Subspace corrected relevance learning with application in neuroimaging.

In machine learning, data often comes from different sources, but combining them can introduce extraneous variation that affects both generalization and interpretability. For example, we investigate the classification of neurodegenerative diseases using FDG-PET data collected from multiple neuroimaging centers. However, data collected at different centers introduces unwanted variation due to differences in scanners, scanning protocols, and processing methods. To address this issue, we propose a two-step approach to limit the influence of center-dependent variation on the classification of healthy controls and early vs. late-stage Parkinson's disease patients. First, we train a Generalized Matrix Learning Vector Quantization (GMLVQ) model on healthy control data to identify a "relevance space" that distinguishes between centers. Second, we use this space to construct a correction matrix that restricts a second GMLVQ system's training on the diagnostic problem. We evaluate the effectiveness of this approach on the real-world multi-center datasets and simulated artificial dataset. Our results demonstrate that the approach produces machine learning systems with reduced bias - being more specific due to eliminating information related to center differences during the training process - and more informative relevance profiles that can be interpreted by medical experts. This method can be adapted to similar problems outside the neuroimaging domain, as long as an appropriate "relevance space" can be identified to construct the correction matrix.

Translating the potential of the urine steroid metabolome to stage NAFLD (TrUSt-NAFLD): study protocol for a multicentre, prospective validation study.

INTRODUCTION: Non-alcoholic fatty liver disease (NAFLD) affects approximately one in four individuals and its prevalence continues to rise. The advanced stages of NAFLD with significant liver fibrosis are associated with adverse morbidity and mortality outcomes. Currently, liver biopsy remains the 'gold-standard' approach to stage NAFLD severity. Although generally well tolerated, liver biopsies are associated with significant complications, are resource intensive, costly, and sample only a very small area of the liver as well as requiring day case admission to a secondary care setting. As a result, there is a significant unmet need to develop non-invasive biomarkers that can accurately stage NAFLD and limit the need for liver biopsy. The aim of this study is to validate the use of the urine steroid metabolome as a strategy to stage NAFLD severity and to compare its performance against other non-invasive NAFLD biomarkers. METHODS AND ANALYSIS: The TrUSt-NAFLD study is a multicentre prospective test validation study aiming to recruit 310 patients with biopsy-proven and staged NAFLD across eight centres within the UK. 150 appropriately matched control patients without liver disease will be recruited through the Oxford Biobank. Blood and urine samples, alongside clinical data, will be collected from all participants. Urine samples will be analysed by liquid chromatography-tandem mass spectroscopy to quantify a panel of predefined steroid metabolites. A machine learning-based classifier, for example, Generalized Matrix Relevance Learning Vector Quantization that was trained on retrospective samples, will be applied to the prospective steroid metabolite data to determine its ability to identify those patients with advanced, as opposed to mild-moderate, liver fibrosis as a consequence of NAFLD. ETHICS AND DISSEMINATION: Research ethical approval was granted by West Midlands, Black Country Research Ethics Committee (REC reference: 21/WM/0177). A substantial amendment (TrUSt-NAFLD-SA1) was approved on 26 November 2021. TRIAL REGISTRATION NUMBER: ISRCTN19370855.

Urine steroid metabolomics as a diagnostic tool in primary aldosteronism.

