Regression plane concept for analysing continuous cellular processes with machine learning.
Ontology highlight
ABSTRACT:
SUBMITTER: Szkalisity A
PROVIDER: S-EPMC8100172 | biostudies-literature | 2021 May
REPOSITORIES: biostudies-literature
Publications
Regression plane concept for analysing continuous cellular processes with machine learning.
Szkalisity Abel A Piccinini Filippo F Beleon Attila A Balassa Tamas T Varga Istvan Gergely IG Migh Ede E Molnar Csaba C Paavolainen Lassi L Timonen Sanna S Banerjee Indranil I Ikonen Elina E Yamauchi Yohei Y Ando Istvan I Peltonen Jaakko J Pietiäinen Vilja V Honti Viktor V Horvath Peter P
Nature communications 20210505 1
Biological processes are inherently continuous, and the chance of phenotypic discovery is significantly restricted by discretising them. Using multi-parametric active regression we introduce the Regression Plane (RP), a user-friendly discovery tool enabling class-free phenotypic supervised machine learning, to describe and explore biological data in a continuous manner. First, we compare traditional classification with regression in a simulated experimental setup. Second, we use our framework to ...[more]
Similar Datasets
Project description:PurposeIn obstetric ultrasound (US) scanning, the learner's ability to mentally build a three-dimensional (3D) map of the fetus from a two-dimensional (2D) US image represents a major challenge in skill acquisition. We aim to build a US plane localisation system for 3D visualisation, training, and guidance without integrating additional sensors.MethodsWe propose a regression convolutional neural network (CNN) using image features to estimate the six-dimensional pose of arbitrarily oriented US planes relative to the fetal brain centre. The network was trained on synthetic images acquired from phantom 3D US volumes and fine-tuned on real scans. Training data was generated by slicing US volumes into imaging planes in Unity at random coordinates and more densely around the standard transventricular (TV) plane.ResultsWith phantom data, the median errors are 0.90 mm/1.17[Formula: see text] and 0.44 mm/1.21[Formula: see text] for random planes and planes close to the TV one, respectively. With real data, using a different fetus with the same gestational age (GA), these errors are 11.84 mm/25.17[Formula: see text]. The average inference time is 2.97 ms per plane.ConclusionThe proposed network reliably localises US planes within the fetal brain in phantom data and successfully generalises pose regression for an unseen fetal brain from a similar GA as in training. Future development will expand the prediction to volumes of the whole fetus and assess its potential for vision-based, freehand US-assisted navigation when acquiring standard fetal planes.
| S-EPMC9110476 | biostudies-literature
Project description:Cells modify their internal organization during continuous state-transitions, supporting functions from cell division to differentiation. However, tools to measure dynamic physiological states of individual transitioning cells are lacking. We combined live-cell imaging and machine learning to monitor ERK1/2-inhibited primary murine skeletal muscle precursor cells, that transition rapidly and robustly from proliferating myoblasts to post-mitotic myocytes and then fuse, forming multinucleated myotubes. Our model, trained using motility and actin intensity features from single cell tracking data, effectively tracked real-time continuous differentiation, revealing that differentiation occurs 7.5-14.5 hours post-induction, followed by fusion ~3 hours later. Co-inhibition of ERK1/2 and p38 led to differentiation without fusion. Our model inferred co-inhibition leads to terminal differentiation, indicating that p38 is specifically required for transitioning from terminal differentiation to fusion. Our model also predicted that co-inhibition leads to changes in actin dynamics. Mass spectrometry supported these in silico predictions and suggested novel fusion and maturation regulators downstream of differentiation. Collectively, this approach can be adapted to various biological processes to uncover novel links between dynamic single-cell states and their functional outcomes.
| S-SCDT-10_1038-S44320-024-00010-3 | biostudies-other
Project description:Transport processes ruled by complex micro-physics and impractical to theoretical investigation may exhibit emergent behavior describable by mathematical expressions. Such information, while implicitly contained in the results of microscopic-scale numerical simulations close to first principles or experiments is not in a form suitable for macroscopic modelling. Here we present a machine learning approach that leverages such information to deploy micro-physics informed transport flux representations applicable to a continuum mechanics description. One issue with deep neural networks, arguably providing the most generic of such representations, is their noisiness which is shown to break the performance of numerical schemes. The matter is addressed and a methodology suitable for schemes characterised by second order convergence rate is presented. The capability of the methodology is demonstrated through an idealized study of the long standing problem of heat flux suppression relevant to fusion and cosmic plasmas. Symbolic representations, although potentially less generic, are straightforward to use in numerical schemes and theoretical analysis, and can be even more accurate as shown by the application to the same problem of an advanced symbolic regression tool. These results are a promising initial step to filling the gap between micro and macro in this important area of modeling.
