Biomedical data science is a multidisciplinary field which leverages large volumes of data to promote biomedical innovation and discovery. Biomedical data science draws from various fields including Biostatistics, Biomedical informatics, and machine learning, with the goal of understanding biological and medical data. It can be viewed as the study and application of data science to solve biomedical problems. Modern biomedical datasets often have specific features which make their analyses difficult, including: Large numbers of feature (sometimes billions), typically far larger than the number of samples (typically tens or hundreds) Noisy and missing data Privacy concerns (e.g., electronic health record confidentiality) Requirement of interpretability from decision makers and regulatory bodies Many biomedical data science projects apply machine learning to such datasets. These characteristics, while also present in many data science applications more generally, make biomedical data science a specific field. Examples of biomedical data science research include: Computational genomics Computational imaging Electronic health records data mining Biomedical network science Clinical Natural Language Processing (NLP) == Computational Imaging and Deep Learning == Computational imaging is a cornerstone of biomedical data science, focusing on the development of algorithms to enhance, analyze, and interpret medical imagery. In recent years, the field has been transformed by the integration of deep learning, particularly through the use of Convolutional Neural Networks. Deep learning started from researchers manually defining characteristics like edge detection or texture representation learning. In a more modern approach of computational imaging, models automatically learn a hierarchy of features directly from raw pixel data. This overlap between data science and deep learning is applied across several key tasks: Classification: Identifying the presence of specific diseases, such as distinguishing between benign and malignant tumors in histopathology slides or detecting pneumonia in chest X-rays. Segmentation: The precise delineation of anatomical structures or lesions. A notable example is the U-Net architecture, which is widely used for biomedical image segmentation to help clinicians quantify organ volume or track tumor growth. Detection: Automating the localization of small objects, such as identifying microcalcifications in mammograms or polyps during colonoscopies. Registration: The process of aligning multiple images to provide a comprehensive view of the patient's anatomy. Even with all of these enhancements, the application of deep learning in medical imaging requires accomplishing vigorous challenges. An example of these changes is building large, annotated datasets and creating the imperative for model interpretability in clinical decision-making. == Electronic Health Records == Electronic Health Records (EHRs) are a digital alternative to patient paper charts, usually including individual records or population health information. EHRs can be used in a wide variety of applications, including research and analysation as they often include demographics, diagnoses, medications, test results, and personal statistics. === History === ==== 1960s ==== The earliest precursor is considered Dr. Lawrence Weed's problem-oriented medical record (POMR) published in the 1968 which sorts and groups medical records by medical diagnoses and symptoms. The POMR was the first system to organize based off of patient information rather than the source (doctors, nurses, attendings, etc.). In 1969, the Regenstrief Institute developed and published the Regenstrief Medical Record System which established electronic writing, storage, and retrieval of records which served as the basis for modern EHR systems. ==== 2000s ==== In 2009, the Health Information Technology for Economic and Clinical Health Act (HITECH Act) was passed in the United States. This act standardized privacy and distribution of EHRs and increased the acceptance and utilization of EHRs within medical and academic settings. == Artificial Intelligence and Machine Learning Applications == Machine Learning and Artificial Intelligence have become central tools in biomedical data science. Recent advances in large language models (LLMs) have expanded their role beyond text, with models trained directly on genomic sequences enabling tasks such as gene function prediction, variant effect analysis, and drug discovery. In clinical settings, Natural Language Processing (NLP) models are applied to electronic health records to extract structured insights from unstructured clinical notes and data, supporting diagnosis and treatment planning. Beyond genomics, AI models have been applied to protein structure prediction. AlphaFold, developed by Google DeepMind, uses deep learning to predict three-dimensional protein structures from amino acid sequences with high accuracy. These predictions have been used to support drug target identification and the study of disease mechanisms. == Knowledge Graphs == Knowledge graphs (KGs) are widely used in biomedical data science to represent and analyze complex relationships among biological and medical entities. By structuring data as nodes (e.g., genes, diseases, drugs) and edges (relationships), KGs enable computational methods to extract insights and support decision-making. These