Primary aldosteronism (PA) causes 5-10% of hypertension cases, but only a minority of patients are currently diagnosed and treated because of a complex, stepwise, and partly invasive workup. We tested the performance of urine steroid metabolomics, the computational analysis of 24-hour urine steroid metabolome data by machine learning, for the identification and subtyping of PA. Mass spectrometry-based multi-steroid profiling was used to quantify the excretion of 34 steroid metabolites in 24-hour urine samples from 158 adults with PA (88 with unilateral PA [UPA] due to aldosterone-producing adenomas [APAs]; 70 with bilateral PA [BPA]) and 65 sex- and age-matched healthy controls. All APAs were resected and underwent targeted gene sequencing to detect somatic mutations associated with UPA. Patients with PA had increased urinary metabolite excretion of mineralocorticoids, glucocorticoids, and glucocorticoid precursors. Urine steroid metabolomics identified patients with PA with high accuracy, both when applied to all 34 or only the three most discriminative steroid metabolites (average areas under the receiver-operating characteristics curve [AUCs-ROC] 0.95-0.97). Whilst machine learning was suboptimal in differentiating UPA from BPA (average AUCs-ROC 0.65-0.73), it readily identified APA cases harbouring somatic KCNJ5 mutations (average AUCs-ROC 0.79-85). These patients showed a distinctly increased urine excretion of the hybrid steroid 18-hydroxycortisol and its metabolite 18-oxo-tetrahydrocortisol, the latter identified by machine learning as by far the most discriminative steroid. In conclusion, urine steroid metabolomics is a non-invasive candidate test for the accurate identification of PA cases and KCNJ5-mutated APAs.

Survey of feature selection and extraction techniques for stock market prediction.

In stock market forecasting, the identification of critical features that affect the performance of machine learning (ML) models is crucial to achieve accurate stock price predictions. Several review papers in the literature have focused on various ML, statistical, and deep learning-based methods used in stock market forecasting. However, no survey study has explored feature selection and extraction techniques for stock market forecasting. This survey presents a detailed analysis of 32 research works that use a combination of feature study and ML approaches in various stock market applications. We conduct a systematic search for articles in the Scopus and Web of Science databases for the years 2011-2022. We review a variety of feature selection and feature extraction approaches that have been successfully applied in the stock market analyses presented in the articles. We also describe the combination of feature analysis techniques and ML methods and evaluate their performance. Moreover, we present other survey articles, stock market input and output data, and analyses based on various factors. We find that correlation criteria, random forest, principal component analysis, and autoencoder are the most widely used feature selection and extraction techniques with the best prediction accuracy for various stock market applications.

FDG-PET combined with learning vector quantization allows classification of neurodegenerative diseases and reveals the trajectory of idiopathic REM sleep behavior disorder.

BACKGROUND AND OBJECTIVES: 18F-fluorodeoxyglucose (FDG) positron emission tomography (PET) combined with principal component analysis (PCA) has been applied to identify disease-related brain patterns in neurodegenerative disorders such as Parkinson's disease (PD), Dementia with Lewy Bodies (DLB) and Alzheimer's disease (AD). These patterns are used to quantify functional brain changes at the single subject level. This is especially relevant in determining disease progression in idiopathic REM sleep behavior disorder (iRBD), a prodromal stage of PD and DLB. However, the PCA method is limited in discriminating between neurodegenerative conditions. More advanced machine learning algorithms may provide a solution. In this study, we apply Generalized Matrix Learning Vector Quantization (GMLVQ) to FDG-PET scans of healthy controls, and patients with AD, PD and DLB. Scans of iRBD patients, scanned twice with an approximate 4 year interval, were projected into GMLVQ space to visualize their trajectory. METHODS: We applied a combination of SSM/PCA and GMLVQ as a classifier on FDG-PET data of healthy controls, AD, DLB, and PD patients. We determined the diagnostic performance by performing a ten times repeated ten fold cross validation. We analyzed the validity of the classification system by inspecting the GMLVQ space. First by the projection of the patients into this space. Second by representing the axis, that span this decision space, into a voxel map. Furthermore, we projected a cohort of RBD patients, whom have been scanned twice (approximately 4 years apart), into the same decision space and visualized their trajectories. RESULTS: The GMLVQ prototypes, relevance diagonal, and decision space voxel maps showed metabolic patterns that agree with previously identified disease-related brain patterns. The GMLVQ decision space showed a plausible quantification of FDG-PET data. Distance traveled by iRBD subjects through GMLVQ space per year (i.e. velocity) was correlated with the change in motor symptoms per year (Spearman's rho =0.62, P=0.004). CONCLUSION: In this proof-of-concept study, we show that GMLVQ provides a classification of patients with neurodegenerative disorders, and may be useful in future studies investigating speed of progression in prodromal disease stages.