| S-EPMC9271097 | biostudies-literature
Project description:Metabolic rewiring allows cells to adapt their metabolism in response to evolving environmental conditions. Traditional metabolomics techniques, whether targeted or untargeted, often struggle to interpret these adaptive shifts. Here, we introduce MetaboLiteLearner, a machine learning framework that harnesses the detailed fragmentation patterns from electron ionization (EI) collected in scan mode during gas chromatography/mass spectrometry (GC/MS) to predict abundance changes in metabolically adapted cells. When tested on breast cancer cells with different preferences to metastasize to specific organs, MetaboLiteLearner predicted the impact of metabolic rewiring on metabolites withheld from the training dataset using only the EI spectra, without metabolite identification or pre-existing knowledge of metabolic networks. The model learned captures shared and unique metabolomic shifts between brain- and lung-homing metastatic lineages, suggesting potential organ-tailored cellular adaptations. Integrating machine learning and metabolomics paves the way for new insights into complex cellular adaptations.
| S-EPMC10462012 | biostudies-literature
Project description:Botnets can simultaneously control millions of Internet-connected devices to launch damaging cyber-attacks that pose significant threats to the Internet. In a botnet, bot-masters communicate with the command and control server using various communication protocols. One of the widely used communication protocols is the 'Domain Name System' (DNS) service, an essential Internet service. Bot-masters utilise Domain Generation Algorithms (DGA) and fast-flux techniques to avoid static blacklists and reverse engineering while remaining flexible. However, botnet's DNS communication generates anomalous DNS traffic throughout the botnet life cycle, and such anomaly is considered an indicator of DNS-based botnets presence in the network. Despite several approaches proposed to detect botnets based on DNS traffic analysis; however, the problem still exists and is challenging due to several reasons, such as not considering significant features and rules that contribute to the detection of DNS-based botnet. Therefore, this paper examines the abnormality of DNS traffic during the botnet lifecycle to extract significant enriched features. These features are further analysed using two machine learning algorithms. The union of the output of two algorithms proposes a novel hybrid rule detection model approach. Two benchmark datasets are used to evaluate the performance of the proposed approach in terms of detection accuracy and false-positive rate. The experimental results show that the proposed approach has a 99.96% accuracy and a 1.6% false-positive rate, outperforming other state-of-the-art DNS-based botnet detection approaches.
| S-EPMC8372004 | biostudies-literature
Project description:The dynamics of the mind are complex. Mental processes unfold continuously in time and may be sensitive to a myriad of interacting variables, especially in naturalistic settings. But statistical models used to analyze data from cognitive experiments often assume simplistic dynamics. Recent advances in deep learning have yielded startling improvements to simulations of dynamical cognitive processes, including speech comprehension, visual perception, and goal-directed behavior. But due to poor interpretability, deep learning is generally not used for scientific analysis. Here, we bridge this gap by showing that deep learning can be used, not just to imitate, but to analyze complex processes, providing flexible function approximation while preserving interpretability. To do so, we define and implement a nonlinear regression model in which the probability distribution over the response variable is parameterized by convolving the history of predictors over time using an artificial neural network, thereby allowing the shape and continuous temporal extent of effects to be inferred directly from time series data. Our approach relaxes standard simplifying assumptions (e.g., linearity, stationarity, and homoscedasticity) that are implausible for many cognitive processes and may critically affect the interpretation of data. We demonstrate substantial improvements on behavioral and neuroimaging data from the language processing domain, and we show that our model enables discovery of novel patterns in exploratory analyses, controls for diverse confounds in confirmatory analyses, and opens up research questions in cognitive (neuro)science that are otherwise hard to study.
| S-EPMC10962694 | biostudies-literature
Project description:Cells dynamically change their internal organization via continuous cell state transitions to mediate a plethora of physiological processes. Understanding such continuous processes is severely limited due to a lack of tools to measure the holistic physiological state of single cells undergoing a transition. We combined live-cell imaging and machine learning to quantitatively monitor skeletal muscle precursor cell (myoblast) differentiation during multinucleated muscle fiber formation. Our machine learning model predicted the continuous differentiation state of single primary murine myoblasts over time and revealed that inhibiting ERK1/2 leads to a gradual transition from an undifferentiated to a terminally differentiated state 7.5-14.5 hours post inhibition. Myoblast fusion occurred ~3 hours after predicted terminal differentiation. Moreover, we showed that our model could predict that cells have reached terminal differentiation under conditions where fusion was stalled, demonstrating potential applications in screening. This method can be adapted to other biological processes to reveal connections between the dynamic single-cell state and virtually any other functional readout.
