Search

This presentation explores how n-grams can be used to automatically classify and learn about music. An overall discussion is provided of various ways in which n-grams can be adapted for use with digital scores, and of how musically meaningful features can be extracted from them. The jSymbolic 3.0 alpha prototype feature extractor is then used in three sets of music classification experiments investigating how n-gram features perform relative to and combined with other types of features extracted from symbolic music files., Funded by the FRQSC and SSHRC.

We present a Web application that facilitates the deep visual search of image collections using contemporary machine learning. We discuss image retrieval as a combined computer vision/human-computer interaction problem, and propose that the standardization of feature extraction is one of the main problems that digital art history faces today.

In this study, we are looking for early mentions of basic principles of sustainability in literary texts using machine learning. With a trained CRF-classifier we automatically annotated a corpus of about 70 novels from German romanticism and singled out passages with a high frequency of annotations, which we analysed in terms of a concept of sustainability. We thus test whether the application of machine learning used to operationalise high-frequency phenomena can also help uncover less frequent and highly interpretive aspects of narrative texts.

Collective sentiment plays a crucial role in financial markets. In this paper, we present our workflow for creating an index that captures the sentiment at the Berlin Stock Exchange from 1872 to 1930. Based on a historical newspaper, we train three models that provide daily aspect-level sentiment data.

The project develops an open-source machine learning platform for East Asian Studies, the first one in the United States.Our platform will be so versatile that humanists will not have to devote time to learning various digital tools. With our sample codes and tutorials, researchers can conduct computer-aided research.

What role does color play in how we imagine our own world and the world(s) of others? Using machine learning and methods from Explainable AI, we study and explain how color use shaped the geographic imaginaries of the Orient and Occident in two different media: photochromes and autochromes

This contribution deals with Dynamic Topic Modelling of Austrian historical newspapers (found in the ANNO Corpus), focusing on the time period from the 18th to the mid-20th Century. The aim of the investigation is to uncover the development of the topic surrounding migration from and via Southeast Europe to Austria.

A decade ago, Johanna Drucker asked: "Is There a 'Digital' Art History?" In this paper, we attempt to reconsider Drucker's question in the light of recent developments in computer vision by investigating the epistemic implications and methodological affordances of large-scale, transformer-based vision models.

This paper explores representations of holiness in a collection of 63.000 lantern slides. Using the multimodal model CLIP, it sheds light on the transition between the real and the imaginary, the holy and the profane. It demonstrates how CLIP can help scholars deal with complex visual concepts such as holiness.

The poster develops and discusses a new technique of modeling prototypicality in genre concepts based on the c@1-score as an uncertainty-based accuracy score and perspectival modeling within the framework of supervised machine learning. The technique is intended to provide better understanding of loosely ordered genres.

We present a modeling of document dates such that it can allow scholars to express uncertainty when annotating data, act as a differentiable loss function for training models and allow for unbiased interpretable performance evaluation under uncertainty.

Kao is a stylized signature used in East Asian cultures. Its location and size are important elements of document manners. This study explores information about their location and size in images through numerical summarization and visualization, and provides quantitative results that support existing tacit knowledge.

In large digital libraries, such as the HathiTrust, metadata is insufficient to identify items of interest. Metadata records are often incomplete and challenging for fiction, where metadata categories, when present, are too broad. This project constructs a machine learning pipeline for fiction classification using the HTRC Extracted Features Dataset, and based on previous work from Underwood et al. We will detail the methodology, early results, and planned future work in generating this dataset.