biomedical relationships can be efficiently modeled and queried using technologies such as Neo4j. === Biomedical Research Applications === KGs provide biomedical researchers with a way to model complex biological systems. They have been used to identify the relationships between diseases and biomolecules, support drug repurposing, and to uncover new biological insights. Additional applications include: Identification of novel antibiotic resistance genes through graph-based link prediction. Finding associations between miRNA and diseases. Prediction of protein-protein interactions. === Clinical Applications === In clinical settings, KGs can be used to make visual representations of a patient's electronic health records. The data obtained from these graphs can assist healthcare providers in improving patient diagnoses and prescribing more effective drugs. Additionally, embeddings derived from resources like the Unified Medical Language System (UMLS) enable natural language processing of clinical text and similarity analysis between medical concepts. === Limitations === Despite their advantages, knowledge graphs face several challenges. Some of these include: High algorithmic complexity and large biological datasets make the process computationally expensive. KG construction can be a time-consuming process that requires careful attention to assign appropriate node types and vocabularies. Using data from a wide range of datasets in one KG requires them to be effectively integrated. == Privacy == A primary challenge in biomedical data science is maintaining medical privacy. Conducting research requires that data be collected on a number of people for training and testing purposes and is stored within biomedical datasets. This poses a risk for violating patient confidentiality and may dissuade people from participating in studies. The main sources of health statistics are surveys administrative and medical records health care claims data, vital records surveillance disease registries grey literature and peer-reviewed literature. Large data collection is a useful tool for researching various medical conditions. Researchers use these large datasets of information to identify factors that may make people more susceptible to certain diseases. Large amounts of collected data can help researchers identify patterns for disease probabilities. The findings can show a person is more likely for a condition, or identify environmental, social, and personal habits that may lead to adverse health issues. Institutions researching using personal medical information come with a moral and legal responsibility to protect the use of that information. Protection of the collected information has become a big concern. Sophisticated and coordinated attacks on certain medical systems happen more frequently. Medical companies, medical insurance and private businesses have invested a great deal into the protection of personal data. Despite this, data breaches continue to be documented. The chart below shows the top healthcare breaches in 2025. For these reasons, many people have reservations about giving up their personal data. Aside from the legitimate use of personal data there have been instances where companies have found methods to profit from brokering medical information. Concerns exist regarding unauthorized use of sensitive information within these data companies. If a person is identified within a dataset, then sensitive data can be used to discriminate against them. For example, insurance companies may charge a hi
Healthy Together
Healthy Together is a health technology company that provides software for Health & Humans Services Departments. Healthy Together supports a “One Door” approach to eligibility, enrollment, and management for programs like Medicaid, Supplemental Nutrition Assistance Program, TANF and WIC, as well as behavioral health (988), disease surveillance, vital records, child welfare and more. The platform's use is to increase the reach and efficacy of program initiatives, improve health equity and reduce cost. Software is available in the United States of America with current deployments in Florida, Oklahoma. The United States Department of Veterans Affairs also utilizes Healthy Together's mobile platform. == Development == Healthy Together launched in March 2020 and builds software for public health and health and human services departments. The Florida Department of Health began using the platform in September 2020 to deliver real-time test results to residents. Over 50% of households in Florida have adopted the mobile application. On December 6, 2022, the Advanced Technology Academic Research Center (ATARC) awarded Healthy Together and the State of Florida's Department of Health with a Digital Experience Award at their 2022 GITEC Emerging Technology Award Ceremony in Washington, D.C. to recognize success of the project. The partnership was also highlighted on the Federal News Network's show Federal Drive. The platform is also used at universities in Oklahoma. In November 2022, the United States Department of Veterans Affairs and Healthy Together announced a collaboration to expand access to health records for Veterans. The platform provides 18 million Veterans with access to their health information through their smartphones and mobile devices. In December 2022, the integration was recognized as one of Healthcare IT News' Top 10 stories of 2022.