2024-05-23 | PXD047198 | Pride
Project description:In recent years, there has been a rapid growth in the use of machine learning in material science. Conventionally, a trained predictive model describes a scalar output variable, such as thermodynamic, electronic, or mechanical properties, as a function of input descriptors that vectorize the compositional or structural features of any given material, such as molecules, chemical compositions, or crystalline systems. In machine learning of material data, on the other hand, the output variable is often given as a function. For example, when predicting the optical absorption spectrum of a molecule, the output variable is a spectral function defined in the wavelength domain. Alternatively, in predicting the microstructure of a polymer nanocomposite, the output variable is given as an image from an electron microscope, which can be represented as a two- or three-dimensional function in the image coordinate system. In this study, we consider two unified frameworks to handle such multidimensional or functional output regressions, which are applicable to a wide range of predictive analyses in material science. The first approach employs generative adversarial networks, which are known to exhibit outstanding performance in various computer vision tasks such as image generation, style transfer, and video generation. We also present another type of statistical modeling inspired by a statistical methodology referred to as functional data analysis. This is an extension of kernel regression to deal with functional outputs, and its simple mathematical structure makes it effective in modeling even with small amounts of data. We demonstrate the proposed methods through several case studies in materials science.
| S-EPMC9597664 | biostudies-literature
Project description:IntroductionBenzodiazepines are the most commonly prescribed psychotropic medications, but they may place users at risk of serious adverse effects. Developing a method to predict benzodiazepine prescriptions could assist in prevention efforts.MethodsThe present study applies machine learning methods to de-identified electronic health record data, in order to develop algorithms for predicting benzodiazepine prescription receipt (yes/no) and number of benzodiazepine prescriptions (0, 1, 2+) at a given encounter. Support-vector machine (SVM) and random forest (RF) approaches were applied to outpatient psychiatry, family medicine, and geriatric medicine data from a large academic medical center. The training sample comprised encounters taking place between January 2020 and December 2021 (N = 204,723 encounters); the testing sample comprised data from encounters taking place between January and March 2022 (N = 28,631 encounters). The following empirically-supported features were evaluated: anxiety and sleep disorders (primary anxiety diagnosis, any anxiety diagnosis, primary sleep diagnosis, any sleep diagnosis), demographic characteristics (age, gender, race), medications (opioid prescription, number of opioid prescriptions, antidepressant prescription, antipsychotic prescription), other clinical variables (mood disorder, psychotic disorder, neurocognitive disorder, prescriber specialty), and insurance status (any insurance, type of insurance). We took a step-wise approach to developing a prediction model, wherein Model 1 included only anxiety and sleep diagnoses, and each subsequent model included an additional group of features.ResultsFor predicting benzodiazepine prescription receipt (yes/no), all models showed good to excellent overall accuracy and area under the receiver operating characteristic curve (AUC) for both SVM (Accuracy = 0.868-0.883; AUC = 0.864-0.924) and RF (Accuracy = 0.860-0.887; AUC = 0.877-0.953). Overall accuracy was also high for predicting number of benzodiazepine prescriptions (0, 1, 2+) for both SVM (Accuracy = 0.861-0.877) and RF (Accuracy = 0.846-0.878).DiscussionResults suggest SVM and RF algorithms can accurately classify individuals who receive a benzodiazepine prescription and can separate patients by the number of benzodiazepine prescriptions received at a given encounter. If replicated, these predictive models could inform system-level interventions to reduce the public health burden of benzodiazepines.
| S-EPMC10036348 | biostudies-literature
Project description:Seizure prediction remains a challenge, with approximately 30% of patients unresponsive to conventional treatments. Addressing this issue is crucial for improving patients' quality of life, as timely intervention can mitigate the impact of seizures. In this research field, it is critical to identify the preictal interval, the transition from regular brain activity to a seizure. While previous studies have explored various Electroencephalogram (EEG) based methodologies for prediction, few have been clinically applicable. Recent studies have underlined the dynamic nature of EEG data, characterised by data changes with time, known as concept drifts, highlighting the need for automated methods to detect and adapt to these changes. In this study, we investigate the effectiveness of automatic concept drift adaptation methods in seizure prediction. Three patient-specific seizure prediction approaches with a 10-minute prediction horizon are compared: a seizure prediction algorithm incorporating a window adjustment method by optimising performance with Support Vector Machines (Backwards-Landmark Window), a seizure prediction algorithm incorporating a data-batch (seizures) selection method using a logistic regression (Seizure-batch Regression), and a seizure prediction algorithm with a dynamic integration of classifiers (Dynamic Weighted Ensemble). These methods incorporate a retraining process after each seizure and use a combination of univariate linear features and SVM classifiers. The Firing Power was used as a post-processing technique to generate alarms before seizures. These methodologies were compared with a control approach based on the typical machine learning pipeline, considering a group of 37 patients with Temporal Lobe Epilepsy from the EPILEPSIAE database. The best-performing approach (Backwards-Landmark Window) achieved results of 0.75 ± 0.33 for sensitivity and 1.03 ± 1.00 for false positive rate per hour. This new strategy performed above chance for 89% of patients with the surrogate predictor, whereas the control approach only validated 46%.
| S-EPMC11001609 | biostudies-literature