Significance: Screening and early detection of oral potentially malignant lesions (OPMLs) are of great significance in reducing the mortality rates associated with head and neck malignancies. Intra-oral multispectral optical imaging of tissues in conjunction with cloud-based machine learning (CBML) can be used to detect oral precancers at the point-of-care (POC) and guide the clinician to the most malignant site for biopsy. Aim: Develop a bimodal multispectral imaging system (BMIS) combining tissue autofluorescence and diffuse reflectance (DR) for mapping changes in oxygenated hemoglobin (HbO2) absorption in the oral mucosa, quantifying tissue abnormalities, and guiding biopsies. Approach: The hand-held widefield BMIS consisting of LEDs emitting at 405, 545, 575, and 610 nm, 5MPx monochrome camera, and proprietary Windows-based software was developed for image capture, processing, and analytics. The DR image ratio (R610/R545) was compared with pathologic classification to develop a CBML algorithm for real-time assessment of tissue status at the POC. Results: Sensitivity of 97.5% and specificity of 92.5% were achieved for discrimination of OPML from patient normal in 40 sites, whereas 82% sensitivity and 96.6% specificity were obtained for discrimination of abnormal (OPML + SCC) in 89 sites. Site-specific algorithms derived for buccal mucosa (27 sites) showed improved sensitivity and specificity of 96.3% for discrimination of OPML from normal. Conclusions: Assessment of oral cancer risk is possible by mapping of HbO2 absorption in tissues, and the BMIS system developed appears to be suitable for biopsy guidance and early detection of oral cancers.

The orbital angular momentum (OAM) of light has been at the center of several classical and quantum applications for imaging, information processing and communication. However, the complex structure inherent in OAM states makes their detection and classification nontrivial in many circumstances. Most of the current detection schemes are based on models of the OAM states built upon the use of Laguerre–Gauss (LG) modes. However, this may not in general be sufficient to capture full information on the generated states. In this paper, we go beyond the LG assumption, and employ hypergeometric-Gaussian (HyGG) modes as the basis states of a refined model that can be used—in certain scenarios—to better tailor OAM detection techniques. We show that enhanced performances in OAM detection are obtained for holographic projection via spatial light modulators in combination with single-mode fibers (SMFs), and for classification techniques based on a machine learning approach. Furthermore, a three-fold enhancement in the SMF coupling efficiency is obtained for the holographic technique, when using the HyGG model with respect to the LG one. This improvement provides a significant boost in the overall efficiency of OAM-encoded single-photon detection systems. Given that most of the experimental works using OAM states are effectively based on the generation of HyGG modes, our findings thus represent a relevant addition to experimental toolboxes for OAM-based protocols in quantum communication, cryptography and simulation.

Significance: Physiological parameters extracted from diffuse reflectance spectroscopy (DRS) provide clinicians quantitative information about tissue that helps aid in diagnosis. There is a great need for an accurate and cost-effective method for extracting parameters from DRS measurements. Aim: The aim is to explore the accuracy and speed of physiological parameter extraction using machine learning models compared to that of the widely used Monte Carlo lookup table (MCLUT) inverse model. Approach: Diffuse reflectance spectra were simulated using a light transport model based on Monte Carlo simulations and weighted to six wavelengths. Deep learning (DL), random forest (RF), gradient boosting machine (GBM), and generalized linear model (GLM) machine learning models were built using a training set of 10,000 spectra from the simulated data. The MCLUT and machine learning models were used to predict physiological parameters from a separate test set of 30,000 simulated spectra. Mean absolute errors were calculated to evaluate the accuracy and compare it among MCLUT and machine learning models. In addition, the computational time to predict parameters from the test set was recorded to compare the speed among MCLUT and machine learning models. Results: The DL, RF, GBM, and GLM models all had significantly lower errors than the MCLUT inverse method for six wavelengths. The DL model proved to have the lowest errors, with all absolute percent errors under 10%. The DL model had much faster runtimes than the MCLUT. Conclusions: Machine learning is promising for extracting physiological parameters from six-wavelength DRS data, with both lower errors and a faster runtime than the widely used MCLUT model.