Kalman filter
In statistics and control theory, Kalman filtering (also known as linear quadratic estimation) is an algorithm that uses a series of measurements observed over time, including statistical noise and other inaccuracies, to produce estimates of unknown variables that tend to be more accurate than those based on a single measurement, by estimating a joint probability distribution over the variables for each time-step. The filter is constructed as a mean squared error minimiser, but an alternative derivation of the filter is also provided showing how the filter relates to maximum likelihood statistics. The filter is named after Rudolf E. Kálmán. Kalman filtering has numerous technological applications. A common application is for guidance, navigation, and control of vehicles, particularly aircraft, spacecraft and ships positioned dynamically. Furthermore, Kalman filtering is much applied in time series analysis tasks such as signal processing and econometrics. Kalman filtering is also important for robotic motion planning and control, and can be used for trajectory optimization. Kalman filtering also works for modeling the central nervous system's control of movement. Due to the time delay between issuing motor commands and receiving sensory feedback, the use of Kalman filters provides a realistic model for making estimates of the current state of a motor system and issuing updated commands. The algorithm works via a two-phase process: a prediction phase and an update phase. In the prediction phase, the Kalman filter produces estimates of the current state variables, including their uncertainties. Once the outcome of the next measurement (necessarily corrupted with some error, including random noise) is observed, these estimates are updated using a weighted average, with more weight given to estimates with greater certainty. The algorithm is recursive. It can operate in real time, using only the present input measurements and the state calculated previously and its uncertainty matrix; no additional past information is required. Optimality of Kalman filtering assumes that errors have a normal (Gaussian) distribution. In the words of Rudolf E. Kálmán, "The following assumptions are made about random processes: Physical random phenomena may be thought of as due to primary random sources exciting dynamic systems. The primary sources are assumed to be independent gaussian random processes with zero mean; the dynamic systems will be linear." Regardless of Gaussianity, however, if the process and measurement covariances are known, then the Kalman filter is the best possible linear estimator in the minimum mean-square-error sense, although there may be better nonlinear estimators. It is a common misconception (perpetuated in the literature) that the Kalman filter cannot be rigorously applied unless all noise processes are assumed to be Gaussian. Extensions and generalizations of the method have also been developed, such as the extended Kalman filter and the unscented Kalman filter which work on nonlinear systems. The basis is a hidden Markov model such that the state space of the latent variables is continuous and all latent and observed variables have Gaussian distributions. Kalman filtering has been used successfully in multi-sensor fusion, and distributed sensor networks to develop distributed or consensus Kalman filtering. == History == The filtering method is named for Hungarian émigré Rudolf E. Kálmán, although Thorvald Nicolai Thiele and Peter Swerling developed a similar algorithm earlier. Richard S. Bucy of the Johns Hopkins Applied Physics Laboratory contributed to the theory, causing it to be known sometimes as Kalman–Bucy filtering. Kalman was inspired to derive the Kalman filter by applying state variables to the Wiener filtering problem. Stanley F. Schmidt is generally credited with developing the first implementation of a Kalman filter. He realized that the filter could be divided into two distinct parts, with one part for time periods between sensor outputs and another part for incorporating measurements. It was during a visit by Kálmán to the NASA Ames Research Center that Schmidt saw the applicability of Kálmán's ideas to the nonlinear problem of trajectory estimation for the Apollo program resulting in its incorporation in the Apollo navigation computer. This digital filter is sometimes termed the Stratonovich–Kalman–Bucy filter because it is a special case of a more general, nonlinear filter developed by the Soviet mathematician Ruslan Stratonovich. In fact, some of the special case linear filter's equations appeared in papers by Stratonovich that were published before the summer of 1961, when Kalman met with Stratonovich during a conference in Moscow. This Kalman filtering was first described and developed partially in technical papers by Swerling (1958), Kalman (1960) and Kalman and Bucy (1961). The Apollo computer used 2k of magnetic core RAM and 36k wire rope [...]. The CPU was built from ICs [...]. Clock speed was under 100 kHz [...]