Data mining in bioinformatics using Weka

The Weka machine learning workbench provides a general purpose environment for automatic classification, regression, clustering and feature selection-common data mining problems in bioinformatics research. It contains an extensive collection of machine learning algorithms and data exploration and the experimental comparison of different machine learning techniques on the same problem. Weka can process data given in the form of a single relational table. Its main objectives are to (a) assist users in extracting useful information from data and (b) enable them to easily identify a suitable algorithm for generating an accurate predictive model from it

Machine Learning and Integrative Analysis of Biomedical Big Data.

Recent developments in high-throughput technologies have accelerated the accumulation of massive amounts of omics data from multiple sources: genome, epigenome, transcriptome, proteome, metabolome, etc. Traditionally, data from each source (e.g., genome) is analyzed in isolation using statistical and machine learning (ML) methods. Integrative analysis of multi-omics and clinical data is key to new biomedical discoveries and advancements in precision medicine. However, data integration poses new computational challenges as well as exacerbates the ones associated with single-omics studies. Specialized computational approaches are required to effectively and efficiently perform integrative analysis of biomedical data acquired from diverse modalities. In this review, we discuss state-of-the-art ML-based approaches for tackling five specific computational challenges associated with integrative analysis: curse of dimensionality, data heterogeneity, missing data, class imbalance and scalability issues

Visual Analytics and Interactive Machine Learning for Human Brain Data

Indiana University-Purdue University Indianapolis (IUPUI)This study mainly focuses on applying visualization techniques on human brain data for data exploration, quality control, and hypothesis discovery. It mainly consists of two parts: multi-modal data visualization and interactive machine learning. For multi-modal data visualization, a major challenge is how to integrate structural, functional and connectivity data to form a comprehensive visual context. We develop a new integrated visualization solution for brain imaging data by combining scientific and information visualization techniques within the context of the same anatomic structure. For interactive machine learning, we propose a new visual analytics approach to interactive machine learning. In this approach, multi-dimensional data visualization techniques are employed to facilitate user interactions with the machine learning process. This allows dynamic user feedback in different forms, such as data selection, data labeling, and data correction, to enhance the efficiency of model building

Are We Closing the Loop Yet? Gaps in the Generalizability of VIS4ML Research

Visualization for machine learning (VIS4ML) research aims to help experts apply their prior knowledge to develop, understand, and improve the performance of machine learning models. In conceiving VIS4ML systems, researchers characterize the nature of human knowledge to support human-in-the-loop tasks, design interactive visualizations to make ML components interpretable and elicit knowledge, and evaluate the effectiveness of human-model interchange. We survey recent VIS4ML papers to assess the generalizability of research contributions and claims in enabling human-in-the-loop ML. Our results show potential gaps between the current scope of VIS4ML research and aspirations for its use in practice. We find that while papers motivate that VIS4ML systems are applicable beyond the specific conditions studied, conclusions are often overfitted to non-representative scenarios, are based on interactions with a small set of ML experts and well-understood datasets, fail to acknowledge crucial dependencies, and hinge on decisions that lack justification. We discuss approaches to close the gap between aspirations and research claims and suggest documentation practices to report generality constraints that better acknowledge the exploratory nature of VIS4ML research

Advancing Building Energy Modeling with Large Language Models: Exploration and Case Studies

The rapid progression in artificial intelligence has facilitated the emergence of large language models like ChatGPT, offering potential applications extending into specialized engineering modeling, especially physics-based building energy modeling. This paper investigates the innovative integration of large language models with building energy modeling software, focusing specifically on the fusion of ChatGPT with EnergyPlus. A literature review is first conducted to reveal a growing trend of incorporating of large language models in engineering modeling, albeit limited research on their application in building energy modeling. We underscore the potential of large language models in addressing building energy modeling challenges and outline potential applications including 1) simulation input generation, 2) simulation output analysis and visualization, 3) conducting error analysis, 4) co-simulation, 5) simulation knowledge extraction and training, and 6) simulation optimization. Three case studies reveal the transformative potential of large language models in automating and optimizing building energy modeling tasks, underscoring the pivotal role of artificial intelligence in advancing sustainable building practices and energy efficiency. The case studies demonstrate that selecting the right large language model techniques is essential to enhance performance and reduce engineering efforts. Besides direct use of large language models, three specific techniques were utilized: 1) prompt engineering, 2) retrieval-augmented generation, and 3) multi-agent large language models. The findings advocate a multidisciplinary approach in future artificial intelligence research, with implications extending beyond building energy modeling to other specialized engineering modeling

Human-Interpretable Explanations for Black-Box Machine Learning Models: An Application to Fraud Detection