Significance: Functional near-infrared spectroscopy (fNIRS) has been widely used to probe human brain function during task state and resting state. However, the existing analysis toolboxes mainly focus on task activation analysis, few software packages can assist resting-state fNIRS studies. Aim: We aimed to provide a versatile and easy-to-use toolbox to perform analysis for both resting state and task fNIRS. Approach: We developed a MATLAB toolbox called NIRS-KIT that works for both resting-state analysis and task activation detection. Results: NIRS-KIT implements common and necessary processing steps for performing fNIRS data analysis, including data preparation, quality control, preprocessing, individual-level analysis, group-level statistics with several popular statistical models, and multiple comparison correction methods, and finally results visualization. For resting-state fNIRS analysis, functional connectivity analysis, graph theory-based network analysis, and amplitude of low-frequency fluctuations analysis are provided. Additionally, NIRS-KIT also supports activation analysis for task fNIRS. Conclusions: NIRS-KIT offers an open source tool for researchers to analyze resting-state and/or task fNIRS data in one suite. It contains several key features: (1) good compatibility, supporting multiple fNIRS recording systems, data formats of NIRS-SPM and Homer2, and the shared near-infrared spectroscopy format data format recommended by the fNIRS society; (2) flexibility, supporting customized preprocessing scripts; (3) ease-to-use, allowing processing fNIRS signals in batch manner with user-friendly graphical user interfaces; and (4) feature-packed data viewing and result visualization. We anticipate that this NIRS-KIT will facilitate the development of the fNIRS field.

Significance: The potential of fluorescence lifetime imaging microscopy (FLIM) is recently being recognized, especially in biological studies. However, FLIM does not directly measure the lifetimes, rather it records the fluorescence decay traces. The lifetimes and/or abundances have to be estimated from these traces during the phase of data processing. To precisely estimate these parameters is challenging and requires a well-designed computer program. Conventionally employed methods, which are based on curve fitting, are computationally expensive and limited in performance especially for highly noisy FLIM data. The graphical analysis, while free of fit, requires calibration samples for a quantitative analysis. Aim: We propose to extract the lifetimes and abundances directly from the decay traces through machine learning (ML). Approach: The ML-based approach was verified with simulated testing data in which the lifetimes and abundances were known exactly. Thereafter, we compared its performance with the commercial software SPCImage based on datasets measured from biological samples on a time-correlated single photon counting system. We reconstructed the decay traces using the lifetime and abundance values estimated by ML and SPCImage methods and utilized the root-mean-squared-error (RMSE) as marker. Results: The RMSE, which represents the difference between the reconstructed and measured decay traces, was observed to be lower for ML than for SPCImage. In addition, we could demonstrate with a three-component analysis the high potential and flexibility of the ML method to deal with more than two lifetime components. Conclusions: The ML-based approach shows great performance in FLIM data analysis.

Automatic segmentation of bones in computed tomography (CT) images is used for instance in beam hardening correction algorithms where it improves the accuracy of resulting CT numbers. Of special interest are pelvic bones, which—because of their strong attenuation—affect the accuracy of brachytherapy in this region. This work evaluated the performance of the JJ2016 algorithm with the performance of MK2014v2 and JS2018 algorithms; all these algorithms were developed by authors. Visual comparison, and, in the latter case, also Dice similarity coefficients derived from the ground truth were used. It was found that the 3D-based JJ2016 performed better than the 2D-based MK2014v2, mainly because of the more accurate hole filling that benefitted from information in adjacent slices. The neural network-based JS2018 outperformed both traditional algorithms. It was, however, limited to the resolution of 1283 owing to the limited amount of memory in the graphical processing unit (GPU). Funding: VetenskapsradetSwedish Research Council [VR-NT 2016-05033]

Deep neural networks achieve stellar generalisation even when they have enough parameters to easily fit all their training data. We study this phenomenon by analysing the dynamics and the performance of over-parameterised two-layer neural networks in the teacher–student setup, where one network, the student, is trained on data generated by another network, called the teacher. We show how the dynamics of stochastic gradient descent (SGD) is captured by a set of differential equations and prove that this description is asymptotically exact in the limit of large inputs. Using this framework, we calculate the final generalisation error of student networks that have more parameters than their teachers. We find that the final generalisation error of the student increases with network size when training only the first layer, but stays constant or even decreases with size when training both layers. We show that these different behaviours have their root in the different solutions SGD finds for different activation functions. Our results indicate that achieving good generalisation in neural networks goes beyond the properties of SGD alone and depends on the interplay of at least the algorithm, the model architecture, and the data set.

