scholarly journals An Interpretable Deep Learning Approach for Biomarker Detection in LC-MS Proteomics Data

2021 ◽  
Author(s):  
Sahar Iravani ◽  
Tim O.F. Conrad

AbstractAnalyzing mass spectrometry-based proteomics data with deep learning (DL) approaches poses several challenges due to the high dimensionality, low sample size, and high level of noise. Besides, DL-based workflows are often hindered to be integrated into medical settings due to the lack of interpretable explanation. We present DLearnMS, a DL biomarker detection framework, to address these challenges on proteomics instances of liquid chromatography-mass spectrometry (LC-MS) - a well-established tool for quantifying complex protein mixtures. Our DLearnMS framework learns the clinical state of LC-MS data instances using convolutional neural networks. Next, based on the trained neural networks, biomarkers can be identified using the layer-wise relevance propagation technique. This enables detecting discriminating regions of the data and the design of more robust networks. We show that DLearnMS outperforms conventional LC-MS biomarker detection approaches in detecting fewer false positive peaks while maintaining a comparable amount of true positives peaks. Unlike other methods, no explicit preprocessing step is needed in DLearnMS.

2022 ◽  
Vol 6 (1) ◽  
Author(s):  
Marco Rossi ◽  
Sofia Vallecorsa

AbstractIn this work, we investigate different machine learning-based strategies for denoising raw simulation data from the ProtoDUNE experiment. The ProtoDUNE detector is hosted by CERN and it aims to test and calibrate the technologies for DUNE, a forthcoming experiment in neutrino physics. The reconstruction workchain consists of converting digital detector signals into physical high-level quantities. We address the first step in reconstruction, namely raw data denoising, leveraging deep learning algorithms. We design two architectures based on graph neural networks, aiming to enhance the receptive field of basic convolutional neural networks. We benchmark this approach against traditional algorithms implemented by the DUNE collaboration. We test the capabilities of graph neural network hardware accelerator setups to speed up training and inference processes.


2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Shisheng Wang ◽  
Hongwen Zhu ◽  
Hu Zhou ◽  
Jingqiu Cheng ◽  
Hao Yang

Abstract Background Mass spectrometry (MS) has become a promising analytical technique to acquire proteomics information for the characterization of biological samples. Nevertheless, most studies focus on the final proteins identified through a suite of algorithms by using partial MS spectra to compare with the sequence database, while the pattern recognition and classification of raw mass-spectrometric data remain unresolved. Results We developed an open-source and comprehensive platform, named MSpectraAI, for analyzing large-scale MS data through deep neural networks (DNNs); this system involves spectral-feature swath extraction, classification, and visualization. Moreover, this platform allows users to create their own DNN model by using Keras. To evaluate this tool, we collected the publicly available proteomics datasets of six tumor types (a total of 7,997,805 mass spectra) from the ProteomeXchange consortium and classified the samples based on the spectra profiling. The results suggest that MSpectraAI can distinguish different types of samples based on the fingerprint spectrum and achieve better prediction accuracy in MS1 level (average 0.967). Conclusion This study deciphers proteome profiling of raw mass spectrometry data and broadens the promising application of the classification and prediction of proteomics data from multi-tumor samples using deep learning methods. MSpectraAI also shows a better performance compared to the other classical machine learning approaches.


Author(s):  
Xiayu Chen ◽  
Ming Zhou ◽  
Zhengxin Gong ◽  
Wei Xu ◽  
Xingyu Liu ◽  
...  