Machine Learning (ML) has been increasingly used to aid humans making high-stakes decisions in a wide range of areas, from public policy to criminal justice, education, healthcare, or financial services. However, it is very hard for humans to grasp the rationale behind every ML model’s prediction, hindering trust in the system. The field of Explainable Artificial Intelligence (XAI) emerged to tackle this problem, aiming to research and develop methods to make those “black-boxes” more interpretable, but there is still no major breakthrough. Additionally, the most popular explanation methods — LIME and SHAP — produce very low-level feature attribution explanations, being of limited usefulness to personas without any ML knowledge. This work was developed at Feedzai, a fintech company that uses ML to prevent financial crime. One of the main Feedzai products is a case management application used by fraud analysts to review suspicious financial transactions flagged by the ML models. Fraud analysts are domain experts trained to look for suspicious evidence in transactions but they do not have ML knowledge, and consequently, current XAI methods do not suit their information needs. To address this, we present JOEL, a neural network-based framework to jointly learn a decision-making task and associated domain knowledge explanations. JOEL is tailored to human-in-the-loop domain experts that lack deep technical ML knowledge, providing high-level insights about the model’s predictions that very much resemble the experts’ own reasoning. Moreover, by collecting the domain feedback from a pool of certified experts (human teaching), we promote seamless and better quality explanations. Lastly, we resort to semantic mappings between legacy expert systems and domain taxonomies to automatically annotate a bootstrap training set, overcoming the absence of concept-based human annotations. We validate JOEL empirically on a real-world fraud detection dataset, at Feedzai. We show that JOEL can generalize the explanations from the bootstrap dataset. Furthermore, obtained results indicate that human teaching is able to further improve the explanations prediction quality.A Aprendizagem de Máquina (AM) tem sido cada vez mais utilizada para ajudar os humanos a tomar decisões de alto risco numa vasta gama de áreas, desde política até à justiça criminal, educação, saúde e serviços financeiros. Porém, é muito difícil para os humanos perceber a razão da decisão do modelo de AM, prejudicando assim a confiança no sistema. O campo da Inteligência Artificial Explicável (IAE) surgiu para enfrentar este problema, visando desenvolver métodos para tornar as “caixas-pretas” mais interpretáveis, embora ainda sem grande avanço. Além disso, os métodos de explicação mais populares — LIME and SHAP — produzem explicações de muito baixo nível, sendo de utilidade limitada para pessoas sem conhecimento de AM. Este trabalho foi desenvolvido na Feedzai, a fintech que usa a AM para prevenir crimes financeiros. Um dos produtos da Feedzai é uma aplicação de gestão de casos, usada por analistas de fraude. Estes são especialistas no domínio treinados para procurar evidências suspeitas em transações financeiras, contudo não tendo o conhecimento em AM, os métodos de IAE atuais não satisfazem as suas necessidades de informação. Para resolver isso, apresentamos JOEL, a framework baseada em rede neuronal para aprender conjuntamente a tarefa de tomada de decisão e as explicações associadas. A JOEL é orientada a especialistas de domínio que não têm conhecimento técnico profundo de AM, fornecendo informações de alto nível sobre as previsões do modelo, que muito se assemelham ao raciocínio dos próprios especialistas. Ademais, ao recolher o feedback de especialistas certificados (ensino humano), promovemos explicações contínuas e de melhor qualidade. Por último, recorremos a mapeamentos semânticos entre sistemas legados e taxonomias de domínio para anotar automaticamente um conjunto de dados, superando a ausência de anotações humanas baseadas em conceitos. Validamos a JOEL empiricamente em um conjunto de dados de detecção de fraude do mundo real, na Feedzai. Mostramos que a JOEL pode generalizar as explicações aprendidas no conjunto de dados inicial e que o ensino humano é capaz de melhorar a qualidade da previsão das explicações

Prognosticating Physique: Machine Learning for Future Body Shape Estimations in Weight Loss

This research presents the development of a predictive model to forecast morphological changes in individuals undergoing weight loss treatment. The initiative, Tech4Diet, draws from the public health imperative to address the global obesity crisis and utilized 3D body scans and supplementary medical data to enhance adherence to treatment. An extensive review of the current literature on 3D human body model representation forms the foundation of this work, leading to the selection of the Skinned Multi-Person Linear Model (SMPL) model for encoding body scans. Long Short-Term Memory (LSTM) networks are employed to analyze these encoded datasets and predict potential body changes before the treatment concludes. The process includes a comprehensive analysis of collected data, body model representation, neural network design, model training, and evaluation. The resulting model successfully generates 3D meshes of predicted body transformations, offering a novel approach to visualizing weight loss progress. Further chapters detail the data acquisition, model design, training process, and results

Fetal brain tissue annotation and segmentation challenge results

In-utero fetal MRI is emerging as an important tool in the diagnosis and analysis of the developing human brain. Automatic segmentation of the developing fetal brain is a vital step in the quantitative analysis of prenatal neurodevelopment both in the research and clinical context. However, manual segmentation of cerebral structures is time-consuming and prone to error and inter-observer variability. Therefore, we organized the Fetal Tissue Annotation (FeTA) Challenge in 2021 in order to encourage the development of automatic segmentation algorithms on an international level. The challenge utilized FeTA Dataset, an open dataset of fetal brain MRI reconstructions segmented into seven different tissues (external cerebrospinal fluid, gray matter, white matter, ventricles, cerebellum, brainstem, deep gray matter). 20 international teams participated in this challenge, submitting a total of 21 algorithms for evaluation. In this paper, we provide a detailed analysis of the results from both a technical and clinical perspective. All participants relied on deep learning methods, mainly U-Nets, with some variability present in the network architecture, optimization, and image pre- and post-processing. The majority of teams used existing medical imaging deep learning frameworks. The main differences between the submissions were the fine tuning done during training, and the specific pre- and post-processing steps performed. The challenge results showed that almost all submissions performed similarly. Four of the top five teams used ensemble learning methods. However, one team's algorithm performed significantly superior to the other submissions, and consisted of an asymmetrical U-Net network architecture. This paper provides a first of its kind benchmark for future automatic multi-tissue segmentation algorithms for the developing human brain in utero