Significance: Melanoma is a deadly cancer that physicians struggle to diagnose early because they lack the knowledge to differentiate benign from malignant lesions. Deep machine learning approaches to image analysis offer promise but lack the transparency to be widely adopted as stand-alone diagnostics. Aim: We aimed to create a transparent machine learning technology (i.e., not deep learning) to discriminate melanomas from nevi in dermoscopy images and an interface for sensory cue integration. Approach: Imaging biomarker cues (IBCs) fed ensemble machine learning classifier (Eclass) training while raw images fed deep learning classifier training. We compared the areas under the diagnostic receiver operator curves. Results: Our interpretable machine learning algorithm outperformed the leading deep-learning approach 75% of the time. The user interface displayed only the diagnostic imaging biomarkers as IBCs. Conclusions: From a translational perspective, Eclass is better than convolutional machine learning diagnosis in that physicians can embrace it faster than black box outputs. Imaging biomarkers cues may be used during sensory cue integration in clinical screening. Our method may be applied to other image-based diagnostic analyses, including pathology and radiology.

Significance: Accurate and objective identification of Alzheimer’s disease (AD) and dementia with Lewy bodies (DLB) is of major clinical importance due to the current lack of low-cost and noninvasive diagnostic tools to differentiate between the two. Developing an approach for such identification can have a great impact in the field of dementia diseases as it would offer physicians a routine objective test to support their diagnoses. The problem is especially acute because these two dementias have some common symptoms and characteristics, which can lead to misdiagnosis of DLB as AD and vice versa, mainly at their early stages. Aim: The aim is to evaluate the potential of mid-infrared (IR) spectroscopy in tandem with machine learning algorithms as a sensitive method to detect minor changes in the biochemical structures that accompany the development of AD and DLB based on a simple peripheral blood test, thus improving the diagnostic accuracy of differentiation between DLB and AD. Approach: IR microspectroscopy was used to examine white blood cells and plasma isolated from 56 individuals: 26 controls, 20 AD patients, and 10 DLB patients. The measured spectra were analyzed via machine learning. Results: Our encouraging results show that it is possible to differentiate between dementia (AD and DLB) and controls with an ∼86% success rate and between DLB and AD patients with a success rate of better than 93%. Conclusions: The success of this method makes it possible to suggest a new, simple, and powerful tool for the mental health professional, with the potential to improve the reliability and objectivity of diagnoses of both AD and DLB.

Significance: We introduce an application of machine learning trained on optical phase features of epithelial and mesenchymal cells to grade cancer cells’ morphologies, relevant to evaluation of cancer phenotype in screening assays and clinical biopsies. Aim: Our objective was to determine quantitative epithelial and mesenchymal qualities of breast cancer cells through an unbiased, generalizable, and linear score covering the range of observed morphologies. Approach: Digital holographic microscopy was used to generate phase height maps of noncancerous epithelial (Gie-No3B11) and fibroblast (human gingival) cell lines, as well as MDA-MB-231 and MCF-7 breast cancer cell lines. Several machine learning algorithms were evaluated as binary classifiers of the noncancerous cells that graded the cancer cells by transfer learning. Results: Epithelial and mesenchymal cells were classified with 96% to 100% accuracy. Breast cancer cells had scores in between the noncancer scores, indicating both epithelial and mesenchymal morphological qualities. The MCF-7 cells skewed toward epithelial scores, while MDA-MB-231 cells skewed toward mesenchymal scores. Linear support vector machines (SVMs) produced the most distinct score distributions for each cell line. Conclusions: The proposed epithelial–mesenchymal score, derived from linear SVM learning, is a sensitive and quantitative approach for detecting epithelial and mesenchymal characteristics of unknown cells based on well-characterized cell lines. We establish a framework for rapid and accurate morphological evaluation of single cells and subtle phenotypic shifts in imaged cell populations.