. The fact that the MIT engineers were able to pack such good software (one of the very first applications of the Kalman filter) into such a tiny computer is truly remarkable. Kalman filters have been vital in the implementation of the navigation systems of U.S. Navy nuclear ballistic missile submarines, and in the guidance and navigation systems of cruise missiles such as the U.S. Navy's Tomahawk missile and the U.S. Air Force's Air Launched Cruise Missile. They are also used in the guidance and navigation systems of reusable launch vehicles and the attitude control and navigation systems of spacecraft which dock at the International Space Station. == Overview of the calculation == Kalman filtering uses a system's dynamic model (e.g., physical laws of motion), known control inputs to that system, and multiple sequential measurements (such as from sensors) to form an estimate of the system's varying quantities (its state) that is better than the estimate obtained by using only one measurement alone. As such, it is a common sensor fusion and data fusion algorithm. Noisy sensor data, approximations in the equations that describe the system evolution, and external factors that are not accounted for, all limit how well it is possible to determine the system's state. The Kalman filter deals effectively with the uncertainty due to noisy sensor data and, to some extent, with random external factors. The Kalman filter produces an estimate of the state of the system as an average of the system's predicted state and of the new measurement using a weighted average. The purpose of the weights is that values with better (i.e., smaller) estimated uncertainty are "trusted" more. The weights are calculated from the covariance, a measure of the estimated uncertainty of the prediction of the system's state. The result of the weighted average is a new state estimate that lies between the predicted and measured state, and has a better estimated uncertainty than either alone. This process is repeated at every time step, with the new estimate and its covariance informing the prediction used in the following iteration. This means that Kalman filter works recursively and requires only the last "best guess", rather than the entire history, of a system's state to calculate a new state. The measurements' certainty-grading and current-state estimate are important considerations. It is common to discuss the filter's response in terms of the Kalman filter's gain. The Kalman gain is the weight given to the measurements and current-state estimate, and can be "tuned" to achieve a particular performance. With a high gain, the filter places more weight on the most recent measurements, and thus conforms to them more responsively. With a low gain, the filter conforms to the model predictions more closely. At the extremes, a high gain (close to one) will result in a more jumpy estimated trajectory, while a low gain (close to zero) will smooth out noise but decrease the responsiveness. When performing the actual calculations for the filter (as discussed below), the state estimate and covariances are coded into matrices because of the multiple dimensions involved in a single set of calculations. This allows for a representation of linear relationships between different state variables (such as position, velocity, and acceleration) in any of the transition models or covariances. == Example application == As an example application, consider the problem of determining the precise location of a truck. The truck can be equipped with a GPS unit that provides an estimate of the position within a few meters. The GPS estimate is likely to be noisy; readings 'jump around' rapidly, though remaining within a few meters of the real position. In addition, since the truck is expected to follow the laws of physics, its position can also be estimated by integrating its velocity over time, determined by keeping track of wheel revolutions and the
Lübke English
The term Lübke English (or, in German, Lübke-Englisch) refers to nonsensical English created by literal word-by-word translation of German phrases, disregarding differences between the languages in syntax and meaning. Lübke English is named after Heinrich Lübke, a president of Germany in the 1960s, whose limited English made him a target of German humorists. In 2006, the German magazine konkret revealed that most of the statements ascribed to Lübke were in fact invented by the editorship of Der Spiegel, mainly by staff writer Ernst Goyke and subsequent letters to the editor. In the 1980s, comedian Otto Waalkes had a routine called "English for Runaways", which is a nonsensical literal translation of Englisch für Fortgeschrittene (actually an idiom for 'English for advanced speakers' in German – note that fortschreiten divides into fort, meaning "away" or "forward", and schreiten, meaning "to walk in steps"). In this mock "course", he translates every sentence back or forth between English and German at least once (usually from German literally into English). Though there are also other, more complex language puns, the title of this routine has gradually replaced the term Lübke English when a German speaker wants to point out naive literal translations.
BFR algorithm
The BFR algorithm, named after its inventors Bradley, Fayyad and Reina, is a variant of k-means algorithm that is designed to cluster data in a high-dimensional Euclidean space. It makes a very strong assumption about the shape of clusters: they must be normally distributed about a centroid. The mean and standard deviation for a cluster may differ for different dimensions, but the dimensions must be independent. In other words, the data must take the shape of axis-aligned ellipses.
