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Pathology Pathology

Multiplex Cellular Communities in Multi-Gigapixel Colorectal Cancer Histology Images for Tissue Phenotyping.

In IEEE transactions on image processing : a publication of the IEEE Signal Processing Society

In computational pathology, automated tissue phenotyping in cancer histology images is a fundamental tool for profiling tumor microenvironments. Current tissue phenotyping methods use features derived from image patches which may not carry biological significance. In this work, we propose a novel multiplex cellular community-based algorithm for tissue phenotyping integrating cell-level features within a graph-based hierarchical framework. We demonstrate that such integration offers better performance compared to prior deep learning and texture-based methods as well as to cellular community based methods using uniplex networks. To this end, we construct celllevel graphs using texture, alpha diversity and multi-resolution deep features. Using these graphs, we compute cellular connectivity features which are then employed for the construction of a patch-level multiplex network. Over this network, we compute multiplex cellular communities using a novel objective function. The proposed objective function computes a low-dimensional subspace from each cellular network and subsequently seeks a common low-dimensional subspace using the Grassmann manifold. We evaluate our proposed algorithm on three publicly available datasets for tissue phenotyping, demonstrating a significant improvement over existing state-of-the-art methods.

Javed Sajid, Mahmood Arif, Werghi Naoufel, Benes Ksenija, Rajpoot Nasir

2020-Sep-23

General General

Heterogeneous Graph Attention Network for Unsupervised Multiple-Target Domain Adaptation.

In IEEE transactions on pattern analysis and machine intelligence ; h5-index 127.0

Domain adaptation, which transfers the knowledge from label-rich source domain to unlabeled target domains, is a challenging task in machine learning. The prior domain adaptation methods focus on pairwise adaptation assumption with a single source and a single target domain, while little work concerns the scenario of one source domain and multiple target domains. Applying pairwise adaptation methods to this setting may be suboptimal, as they fail to consider the semantic association among multiple target domains. In this work we propose a deep semantic information propagation approach in the novel context of multiple unlabeled target domains and one labeled source domain. Our model aims to learn a unified subspace common for all domains with a heterogeneous graph attention network, where the transductive ability of the graph attention network can conduct semantic propagation of the related samples among multiple domains. In particular, the attention mechanism is applied to optimize the relationships of multiple domain samples for better semantic transfer. Then, the pseudo labels of the target domains predicted by the graph attention network are utilized to learn domain-invariant representations by aligning labeled source centroid and pseudo-labeled target centroid. We test our approach on four challenging public datasets, and it outperforms several popular domain adaptation methods.

Yang Xu, Deng Cheng, Liu Tongliang, Tao Dacheng

2020-Sep-23

General General

Predicting Hydrophobicity by Learning Spatiotemporal Features of Interfacial Water Structure: Combining Molecular Dynamics Simulations with Convolutional Neural Networks.

In The journal of physical chemistry. B

The hydrophobicity of functionalized interfaces can be quantified by the structure and dynamics of water molecules using molecular dynamics (MD) simulations, but existing methods to quantify interfacial hydrophobicity are computationally expensive. In this work, we develop a new machine learning approach that leverages convolutional neural networks (CNNs) to predict the hydration free energy (HFE) as a measure of interfacial hydrophobicity based on water positions sampled from MD simulations. We construct a set of idealized self-assembled monolayers (SAMs) with varying surface polarities and calculate their HFEs using indirect umbrella sampling calculations (INDUS). Using the INDUS-calculated HFEs as labels and physically informed representations of interfacial water density from MD simulations as input, we train and evaluate a series of neural networks to predict SAM HFEs. By systematically varying model hyperparameters, we demonstrate that a 3D CNN trained to analyze both spatial and temporal correlations between interfacial water molecule positions leads to HFE predictions that require an order of magnitude less MD simulation time than INDUS. We showcase the power of this model to explore a large design space by predicting HFEs for a set of 71 chemically heterogeneous SAMs with varying patterns and mole fractions.

Kelkar Atharva Shailendra, Dallin Bradley C, Van Lehn Reid C

2020-Sep-23

General General

Machine Learning Predicts Degree of Aromaticity from Structural Fingerprints.