Deep neural networks (DNNs) have attained human-level performance on dozens of challenging tasks via an end-to-end deep learning strategy. Deep learning allows data representations that have multiple levels of abstraction; however, it does not explicitly provide any insights into the internal operations of DNNs. Deep learning's success is appealing to neuroscientists not only as a method for applying DNNs to model biological neural systems but also as a means of adopting concepts and methods from cognitive neuroscience to understand the internal representations of DNNs. Although general deep learning frameworks, such as PyTorch and TensorFlow, could be used to allow such cross-disciplinary investigations, the use of these frameworks typically requires high-level programming expertise and comprehensive mathematical knowledge. A toolbox specifically designed as a mechanism for cognitive neuroscientists to map both DNNs and brains is urgently needed. Here, we present DNNBrain, a Python-based toolbox designed for exploring the internal representations of DNNs as well as brains. Through the integration of DNN software packages and well-established brain imaging tools, DNNBrain provides application programming and command line interfaces for a variety of research scenarios. These include extracting DNN activation, probing and visualizing DNN representations, and mapping DNN representations onto the brain. We expect that our toolbox will accelerate scientific research by both applying DNNs to model biological neural systems and utilizing paradigms of cognitive neuroscience to unveil the black box of DNNs.


2021 ◽  
Author(s):  
Qihang Wang ◽  
Feng Liu ◽  
Guihong Wan ◽  
Ying Chen

AbstractMonitoring the depth of unconsciousness during anesthesia is useful in both clinical settings and neuroscience investigations to understand brain mechanisms. Electroencephalogram (EEG) has been used as an objective means of characterizing brain altered arousal and/or cognition states induced by anesthetics in real-time. Different general anesthetics affect cerebral electrical activities in different ways. However, the performance of conventional machine learning models on EEG data is unsatisfactory due to the low Signal to Noise Ratio (SNR) in the EEG signals, especially in the office-based anesthesia EEG setting. Deep learning models have been used widely in the field of Brain Computer Interface (BCI) to perform classification and pattern recognition tasks due to their capability of good generalization and handling noises. Compared to other BCI applications, where deep learning has demonstrated encouraging results, the deep learning approach for classifying different brain consciousness states under anesthesia has been much less investigated. In this paper, we propose a new framework based on meta-learning using deep neural networks, named Anes-MetaNet, to classify brain states under anesthetics. The Anes-MetaNet is composed of Convolutional Neural Networks (CNN) to extract power spectrum features, and a time consequence model based on Long Short-Term Memory (LSTM) Networks to capture the temporal dependencies, and a meta-learning framework to handle large cross-subject variability. We used a multi-stage training paradigm to improve the performance, which is justified by visualizing the high-level feature mapping. Experiments on the office-based anesthesia EEG dataset demonstrate the effectiveness of our proposed Anes-MetaNet by comparison of existing methods.


2016 ◽  
Vol 10 (03) ◽  
pp. 417-439 ◽  
Author(s):  
Xing Hao ◽  
Guigang Zhang ◽  
Shang Ma

Deep learning is a branch of machine learning that tries to model high-level abstractions of data using multiple layers of neurons consisting of complex structures or non-liner transformations. With the increase of the amount of data and the power of computation, neural networks with more complex structures have attracted widespread attention and been applied to various fields. This paper provides an overview of deep learning in neural networks including popular architecture models and training algorithms.


2020 ◽  
Vol 8 (6) ◽  
pp. 4781-4784

Dermatological diseases are found to induce a serious impact on the health of millions of people as everyone is affected by almost all types of skin disorders every year. Since the human analysis of such diseases takes some time and effort, and current methods are only used to analyse singular types of skin diseases, there is a need for a more high-level computer-aided expertise in the analysis and diagnosis of multi-type skin diseases. This paper proposes an approach to use computer-aided techniques in deep learning neural networks such as Convolutional neural networks (CNN) and Residual Neural Networks (ResNet) to predict skin diseases real-time and thus provides more accuracy than other neural networks.


2020 ◽  
Author(s):  
Qianli Liao

(Performed in 2018 as a class project) Deep learning is a field that has been mainly driven by connectionist models like neural networks, characterized by layered processing of distributed, sub-symbolic and statistical features. However, human high-level thoughts appear to be highly symbolic, focusing on objects and relations.To bridge the gap between perception and symbols, a series of models on "Object Oriented Deep Learning" was proposed [9,8,7]. In this project we further explore this class of models. We implement a generative version of OODL that can generate images instead of performing object recognition, in a similar way to Generative Adversarial Networks (GANs). In comparison to conventional “feature-oriented” deep learning, OODL naturally handles properties of objects by incorporating them as fields. It offers exact equivariance [8] to translation, rotation and scaling. When implementing it as a generative model, one should be able to precisely control such geometric properties of the generated objects.