Noninvasive in vivo imaging of microcirculatory blood flow or perfusion (average speed times concentration of moving red blood cells) is of interest in several clinical applications, including monitoring of burn wounds1,2 and investigation of peripheral arterial disease,3 as well as several others.4 One technique that has gained a lot of focus in the last decades is laser speckle contrast imaging [LSCI; sometimes laser speckle contrast analysis (LASCA)] in which tissue is illuminated with a laser and the resulting speckle pattern is detected with a camera. Light that scatters when interacting with moving particles in the tissue will obtain a Doppler frequency shift depending on the velocity of the particles. The interference of light with different frequencies will give rise to fluctuations in the speckle pattern formed on the imaging sensor. The movement of the speckles on the sensor will cause an image blur that increases with exposure time. The local spatial statistics of this blur can be related to the movement of particles in the tissue, as is done in LSCI.5 LSCI has been increasingly used over laser Doppler imaging mainly due to its simple setup and fast acquisition and data processing. However, conventional LSCI has drawbacks such as a nonlinear response to perfusion, dependency to static scattering contrast, and a high variability in the presence of noise.5,6 Recent work has gone into calibrating and correcting for these issues to make LSCI a more accurate technique.7 Despite this, while it is generally accepted that LSCI is related to microcirculatory perfusion, the relationship is complex and a direct mapping is still not known.4,8 For the older laser Doppler flowmetry (LDF) technique, the relation to microcircular perfusion is better understood, where it is, for example, possible to theoretically show that the perfusion estimate is linearly related to the flow speed.9,10 To address the nonlinearity of LSCI to perfusion, Parthasarathy et al.11 proposed a new setup using multiple exposure times. The technique, called multi-exposure laser speckle contrast imaging (MELSCI, sometimes MESI), obtains information about the speckle motion blur at various exposures, enabling more advanced models to be used when estimating perfusion from the contrast.5,12 Several approaches to capture multi-exposure images have been proposed. The initial approach by Parthasarathy et al.11 was to use a time-modulated laser to achieve multi-exposure images. By capturing all images with a fixed exposure time but only illuminating the tissue during parts of that time, multi-exposures can be generated. However, a problem with this approach is that images with different exposure times are separated in time since they are captured sequentially. Dragojevic et al.13 suggested another approach that addressed this drawback. This was based on a high-speed camera, only capturing images at the shortest exposure time required, and in postprocessing adding successive images together to create longer exposure times. These synthetic exposure times are valid if the interframe delay in the camera is negligible. This method is faster and more accurate than previous methods due to all exposure times essentially being captured simultaneously, but it produces immense amounts of data that must be transferred and processed. At the time, this was, therefore, limited to an offline technique. Hence, MELSCI has so far been held back by technical limitations in both the imaging setup and the computation time of the models. To address this problem of a data and processing bottleneck, we have previously presented a system for synthetic MELSCI,14 based on a high-speed 1000-frames per second (fps) 1-megapixel camera directly interfaced to a field programmable gate array (FPGA) performing the multi-exposure contrast algorithm outlined by Dragojevic13 in real-time. Processed contrast images were sent to a computer, massively reducing the data throughput requirements. This system could produce multi-exposure contrast images at 15.6 fps, using all available frames from the 1000-fps camera, without any loss of data. However, due to insufficient processing power, the system was not able to transfer the processed images to the computer fast enough, and thus could not provide a real-time video-rate output. Furthermore, while the calculation of multi-exposure contrast images was fast enough, at the time there was no multi-exposure perfusion algorithm fast enough to keep up with the continuous stream of contrast images. The model proposed by Parthasarathy et al.11 and later refined by Kazmi et al.15 requires nonlinear fitting to extract perfusion-related parameters from the multi-exposure contrast. This process must be performed individually in each pixel for full field perfusion images, which is not feasible in real-time with satisfactory frame rates.6 We have previously presented a method using machine learning and simulated data from thousands of Monte Carlo tissue models from which we train an artificial neural network (ANN) to translate multi-exposure contrast to laser Doppler perfusion. We showed that this technique not only achieves a model-inference time of