Data-driven model
Data-driven models are a class of computational models that primarily rely on historical data collected throughout a system's or process' lifetime to establish relationships between input, internal, and output variables. Commonly found in numerous articles and publications, data-driven models have evolved from earlier statistical models, overcoming limitations posed by strict assumptions about probability distributions. These models have gained prominence across various fields, particularly in the era of big data, artificial intelligence, and machine learning, where they offer valuable insights and predictions based on the available data. == Background == These models have evolved from earlier statistical models, which were based on certain assumptions about probability distributions that often proved to be overly restrictive. The emergence of data-driven models in the 1950s and 1960s coincided with the development of digital computers, advancements in artificial intelligence research, and the introduction of new approaches in non-behavioural modelling, such as pattern recognition and automatic classification. == Key Concepts == Data-driven models encompass a wide range of techniques and methodologies that aim to intelligently process and analyse large datasets. Examples include fuzzy logic, fuzzy and rough sets for handling uncertainty, neural networks for approximating functions, global optimization and evolutionary computing, statistical learning theory, and Bayesian methods. These models have found applications in various fields, including economics, customer relations management, financial services, medicine, and the military, among others. Machine learning, a subfield of artificial intelligence, is closely related to data-driven modelling as it also focuses on using historical data to create models that can make predictions and identify patterns. In fact, many data-driven models incorporate machine learning techniques, such as regression, classification, and clustering algorithms, to process and analyse data. In recent years, the concept of data-driven models has gained considerable attention in the field of water resources, with numerous applications, academic courses, and scientific publications using the term as a generalization for models that rely on data rather than physics. This classification has been featured in various publications and has even spurred the development of hybrid models in the past decade. Hybrid models attempt to quantify the degree of physically based information used in hydrological models and determine whether the process of building the model is primarily driven by physics or purely data-based. As a result, data-driven models have become an essential topic of discussion and exploration within water resources management and research. The term "data-driven modelling" (DDM) refers to the overarching paradigm of using historical data in conjunction with advanced computational techniques, including machine learning and artificial intelligence, to create models that can reveal underlying trends, patterns, and, in some cases, make predictions Data-driven models can be built with or without detailed knowledge of the underlying processes governing the system behavior, which makes them particularly useful when such knowledge is missing or fragmented.
Supervised learning
In machine learning, supervised learning (SL) is a type of machine learning paradigm where an algorithm learns to map input data to a specific output based on example input-output pairs. This process involves training a statistical model using labeled data, meaning each piece of input data is provided with the correct output. The term "supervised" refers to the role of a teacher or supervisor who provides this training data, guiding the algorithm towards correct predictions. For instance, if you want a model to identify cats in images, supervised learning would involve feeding it many images of cats (inputs) that are explicitly labeled "cat" (outputs). The goal of supervised learning is for the trained model to accurately predict the output for new, unseen data. This requires the algorithm to effectively generalize from the training examples, a quality measured by its generalization error. Supervised learning is commonly used for tasks like classification (predicting a category, e.g., spam or not spam) and regression (predicting a continuous value, e.g., house prices). == Steps to follow == To solve a given problem of supervised learning, the following steps must be performed: Determine the type of training samples. Before doing anything else, the user should decide what kind of data is to be used as a training set. In the case of handwriting analysis, for example, this might be a single handwritten character, an entire handwritten word, an entire sentence of handwriting, or a full paragraph of handwriting. Gather a training set. The training set needs to be representative of the real-world use of the function. Thus, a set of input objects is gathered together with corresponding outputs, either from human experts or from measurements. Determine the input feature representation of the learned function. The accuracy of the learned function depends strongly on how the input object is represented. Typically, the input object is transformed into a feature vector, which contains a number of features that are descriptive of the object. The number of features should not be too large, because of the curse of dimensionality; but should contain enough information to accurately predict the output. Determine the structure of the learned function and corresponding learning algorithm. For example, one may choose to use support-vector machines or decision trees. Complete the design. Run the learning algorithm on the gathered training set. Some supervised learning algorithms require the user to determine certain control parameters. These parameters may be adjusted by optimizing performance on a subset (called a validation set) of the training set, or via cross-validation. Evaluate the accuracy of the learned function. After parameter adjustment and learning, the performance of