An application of generalized matrix learning vector quantization in neuroimaging.

BACKGROUND AND OBJECTIVE: Neurodegenerative diseases like Parkinson's disease often take several years before they can be diagnosed reliably based on clinical grounds. Imaging techniques such as MRI are used to detect anatomical (structural) pathological changes. However, these kinds of changes are usually seen only late in the development. The measurement of functional brain activity by means of [18F]fluorodeoxyglucose positron emission tomography (FDG-PET) can provide useful information, but its interpretation is more difficult. The scaled sub-profile model principal component analysis (SSM/PCA) was shown to provide more useful information than other statistical techniques. Our objective is to improve the performance further by combining SSM/PCA and prototype-based generalized matrix learning vector quantization (GMLVQ). METHODS: We apply a combination of SSM/PCA and GMLVQ as a classifier. In order to demonstrate the combination's validity, we analyze FDG-PET data of Parkinson's disease (PD) patients collected at three different neuroimaging centers in Europe. We determine the diagnostic performance by performing a ten times repeated ten fold cross validation. Additionally, discriminant visualizations of the data are included. The prototypes and relevance of GMLVQ are transformed back to the original voxel space by exploiting the linearity of SSM/PCA. The resulting prototypes and relevance profiles have then been assessed by three neurologists. RESULTS: One important finding is that discriminative visualization can help to identify disease-related properties as well as differences which are due to center-specific factors. Secondly, the neurologist assessed the interpretability of the method and confirmed that prototypes are similar to known activity profiles of PD patients. CONCLUSION: We have shown that the presented combination of SSM/PCA and GMLVQ can provide useful means to assess and better understand characteristic differences in FDG-PET data from PD patients and HCs. Based on the assessments by medical experts and the results of our computational analysis we conclude that the first steps towards a diagnostic support system have been taken successfully.

Tissue- and development-stage-specific mRNA and heterogeneous CNV signatures of human ribosomal proteins in normal and cancer samples.

We give results from a detailed analysis of human Ribosomal Protein (RP) levels in normal and cancer samples and cell lines from large mRNA, copy number variation and ribosome profiling datasets. After normalizing total RP mRNA levels per sample, we find highly consistent tissue specific RP mRNA signatures in normal and tumor samples. Multiple RP mRNA-subtypes exist in several cancers, with significant survival and genomic differences. Some RP mRNA variations among subtypes correlate with copy number loss of RP genes. In kidney cancer, RP subtypes map to molecular subtypes related to cell-of-origin. Pan-cancer analysis of TCGA data showed widespread single/double copy loss of RP genes, without significantly affecting survival. In several cancer cell lines, CRISPR-Cas9 knockout of RP genes did not affect cell viability. Matched RP ribosome profiling and mRNA data in humans and rodents stratified by tissue and development stage and were strongly correlated, showing that RP translation rates were proportional to mRNA levels. In a small dataset of human adult and fetal tissues, RP protein levels showed development stage and tissue specific heterogeneity of RP levels. Our results suggest that heterogeneous RP levels play a significant functional role in cellular physiology, in both normal and disease states.

Accurate non-invasive diagnosis and staging of non-alcoholic fatty liver disease using the urinary steroid metabolome.