Significance: Machine learning is increasingly being applied to the classification of microscopic data. In order to detect some complex and dynamic cellular processes, time-resolved live-cell imaging might be necessary. Incorporating the temporal information into the classification process may allow for a better and more specific classification. Aim: We propose a methodology for cell classification based on the time-lapse quantitative phase images (QPIs) gained by digital holographic microscopy (DHM) with the goal of increasing performance of classification of dynamic cellular processes. Approach: The methodology was demonstrated by studying epithelial-mesenchymal transition (EMT) which entails major and distinct time-dependent morphological changes. The time-lapse QPIs of EMT were obtained over a 48-h period and specific novel features representing the dynamic cell behavior were extracted. The two distinct end-state phenotypes were classified by several supervised machine learning algorithms and the results were compared with the classification performed on single-time-point images. Results: In comparison to the single-time-point approach, our data suggest the incorporation of temporal information into the classification of cell phenotypes during EMT improves performance by nearly 9% in terms of accuracy, and further indicate the potential of DHM to monitor cellular morphological changes. Conclusions: Proposed approach based on the time-lapse images gained by DHM could improve the monitoring of live cell behavior in an automated fashion and could be further developed into a tool for high-throughput automated analysis of unique cell behavior. (C) The Authors. Published by SPIE under a Creative Commons Attribution 4.0 Unported License.

The bipartite network representation of the drug–target interactions (DTIs) in a biosystem enhances understanding of the drugs’ multifaceted action modes, suggests therapeutic switching for approved drugs and unveils possible side effects. As experimental testing of DTIs is costly and time-consuming, computational predictors are of great aid. Here, for the first time, state-of-the-art DTI supervised predictors custom-made in network biology were compared—using standard and innovative validation frameworks—with unsupervised pure topological-based models designed for general-purpose link prediction in bipartite networks. Surprisingly, our results show that the bipartite topology alone, if adequately exploited by means of the recently proposed local-community-paradigm (LCP) theory—initially detected in brain-network topological self-organization and afterwards generalized to any complex network—is able to suggest highly reliable predictions, with comparable performance with the state-of-the-art-supervised methods that exploit additional (non-topological, for instance biochemical) DTI knowledge. Furthermore, a detailed analysis of the novel predictions revealed that each class of methods prioritizes distinct true interactions; hence, combining methodologies based on diverse principles represents a promising strategy to improve drug–target discovery. To conclude, this study promotes the power of bio-inspired computing, demonstrating that simple unsupervised rules inspired by principles of topological self-organization and adaptiveness arising during learning in living intelligent systems (like the brain) can efficiently equal perform complicated algorithms based on advanced, supervised and knowledge-based engineering.

Small RNAs (sRNAs) are important short-length molecules with regulatory functions essential for plant development and plasticity. High-throughput sequencing of total sRNA populations has revealed that the largest share of sRNA remains uncategorized. To better understand the role of sRNA-mediated cellular regulation, it is necessary to create accurate and comprehensive catalogues of sRNA and their sequence features, a task that currently relies on nontrivial bioinformatic approaches. Although a large number of computational tools have been developed to predict features of sRNA sequences, these tools are mostly dedicated to microRNAs and none integrates the functionalities necessary to describe units from all sRNA pathways thus far discovered in plants. Here, we review the different classes of sRNA found in plants and describe available bioinformatics tools that can help in their detection and categorization.