the resulting function should be measured on a test set that is separate from the training set. == Algorithm choice == A wide range of supervised learning algorithms are available, each with its strengths and weaknesses. There is no single learning algorithm that works best on all supervised learning problems (see the No free lunch theorem). There are four major issues to consider in supervised learning: === Bias–variance tradeoff === A first issue is the tradeoff between bias and variance. Imagine that we have available several different, but equally good, training data sets. A learning algorithm is biased for a particular input x {\displaystyle x} if, when trained on each of these data sets, it is systematically incorrect when predicting the correct output for x {\displaystyle x} . A learning algorithm has high variance for a particular input x {\displaystyle x} if it predicts different output values when trained on different training sets. The prediction error of a learned classifier is related to the sum of the bias and the variance of the learning algorithm. Generally, there is a tradeoff between bias and variance. A learning algorithm with low bias must be "flexible" so that it can fit the data well. But if the learning algorithm is too flexible, it will fit each training data set differently, and hence have high variance. A key aspect of many supervised learning methods is that they are able to adjust this tradeoff between bias and variance (either automatically or by providing a bias/variance parameter that the user can adjust). === Function complexity and amount of training data === The second issue is of the amount of training data available relative to the complexity of the "true" function (classifier or regression function). If the true function is simple, then an "inflexible" learning algorithm with high bias and low variance will be able to learn it from a small amount of data. But if the true function is highly complex (e.g., because it involves complex interactions among many different input features and behaves differently in different parts of the input space), then the function will only be able to learn with a large amount of training data paired with a "flexible" learning algorithm with low bias and high variance. === Dimensionality of the input space === A third issue is the dimensionality of the input space. If the input feature vectors have large dimensions, learning the function can be difficult even if the true function only depends on a small number of those features. This is because the many "extra" dimensions can confuse the learning algorithm and cause it to have high variance. Hence, input data of large dimensions typically requires tuning the classifier to have low variance and high bias. In practice, if the engineer can manually remove irrelevant features from the input data, it will likely improve the accuracy of the learned function. In addition, there are many algorithms for feature selection that seek to identify the relevant features and discard the irrelevant ones. This is an instance of the more general strategy of dimensionality reduction, which seeks to map the input data into a lower-dimensional space prior to running the supervised learning algorithm. === Noise in the output values === A fourth issue is the degree of noise in the desired output values (the supervisory target variables). If the desired output values are often incorrect (because of human error or sensor errors), then the learning algorithm should not attempt to find a function that exactly matches the training examples. Attempting to fit the data too carefully leads to overfitting. You can overfit even when there are no measurement errors (stochastic noise) if the function you are trying to learn is too complex for your learning model. In such a situation, the part of the target function that cannot be modeled "corrupts" your training data – this phenomenon has been called deterministic noise. When either type of noise is present, it is better to go with a higher bias, lower variance estimator. In practice, there are several approaches to alleviate noise in the output values such as early stopping to prevent overfitting as well as detecting and removing the noisy training examples prior to training the supervised learning algorithm. There are several algorithms that identify noisy training examples and removing the suspected noisy training examples prior to training has decreased generalization error with statistical significance. === Other factors to consider === Other factors to consider when choosing and applying a learning algorithm include the following: Heterogeneity of the data. If the feature vectors include features of many different kinds (discrete, discrete ordered, counts, continuous values), some algorithms are easier to apply than others. Many algorithms, including support-vector machines, linear regression, logistic regression, neural networks, and nearest neighbor methods, require that the input features be numerical and scaled to similar ranges (e.g., to the [-1,1] interval). Methods that employ a distance function, such as nearest neighbor methods and support-vector machines with Gaussian kernels, are particularly sensitive to this. An advantage of decision trees is that they easily handle heterogeneous data. Redundancy in the data. If the input features contain redundant information (e.g., highly correlated features), some learning algorithms (e.g., linear regression, logistic regression, and distance-based methods) will perform poorly because of numerical instabilities. These problems can often be solved by imposing some form of regularization. Presence of interactions and non-linearities. If each of the features makes an independent contribution to the output, then algorithms based on linear functions (e.g., linear regression, logistic regression, support-vector machines, naive Bayes) and distance functions (e.g., nearest neighbor methods, support-vector machines with Gaussian kernels) generally perform well. However, if there are complex interactions among features, then algorithms such as decision trees and neural networks work better, becaus