have been successfully applied to solve many complex pattern recognition problems. Highlighting the role of DL in recognizing patterns in biological data, this article provides - applications of DL to biological sequences, images, and signals data; overview of open access sources of these data; description of open source DL tools applicable on these data; and comparison of these tools from qualitative and quantitative perspectives. At the end, it outlines some open research challenges in mining biological data and puts forward a number of possible future perspectives.

In this dissertation, we cover some recent advances in collaborative filtering and ranking. In chapter 1, we give a brief introduction of the history and the current landscape of collaborative filtering and ranking; chapter 2 we first talk about pointwise collaborative filtering problem with graph information, and how our proposed new method can encode very deep graph information which helps four existing graph collaborative filtering algorithms; chapter 3 is on the pairwise approach for collaborative ranking and how we speed up the algorithm to near-linear time complexity; chapter 4 is on the new listwise approach for collaborative ranking and how the listwise approach is a better choice of loss for both explicit and implicit feedback over pointwise and pairwise loss; chapter 5 is about the new regularization technique Stochastic Shared Embeddings (SSE) we proposed for embedding layers and how it is both theoretically sound and empirically effectively for 6 different tasks across recommendation and natural language processing; chapter 6 is how we introduce personalization for the state-of-the-art sequential recommendation model with the help of SSE, which plays an important role in preventing our personalized model from overfitting to the training data; chapter 7, we summarize what we have achieved so far and predict what the future directions can be; chapter 8 is the appendix to all the chapters.

Credit scoring is without a doubt one of the oldest applications of analytics. In recent years, a multitude of sophisticated classification techniques have been developed to improve the statistical performance of credit scoring models. Instead of focusing on the techniques themselves, this paper leverages alternative data sources to enhance both statistical and economic model performance. The study demonstrates how including call networks, in the context of positive credit information, as a new Big Data source has added value in terms of profit by applying a profit measure and profit-based feature selection. A unique combination of datasets, including call-detail records, credit and debit account information of customers is used to create scorecards for credit card applicants. Call-detail records are used to build call networks and advanced social network analytics techniques are applied to propagate influence from prior defaulters throughout the network to produce influence scores. The results show that combining call-detail records with traditional data in credit scoring models significantly increases their performance when measured in AUC. In terms of profit, the best model is the one built with only calling behavior features. In addition, the calling behavior features are the most predictive in other models, both in terms of statistical and economic performance. The results have an impact in terms of ethical use of call-detail records, regulatory implications, financial inclusion, as well as data sharing and privacy.

t-Distributed Stochastic Neighbor Embedding (t-SNE) for the visualization of multidimensional data has proven to be a popular approach, with successful applications in a wide range of domains. Despite their usefulness, t-SNE projections can be hard to interpret or even misleading, which hurts the trustworthiness of the results. Understanding the details of t-SNE itself and the reasons behind specific patterns in its output may be a daunting task, especially for non-experts in dimensionality reduction. In this work, we present t-viSNE, an interactive tool for the visual exploration of t-SNE projections that enables analysts to inspect different aspects of their accuracy and meaning, such as the effects of hyper-parameters, distance and neighborhood preservation, densities and costs of specific neighborhoods, and the correlations between dimensions and visual patterns. We propose a coherent, accessible, and well-integrated collection of different views for the visualization of t-SNE projections. The applicability and usability of t-viSNE are demonstrated through hypothetical usage scenarios with real data sets. Finally, we present the results of a user study where the tool's effectiveness was evaluated. By bringing to light information that would normally be lost after running t-SNE, we hope to support analysts in using t-SNE and making its results better understandable.

Music making is increasingly digitized here in 2020, but some analog audio effects are still very difficult to reproduce in this way. One of those effects is the kind of screeching guitar distortion favored by rock gods everywhere. Up to now, these effects, which involve guitar amplifiers, have been next to impossible to re-create digitally. That's now changed thanks to the work of researchers in the department of signal processing and acoustics at Finland's Aalto University. Using deep learning artificial intelligence (A.I.), they have created a neural network for guitar distortion modeling that, for the first time, can fool blind-test listeners into thinking it's the genuine article.

Companies may be achieving only a third of the value they could be getting from data science in industry applications. In this paper, we propose a methodology for categorizing and answering 'The Big Three' questions (what is going on, what is causing it, and what actions can I take that will optimize what I care about) using data science. The applications of data science seem to be nearly endless in today's modern landscape, with each company jockeying for position in the new data and insights economy. Yet, data scientists seem to be solely focused on using classification, regression, and clustering methods to answer the question 'what is going on'. Answering questions about why things are happening or how to take optimal actions to improve metrics are relegated to niche fields of research and generally neglected in industry data science analysis. We survey technical methods to answer these other important questions, describe areas in which some of these methods are being applied, and provide a practical example of how to apply our methodology and selected methods to a real business use case.