BACKGROUND: The development of accurate, non-invasive markers to diagnose and stage non-alcoholic fatty liver disease (NAFLD) is critical to reduce the need for an invasive liver biopsy and to identify patients who are at the highest risk of hepatic and cardio-metabolic complications. Disruption of steroid hormone metabolic pathways has been described in patients with NAFLD. AIM(S): To assess the hypothesis that assessment of the urinary steroid metabolome may provide a novel, non-invasive biomarker strategy to stage NAFLD. METHODS: We analysed the urinary steroid metabolome in 275 subjects (121 with biopsy-proven NAFLD, 48 with alcohol-related cirrhosis and 106 controls), using gas chromatography-mass spectrometry (GC-MS) coupled with machine learning-based Generalised Matrix Learning Vector Quantisation (GMLVQ) analysis. RESULTS: Generalised Matrix Learning Vector Quantisation analysis achieved excellent separation of early (F0-F2) from advanced (F3-F4) fibrosis (AUC receiver operating characteristics [ROC]: 0.92 [0.91-0.94]). Furthermore, there was near perfect separation of controls from patients with advanced fibrotic NAFLD (AUC ROC = 0.99 [0.98-0.99]) and from those with NAFLD cirrhosis (AUC ROC = 1.0 [1.0-1.0]). This approach was also able to distinguish patients with NAFLD cirrhosis from those with alcohol-related cirrhosis (AUC ROC = 0.83 [0.81-0.85]). CONCLUSIONS: Unbiased GMLVQ analysis of the urinary steroid metabolome offers excellent potential as a non-invasive biomarker approach to stage NAFLD fibrosis as well as to screen for NAFLD. A highly sensitive and specific urinary biomarker is likely to have clinical utility both in secondary care and in the broader general population within primary care and could significantly decrease the need for liver biopsy.

Urine Steroid Metabolomics as a Novel Tool for Detection of Recurrent Adrenocortical Carcinoma.

CONTEXT: Urine steroid metabolomics, combining mass spectrometry-based steroid profiling and machine learning, has been described as a novel diagnostic tool for detection of adrenocortical carcinoma (ACC). OBJECTIVE, DESIGN, SETTING: This proof-of-concept study evaluated the performance of urine steroid metabolomics as a tool for postoperative recurrence detection after microscopically complete (R0) resection of ACC. PATIENTS AND METHODS: 135 patients from 14 clinical centers provided postoperative urine samples, which were analyzed by gas chromatography-mass spectrometry. We assessed the utility of these urine steroid profiles in detecting ACC recurrence, either when interpreted by expert clinicians or when analyzed by random forest, a machine learning-based classifier. Radiological recurrence detection served as the reference standard. RESULTS: Imaging detected recurrent disease in 42 of 135 patients; 32 had provided pre- and post-recurrence urine samples. 39 patients remained disease-free for ≥3 years. The urine "steroid fingerprint" at recurrence resembled that observed before R0 resection in the majority of cases. Review of longitudinally collected urine steroid profiles by 3 blinded experts detected recurrence by the time of radiological diagnosis in 50% to 72% of cases, improving to 69% to 92%, if a preoperative urine steroid result was available. Recurrence detection by steroid profiling preceded detection by imaging by more than 2 months in 22% to 39% of patients. Specificities varied considerably, ranging from 61% to 97%. The computational classifier detected ACC recurrence with superior accuracy (sensitivity = specificity = 81%). CONCLUSION: Urine steroid metabolomics is a promising tool for postoperative recurrence detection in ACC; availability of a preoperative urine considerably improves the ability to detect ACC recurrence.

Effect estimate comparison between the prescription sequence symmetry analysis (PSSA) and parallel group study designs: A systematic review.

Prescription sequence symmetry analysis (PSSA), a case-only design introduced in 1996, has been increasingly used to identify unintentional drug effects, and has potential applications as a hypothesis-testing and a hypothesis-generating method, due to its easy application and effective control of time-invariant confounders. The aim of this study is to systematically compare effect estimates from the PSSA to effect estimates from conventional observational parallel group study designs, to assess the validity and constraints of the PSSA study design. We reviewed the MEDLINE, EMBASE, and Web of Science databases until February 2016 to identify studies that compared PSSA to a parallel group design. Data from the eligible articles was extracted and analyzed, including making a Bland-Altman plot and calculating the number of discrepancies between the designs. 63 comparisons (from two studies) were included in the review. There was a significant correlation (p < 0.001) between the effect estimates of the PSSA and the parallel group designs, but the bias indicated by the Bland-Altman plot (0.20) and the percentage of discrepancies (70-80%) showed that this correlation was not accompanied by a considerable similarity of the effect estimates. Overall, the effect estimates of the parallel group designs were higher than those of the PSSA, not necessarily further away from 1, and the parallel group designs also generated more significant signals. However, these results should be approached with caution, as the effect estimates were only retrieved from two separate studies. This review indicates that, even though PSSA has a lot of potential, the effect estimates generated by the PSSA are usually lower than the effect estimates generated by parallel group designs, and PSSA mostly has a lower power than the conventional study designs, but this is based on limited comparisons, and more comparisons are needed to make a proper conclusion.