In Journal of chemical information and modeling

Prediction of whether a compound is 'aromatic' is at first glance a relatively simple task - does it obey Hückel's rule (planar cyclic π-system with 4n+2 electrons) or not? However, aromaticity is far from a binary property, and there are distinct variations in chemical and biological behaviour between different systems which obey Hückel's rule and are thus classified as aromatic. To that end, the aromaticity of each molecule in a large public dataset [1] [2] was quantified by an extension of the work of Raczyńska et al. [3]. Building on this data, a method is proposed for machine-learning the degree of aromaticity for each aromatic ring in a molecule. Categories are derived from the numeric results, allowing the differentiation of structural patterns between them and thus better representation of the underlying chemical and biological behaviour in expert and (Q)SAR systems.

Ponting David John, van Deursen Ruud, Ott Martin A

2020-Sep-23

Radiology Radiology

Assessing and mitigating the effects of class imbalance in machine learning with application to X-ray imaging.

In International journal of computer assisted radiology and surgery

PURPOSE : Machine learning (ML) algorithms are well known to exhibit variations in prediction accuracy when provided with imbalanced training sets typically seen in medical imaging (MI) due to the imbalanced ratio of pathological and normal cases. This paper presents a thorough investigation of the effects of class imbalance and methods for mitigating class imbalance in ML algorithms applied to MI.

METHODS : We first selected five classes from the Image Retrieval in Medical Applications (IRMA) dataset, performed multiclass classification using the random forest model (RFM), and then performed binary classification using convolutional neural network (CNN) on a chest X-ray dataset. An imbalanced class was created in the training set by varying the number of images in that class. Methods tested to mitigate class imbalance included oversampling, undersampling, and changing class weights of the RFM. Model performance was assessed by overall classification accuracy, overall F1 score, and specificity, recall, and precision of the imbalanced class.

RESULTS : A close-to-balanced training set resulted in the best model performance, and a large imbalance with overrepresentation was more detrimental to model performance than underrepresentation. Oversampling and undersampling methods were both effective in mitigating class imbalance, and efficacy of oversampling techniques was class specific.

CONCLUSION : This study systematically demonstrates the effect of class imbalance on two public X-ray datasets on RFM and CNN, making these findings widely applicable as a reference. Furthermore, the methods employed here can guide researchers in assessing and addressing the effects of class imbalance, while considering the data-specific characteristics to optimize imbalance mitigating methods.

Qu Wendi, Balki Indranil, Mendez Mauro, Valen John, Levman Jacob, Tyrrell Pascal N

2020-Sep-23

Class imbalance, Machine learning, Medical imaging, Radiology, X-ray

General General

Ethical dilemmas in COVID-19 times: how to decide who lives and who dies?

In Revista da Associacao Medica Brasileira (1992)

The respiratory disease caused by the coronavirus SARS-CoV-2 (COVID-19) is a pandemic that produces a large number of simultaneous patients with severe symptoms and in need of special hospital care, overloading the infrastructure of health services. All of these demands generate the need to ration equipment and interventions. Faced with this imbalance, how, when, and who decides, there is the impact of the stressful systems of professionals who are at the front line of care and, in the background, issues inherent to human subjectivity. Along this path, the idea of using artificial intelligence algorithms to replace health professionals in the decision-making process also arises. In this context, there is the ethical question of how to manage the demands produced by the pandemic. The objective of this work is to reflect, from the point of view of medical ethics, on the basic principles of the choices made by the health teams, during the COVID-19 pandemic, whose resources are scarce and decisions cause anguish and restlessness. The ethical values for the rationing of health resources in an epidemic must converge to some proposals based on fundamental values such as maximizing the benefits produced by scarce resources, treating people equally, promoting and recommending instrumental values, giving priority to critical situations. Naturally, different judgments will occur in different circumstances, but transparency is essential to ensure public trust. In this way, it is possible to develop prioritization guidelines using well-defined values and ethical recommendations to achieve fair resource allocation.

Neves Nedy M B C, Bitencourt Flávia B C S N, Bitencourt Almir G V

2020