Accurate assessment of burn severity is critical for wound care and the course of treatment. Delays in classification translate to delays in burn management, increasing the risk of scarring and infection. To this end, numerous imaging techniques have been used to examine tissue properties to infer burn severity. Spatial frequency-domain imaging (SFDI) has also been used to characterize burns based on the relationships between histologic observations and changes in tissue properties. Recently, machine learning has been used to classify burns by combining optical features from multispectral or hyperspectral imaging. Rather than employ models of light propagation to deduce tissue optical properties, we investigated the feasibility of using SFDI reflectance data at multiple spatial frequencies, with a support vector machine (SVM) classifier, to predict severity in a porcine model of graded burns. Calibrated reflectance images were collected using SFDI at eight wavelengths (471 to 851 nm) and five spatial frequencies (0 to 0.2 mm−1). Three models were built from subsets of this initial dataset. The first subset included data taken at all wavelengths with the planar (0 mm−1) spatial frequency, the second comprised data at all wavelengths and spatial frequencies, and the third used all collected data at values relative to unburned tissue. These data subsets were used to train and test cubic SVM models, and compared against burn status 28 days after injury. Model accuracy was established through leave-one-out cross-validation testing. The model based on images obtained at all wavelengths and spatial frequencies predicted burn severity at 24 h with 92.5% accuracy. The model composed of all values relative to unburned skin was 94.4% accurate. By comparison, the model that employed only planar illumination was 88.8% accurate. This investigation suggests that the combination of SFDI with machine learning has potential for accurately predicting burn severity.

While novel technologies such as high-throughput screening have advanced together with significant investment by pharmaceutical companies during the past decades, the success rate for drug development has not yet been improved prompting researchers looking for new strategies of drug discovery. Drug repositioning is a potential approach to solve this dilemma. However, experimental identification and validation of potential drug targets encoded by the human genome is both costly and time-consuming. Therefore, effective computational approaches have been proposed to facilitate drug repositioning, which have proved to be successful in drug discovery. Doubtlessly, the availability of open-accessible data from basic chemical biology research and the success of human genome sequencing are crucial to develop effective in silico drug repositioning methods allowing the identification of potential targets for existing drugs. In this work, we review several chemogenomic data-driven computational algorithms with source codes publicly accessible for predicting drug–target interactions (DTIs). We organize these algorithms by model properties and model evolutionary relationships. We re-implemented five representative algorithms in R programming language, and compared these algorithms by means of mean percentile ranking, a new recall-based evaluation metric in the DTI prediction research field. We anticipate that this review will be objective and helpful to researchers who would like to further improve existing algorithms or need to choose appropriate algorithms to infer potential DTIs in the projects. The source codes for DTI predictions are available at: https://github.com/minghao2016/chemogenomicAlg4DTIpred.

In the past decade, significant progress has been made in complex disease research across multiple omics layers from genome, transcriptome and proteome to metabolome. There is an increasing awareness of the importance of biological interconnections, and much success has been achieved using systems biology approaches. However, because of the typical focus on one single omics layer at a time, existing systems biology findings explain only a modest portion of complex disease. Recent advances in multi-omics data collection and sharing present us new opportunities for studying complex diseases in a more comprehensive fashion, and yet simultaneously create new challenges considering the unprecedented data dimensionality and diversity. Here, our goal is to review extant and emerging network approaches that can be applied across multiple biological layers to facilitate a more comprehensive and integrative multilayered omics analysis of complex diseases.

RNA-Seq is a widely-used method for studying the behavior of genes under different biological conditions. An essential step in an RNA-Seq study is normalization, in which raw data are adjusted to account for factors that prevent direct comparison of expression measures. Errors in normalization can have a significant impact on downstream analysis, such as inflated false positives in differential expression analysis. An under-emphasized feature of normalization is the assumptions upon which the methods rely and how the validity of these assumptions can have a substantial impact on the performance of the methods. In this paper, we explain how assumptions provide the link between raw RNA-Seq read counts and meaningful measures of gene expression. We examine normalization methods from the perspective of their assumptions, as an understanding of methodological assumptions is necessary for choosing methods appropriate for the data at hand. Furthermore, we discuss why normalization methods perform poorly when their assumptions are violated and how this causes problems in subsequent analysis. To analyze a biological experiment, researchers must select a normalization method with assumptions that are met and that produces a meaningful measure of expression for the given experiment., Comment: 20 pages, 6 figures, 1 table. Supplementary information contains 9 pages, 1 table. For associated simulation code, see https://github.com/ciaranlevans/rnaSeqAssumptions