Statistical Mechanics of On-Line Learning Under Concept Drift.

We introduce a modeling framework for the investigation of on-line machine learning processes in non-stationary environments. We exemplify the approach in terms of two specific model situations: In the first, we consider the learning of a classification scheme from clustered data by means of prototype-based Learning Vector Quantization (LVQ). In the second, we study the training of layered neural networks with sigmoidal activations for the purpose of regression. In both cases, the target, i.e., the classification or regression scheme, is considered to change continuously while the system is trained from a stream of labeled data. We extend and apply methods borrowed from statistical physics which have been used frequently for the exact description of training dynamics in stationary environments. Extensions of the approach allow for the computation of typical learning curves in the presence of concept drift in a variety of model situations. First results are presented and discussed for stochastic drift processes in classification and regression problems. They indicate that LVQ is capable of tracking a classification scheme under drift to a non-trivial extent. Furthermore, we show that concept drift can cause the persistence of sub-optimal plateau states in gradient based training of layered neural networks for regression.

Steroid metabolome analysis reveals prevalent glucocorticoid excess in primary aldosteronism.

BACKGROUND: Adrenal aldosterone excess is the most common cause of secondary hypertension and is associated with increased cardiovascular morbidity. However, adverse metabolic risk in primary aldosteronism extends beyond hypertension, with increased rates of insulin resistance, type 2 diabetes, and osteoporosis, which cannot be easily explained by aldosterone excess. METHODS: We performed mass spectrometry-based analysis of a 24-hour urine steroid metabolome in 174 newly diagnosed patients with primary aldosteronism (103 unilateral adenomas, 71 bilateral adrenal hyperplasias) in comparison to 162 healthy controls, 56 patients with endocrine inactive adrenal adenoma, 104 patients with mild subclinical, and 47 with clinically overt adrenal cortisol excess. We also analyzed the expression of cortisol-producing CYP11B1 and aldosterone-producing CYP11B2 enzymes in adenoma tissue from 57 patients with aldosterone-producing adenoma, employing immunohistochemistry with digital image analysis. RESULTS: Primary aldosteronism patients had significantly increased cortisol and total glucocorticoid metabolite excretion (all P < 0.001), only exceeded by glucocorticoid output in patients with clinically overt adrenal Cushing syndrome. Several surrogate parameters of metabolic risk correlated significantly with glucocorticoid but not mineralocorticoid output. Intratumoral CYP11B1 expression was significantly associated with the corresponding in vivo glucocorticoid excretion. Unilateral adrenalectomy resolved both mineralocorticoid and glucocorticoid excess. Postoperative evidence of adrenal insufficiency was found in 13 (29%) of 45 consecutively tested patients. CONCLUSION: Our data indicate that glucocorticoid cosecretion is frequently found in primary aldosteronism and contributes to associated metabolic risk. Mineralocorticoid receptor antagonist therapy alone may not be sufficient to counteract adverse metabolic risk in medically treated patients with primary aldosteronism. FUNDING: Medical Research Council UK, Wellcome Trust, European Commission.

Prototype-based models in machine learning.