Biochemical methods that measure affinity and biophysical methods that describe the interaction in atomistic level detail have provided valuable information toward a mechanistic explanation for bimolecular recognition [1]. However, more often than not, compounds with drug potential are discovered serendipitously or by phenotypic drug discovery [2] since this highly specific interaction is still difficult to predict [3]. Protein structure based computational strategies such as docking [4], ultra-large library docking for discovering new chemotypes [5], and molecular dynamics simulations [4] or ligand based strategies such as quantitative structure-activity relationship (QSAR) [6, 7], and molecular similarity [8] have been powerful at narrowing down the list of compounds to be tested experimentally. With the increase in available data, machine learning and deep learning architectures are also starting to play a significant role in cheminformatics and drug discovery [9]. These approaches often require extensive computational resources or they are limited by the availability of 3D information. On the other hand, text based representations of biochemical entities are more readily available as evidenced by the 19,588 biomolecular complexes (3D structures) in PDB-Bind [10] (accessed on Nov 13, 2019) compared with 561,356 (manually annotated and reviewed) protein sequences in Uniprot [11] (accessed on Nov 13, 2019) or 97 million compounds in Pubchem [12] (accessed on Nov 13, 2019). The advances in natural language processing (NLP) methodologies make processing of text based representations of biomolecules an area of intense research interest. The discipline of natural language processing (NLP) comprises a variety of methods that explore a large amount of textual data in order to bring unstructured, latent (or hidden) knowledge to the fore [13]. Advances in this field are beneficial for tasks that use language (textual data) to build insight.

Computational intelligence in finance has been a very popular topic for both academia and financial industry in the last few decades. Numerous studies have been published resulting in various models. Meanwhile, within the Machine Learning (ML) field, Deep Learning (DL) started getting a lot of attention recently, mostly due to its outperformance over the classical models. Lots of different implementations of DL exist today, and the broad interest is continuing. Finance is one particular area where DL models started getting traction, however, the playfield is wide open, a lot of research opportunities still exist. In this paper, we tried to provide a state-of-the-art snapshot of the developed DL models for financial applications, as of today. We not only categorized the works according to their intended subfield in finance but also analyzed them based on their DL models. In addition, we also aimed at identifying possible future implementations and highlighted the pathway for the ongoing research within the field.

The trustworthiness of data science systems in applied and real-world settings emerges from the resolution of specific tensions through situated, pragmatic, and ongoing forms of work. Drawing on research in CSCW, critical data studies, and history and sociology of science, and six months of immersive ethnographic fieldwork with a corporate data science team, we describe four common tensions in applied data science work: (un)equivocal numbers, (counter)intuitive knowledge, (in)credible data, and (in)scrutable models. We show how organizational actors establish and re-negotiate trust under messy and uncertain analytic conditions through practices of skepticism, assessment, and credibility. Highlighting the collaborative and heterogeneous nature of real-world data science, we show how the management of trust in applied corporate data science settings depends not only on pre-processing and quantification, but also on negotiation and translation. We conclude by discussing the implications of our findings for data science research and practice, both within and beyond CSCW.

Advances in Data Science are lately permeating every field of Transportation Science and Engineering, making it straightforward to imagine that developments in the transportation sector will be data-driven. Nowadays, Intelligent Transportation Systems (ITS) could be arguably approached as a "story" intensively producing and consuming large amounts of data. A diversity of sensing devices densely spread over the infrastructure, vehicles or the travelers' personal devices act as sources of data flows that are eventually fed to software running on automatic devices, actuators or control systems producing, in turn, complex information flows between users, traffic managers, data analysts, traffic modeling scientists, etc. These information flows provide enormous opportunities to improve model development and decision-making. The present work aims to describe how data, coming from diverse ITS sources, can be used to learn and adapt data-driven models for efficiently operating ITS assets, systems and processes; in other words, for data-based models to fully become actionable. Grounded on this described data modeling pipeline for ITS, we define the characteristics, engineering requisites and challenges intrinsic to its three compounding stages, namely, data fusion, adaptive learning and model evaluation. We deliberately generalize model learning to be adaptive, since, in the core of our paper is the firm conviction that most learners will have to adapt to the everchanging phenomenon scenario underlying the majority of ITS applications. Finally, we provide a prospect of current research lines within the Data Science realm that can bring notable advances to data-based ITS modeling, which will eventually bridge the gap towards the practicality and actionability of such models.