2021 ◽  
Author(s):  
Matan Fintz ◽  
Margarita Osadchy ◽  
Uri Hertz

AbstractDeep neural networks (DNN) models have the potential to provide new insights in the study of human decision making, due to their high capacity and data-driven design. While these models may be able to go beyond theory-driven models in predicting human behaviour, their opaque nature limits their ability to explain how an operation is carried out. This explainability problem remains unresolved. Here we demonstrate the use of a DNN model as an exploratory tool to identify predictable and consistent human behaviour in value-based decision making beyond the scope of theory-driven models. We then propose using theory-driven models to characterise the operation of the DNN model. We trained a DNN model to predict human decisions in a four-armed bandit task. We found that this model was more accurate than a reinforcement-learning reward-oriented model geared towards choosing the most rewarding option. This disparity in accuracy was more pronounced during times when the expected reward from all options was similar, i.e., no unambiguous good option. To investigate this disparity, we introduced a reward-oblivious model, which was trained to predict human decisions without information about the rewards obtained from each option. This model captured decision-sequence patterns made by participants (e.g., a-b-c-d). In a series of experimental offline simulations of all models we found that the general model was in line with a reward-oriented model’s predictions when one option was clearly better than the others.However, when options’ expected rewards were similar to each other, it was in-line with the reward-oblivious model’s pattern completion predictions. These results indicate the contribution of predictable but task-irrelevant decision patterns to human decisions, especially when task-relevant choices are not immediately apparent. Importantly, we demonstrate how theory-driven cognitive models can be used to characterise the operation of DNNs, making them a useful explanatory tool in scientific investigation.Author SummaryDeep neural networks (DNN) models are an extremely useful tool across multiple domains, and specifically for performing tasks that mimic and predict human behaviour. However, due to their opaque nature and high level of complexity, their ability to explain human behaviour is limited. Here we used DNN models to uncover hitherto overlooked aspects of human decision making, i.e., their reliance on predictable patterns for exploration. For this purpose, we trained a DNN model to predict human choices in a decision-making task. We then characterised this data-driven model using explicit, theory-driven cognitive models, in a set of offline experimental simulations. This relationship between explicit and data-driven approaches, where high-capacity models are used to explore beyond the scope of established models and theory-driven models are used to explain and characterise these new grounds, make DNN models a powerful scientific tool.


Sensors ◽  
2020 ◽  
Vol 20 (19) ◽  
pp. 5707 ◽  
Author(s):  
Saedeh Abbaspour ◽  
Faranak Fotouhi ◽  
Ali Sedaghatbaf ◽  
Hossein Fotouhi ◽  
Maryam Vahabi ◽  
...  

Recent advances in artificial intelligence and machine learning (ML) led to effective methods and tools for analyzing the human behavior. Human Activity Recognition (HAR) is one of the fields that has seen an explosive research interest among the ML community due to its wide range of applications. HAR is one of the most helpful technology tools to support the elderly’s daily life and to help people suffering from cognitive disorders, Parkinson’s disease, dementia, etc. It is also very useful in areas such as transportation, robotics and sports. Deep learning (DL) is a branch of ML based on complex Artificial Neural Networks (ANNs) that has demonstrated a high level of accuracy and performance in HAR. Convolutional Neural Networks (CNNs) and Recurrent Neural Networks (RNNs) are two types of DL models widely used in the recent years to address the HAR problem. The purpose of this paper is to investigate the effectiveness of their integration in recognizing daily activities, e.g., walking. We analyze four hybrid models that integrate CNNs with four powerful RNNs, i.e., LSTMs, BiLSTMs, GRUs and BiGRUs. The outcomes of our experiments on the PAMAP2 dataset indicate that our proposed hybrid models achieve an outstanding level of performance with respect to several indicative measures, e.g., F-score, accuracy, sensitivity, and specificity.


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