An overview is given of prototype-based models in machine learning. In this framework, observations, i.e., data, are stored in terms of typical representatives. Together with a suitable measure of similarity, the systems can be employed in the context of unsupervised and supervised analysis of potentially high-dimensional, complex datasets. We discuss basic schemes of competitive vector quantization as well as the so-called neural gas approach and Kohonen's topology-preserving self-organizing map. Supervised learning in prototype systems is exemplified in terms of learning vector quantization. Most frequently, the familiar Euclidean distance serves as a dissimilarity measure. We present extensions of the framework to nonstandard measures and give an introduction to the use of adaptive distances in relevance learning.

Modeling spontaneous activity across an excitable epithelium: Support for a coordination scenario of early neural evolution.

Internal coordination models hold that early nervous systems evolved in the first place to coordinate internal activity at a multicellular level, most notably the use of multicellular contractility as an effector for motility. A recent example of such a model, the skin brain thesis, suggests that excitable epithelia using chemical signaling are a potential candidate as a nervous system precursor. We developed a computational model and a measure for whole body coordination to investigate the coordinative properties of such excitable epithelia. Using this measure we show that excitable epithelia can spontaneously exhibit body-scale patterns of activation. Relevant factors determining the extent of patterning are the noise level for exocytosis, relative body dimensions, and body size. In smaller bodies whole-body coordination emerges from cellular excitability and bidirectional excitatory transmission alone. Our results show that basic internal coordination as proposed by the skin brain thesis could have arisen in this potential nervous system precursor, supporting that this configuration may have played a role as a proto-neural system and requires further investigation.

Reach of Supplemental Nutrition Assistance Program-Education (SNAP-Ed) interventions and nutrition and physical activity-related outcomes, California, 2011-2012.

INTRODUCTION: This study combined information on the interventions of the US Department of Agriculture's Supplemental Nutrition Assistance Program-Education with 5,927 interview responses from the California Health Interview Survey to investigate associations between levels of intervention reach in low-income census tracts in California and self-reported physical activity and consumption of fruits and vegetables, fast food, and sugar-sweetened beverages. METHODS: We determined 4 levels of intervention reach (low reach, moderate reach, high reach, and no intervention) across 1,273 program-eligible census tracts from data on actual and eligible number of intervention participants. The locations of California Health Interview Survey respondents were geocoded and linked with program data. Regression analyses included measures for sex, age, race/ethnicity, and education. RESULTS: Adults and children from high-reach census tracts reported eating more fruits and vegetables than adults and children from no-intervention census tracts. Adults from census tracts with low, moderate, or high levels of reach reported eating fast food less often than adults from no-intervention census tracts. Teenagers from low-reach census tracts reported more physical activity than teenagers in no-intervention census tracts. CONCLUSION: The greatest concentration of Supplemental Nutrition Assistance Program-Education interventions was associated with adults and children eating more fruits and vegetables and adults eating fast food less frequently. These findings demonstrate the potential impact of such interventions as implemented by numerous organizations with diverse populations; these interventions can play an important role in addressing the obesity epidemic in the United States. Limitations of this study include the absence of measures of exposure to the intervention at the individual level and low statistical power for the teenager sample.

Inter-species inference of gene set enrichment in lung epithelial cells from proteomic and large transcriptomic datasets.

MOTIVATION: Translating findings in rodent models to human models has been a cornerstone of modern biology and drug development. However, in many cases, a naive 'extrapolation' between the two species has not succeeded. As a result, clinical trials of new drugs sometimes fail even after considerable success in the mouse or rat stage of development. In addition to in vitro studies, inter-species translation requires analytical tools that can predict the enriched gene sets in human cells under various stimuli from corresponding measurements in animals. Such tools can improve our understanding of the underlying biology and optimize the allocation of resources for drug development. RESULTS: We developed an algorithm to predict differential gene set enrichment as part of the sbv IMPROVER (systems biology verification in Industrial Methodology for Process Verification in Research) Species Translation Challenge, which focused on phosphoproteomic and transcriptomic measurements of normal human bronchial epithelial (NHBE) primary cells under various stimuli and corresponding measurements in rat (NRBE) primary cells. We find that gene sets exhibit a higher inter-species correlation compared with individual genes, and are potentially more suited for direct prediction. Furthermore, in contrast to a similar cross-species response in protein phosphorylation states 5 and 25 min after exposure to stimuli, gene set enrichment 6 h after exposure is significantly different in NHBE cells compared with NRBE cells. In spite of this difference, we were able to develop a robust algorithm to predict gene set activation in NHBE with high accuracy using simple analytical methods. AVAILABILITY AND IMPLEMENTATION: Implementation of all algorithms is available as source code (in Matlab) at http://bhanot.biomaps.rutgers.edu/wiki/codes_SC3_Predicting_GeneSets.zip, along with the relevant data used in the analysis. Gene sets, gene expression and protein phosphorylation data are available on request. CONTACT: hormoz@kitp.ucsb.edu.

Predicting protein phosphorylation from gene expression: top methods from the IMPROVER Species Translation Challenge.

MOTIVATION: Using gene expression to infer changes in protein phosphorylation levels induced in cells by various stimuli is an outstanding problem. The intra-species protein phosphorylation challenge organized by the IMPROVER consortium provided the framework to identify the best approaches to address this issue. RESULTS: Rat lung epithelial cells were treated with 52 stimuli, and gene expression and phosphorylation levels were measured. Competing teams used gene expression data from 26 stimuli to develop protein phosphorylation prediction models and were ranked based on prediction performance for the remaining 26 stimuli. Three teams were tied in first place in this challenge achieving a balanced accuracy of about 70%, indicating that gene expression is only moderately predictive of protein phosphorylation. In spite of the similar performance, the approaches used by these three teams, described in detail in this article, were different, with the average number of predictor genes per phosphoprotein used by the teams ranging from 3 to 124. However, a significant overlap of gene signatures between teams was observed for the majority of the proteins considered, while Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were enriched in the union of the predictor genes of the three teams for multiple proteins. AVAILABILITY AND IMPLEMENTATION: Gene expression and protein phosphorylation data are available from ArrayExpress (E-MTAB-2091). Software implementation of the approach of Teams 49 and 75 are available at http://bioinformaticsprb.med.wayne.edu and http://people.cs.clemson.edu/∼luofeng/sbv.rar, respectively. CONTACT: gyanbhanot@gmail.com or luofeng@clemson.edu or atarca@med.wayne.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Inter-species prediction of protein phosphorylation in the sbv IMPROVER species translation challenge.

MOTIVATION: Animal models are widely used in biomedical research for reasons ranging from practical to ethical. An important issue is whether rodent models are predictive of human biology. This has been addressed recently in the framework of a series of challenges designed by the systems biology verification for Industrial Methodology for Process Verification in Research (sbv IMPROVER) initiative. In particular, one of the sub-challenges was devoted to the prediction of protein phosphorylation responses in human bronchial epithelial cells, exposed to a number of different chemical stimuli, given the responses in rat bronchial epithelial cells. Participating teams were asked to make inter-species predictions on the basis of available training examples, comprising transcriptomics and phosphoproteomics data. RESULTS: Here, the two best performing teams present their data-driven approaches and computational methods. In addition, post hoc analyses of the datasets and challenge results were performed by the participants and challenge organizers. The challenge outcome indicates that successful prediction of protein phosphorylation status in human based on rat phosphorylation levels is feasible. However, within the limitations of the computational tools used, the inclusion of gene expression data does not improve the prediction quality. The post hoc analysis of time-specific measurements sheds light on the signaling pathways in both species. AVAILABILITY AND IMPLEMENTATION: A detailed description of the dataset, challenge design and outcome is available at www.sbvimprover.com. The code used by team IGB is provided under http://github.com/uci-igb/improver2013. Implementations of the algorithms applied by team AMG are available at http://bhanot.biomaps.rutgers.edu/wiki/AMG-sc2-code.zip. CONTACT: meikelbiehl@gmail.com.