Usability of Telehealth Systems for Noncommunicable Diseases in Primary Care From the COVID-19 Pandemic Onward: Systematic Review.

BACKGROUND: During the COVID-19 pandemic, telehealth was expanded without the opportunity to extensively evaluate the adopted technology's usability. OBJECTIVE: We aimed to synthesize evidence on health professionals' perceptions regarding the usability of telehealth systems in the primary care of individuals with noncommunicable diseases (NCDs; hypertension and diabetes) from the COVID-19 pandemic onward. METHODS: A systematic review was performed of clinical trials, prospective cohort studies, retrospective observational studies, and studies that used qualitative data collection and analysis methods published in English, Spanish, and Portuguese from March 2020 onward. The databases queried were MEDLINE, Embase, BIREME, IEEE Xplore, BVS, Google Scholar, and grey literature. Studies involving health professionals who used telehealth systems in primary care and managed patients with NCDs from the COVID-19 pandemic onward were considered eligible. Titles, abstracts, and full texts were reviewed. Data were extracted to provide a narrative qualitative evidence synthesis of the included articles. The risk of bias and methodological quality of the included studies were analyzed. The primary outcome was the usability of telehealth systems, while the secondary outcomes were satisfaction and the contexts in which the telehealth system was used. RESULTS: We included 11 of 417 retrieved studies, which had data from 248 health care professionals. These health care professionals were mostly doctors and nurses with prior experience in telehealth in high- and middle-income countries. Overall, 9 studies (82%) were qualitative studies and 2 (18%) were quasiexperimental or multisite trial studies. Moreover, 7 studies (64%) addressed diabetes, 1 (9%) addressed diabetes and hypertension, and 3 (27%) addressed chronic diseases. Most studies used a survey to assess usability. With a moderate confidence level, we concluded that health professionals considered the usability of telehealth systems to be good and felt comfortable and satisfied. Patients felt satisfied using telehealth. The most important predictor for using digital health technologies was ease of use. The main barriers were technological challenges, connectivity issues, low computer literacy, inability to perform complete physical examination, and lack of training. Although the usability of telehealth systems was considered good, there is a need for research that investigates factors that may influence the perceptions of telehealth usability, such as differences between private and public services; differences in the level of experience of professionals, including professional experience and experience with digital tools; and differences in gender, age groups, occupations, and settings. CONCLUSIONS: The COVID-19 pandemic has generated incredible demand for virtual care. Professionals' favorable perceptions of the usability of telehealth indicate that it can facilitate access to quality care. Although there are still challenges to telehealth, more than infrastructure challenges, the most reported challenges were related to empowering people for digital health. TRIAL REGISTRATION: PROSPERO International Prospective Register of Systematic Reviews CRD42021296887; https://www.crd.york.ac.uk/PROSPERO/display_record.php?RecordID=296887. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID): RR2-10.21801/ppcrj.2022.82.6.

Selective visuoconstructional impairment following mild COVID-19 with inflammatory and neuroimaging correlation findings.

People recovered from COVID-19 may still present complications including respiratory and neurological sequelae. In other viral infections, cognitive impairment occurs due to brain damage or dysfunction caused by vascular lesions and inflammatory processes. Persistent cognitive impairment compromises daily activities and psychosocial adaptation. Some level of neurological and psychiatric consequences were expected and described in severe cases of COVID-19. However, it is debatable whether neuropsychiatric complications are related to COVID-19 or to unfoldings from a severe infection. Nevertheless, the majority of cases recorded worldwide were mild to moderate self-limited illness in non-hospitalized people. Thus, it is important to understand what are the implications of mild COVID-19, which is the largest and understudied pool of COVID-19 cases. We aimed to investigate adults at least four months after recovering from mild COVID-19, which were assessed by neuropsychological, ocular and neurological tests, immune markers assay, and by structural MRI and 18FDG-PET neuroimaging to shed light on putative brain changes and clinical correlations. In approximately one-quarter of mild-COVID-19 individuals, we detected a specific visuoconstructive deficit, which was associated with changes in molecular and structural brain imaging, and correlated with upregulation of peripheral immune markers. Our findings provide evidence of neuroinflammatory burden causing cognitive deficit, in an already large and growing fraction of the world population. While living with a multitude of mild COVID-19 cases, action is required for a more comprehensive assessment and follow-up of the cognitive impairment, allowing to better understand symptom persistence and the necessity of rehabilitation of the affected individuals.

Political polarization on Twitter during the COVID-19 pandemic: a case study in Brazil.

The debate over the COVID-19 pandemic is constantly trending at online conversations since its beginning in 2019. The discussions in many social media platforms is related not only to health aspects of the disease, but also public policies and non-pharmacological measures to mitigate the spreading of the virus and propose alternative treatments. Divergent opinions regarding these measures are leading to heated discussions and polarization. Particularly in highly politically polarized countries, users tend to be divided in those in-favor or against government policies. In this work we present a computational method to analyze Twitter data and: (i) identify users with a high probability of being bots using only COVID-19 related messages; (ii) quantify the political polarization of the Brazilian general public in the context of the COVID-19 pandemic; (iii) analyze how bots tweet and affect political polarization. We collected over 100 million tweets from 26 April 2020 to 3 January 2021, and observed in general a highly polarized population (with polarization index varying from 0.57 to 0.86), which focuses on very different topics of discussions over the most polarized weeks-but all related to government and health-related events.

Semantic Academic Profiler (SAP): a framework for researcher assessment based on semantic topic modeling.

Recent efforts have focused on identifying multidisciplinary teams and detecting co-Authorship Networks based on exploring topic modeling to identify researchers' expertise. Though promising, none of these efforts perform a real-life evaluation of the quality of the built topics. This paper proposes a Semantic Academic Profiler (SAP) framework that allows summarizing articles written by researchers to automatically build research profiles and perform online evaluations regarding these built profiles. SAP exploits and extends state-of-the-art Topic Modeling strategies based on Cluwords considering n-grams and introduces a new visual interface able to highlight the main topics related to articles, researchers and institutions. To evaluate SAP's capability of summarizing the profile of such entities as well as its usefulness for supporting online assessments of the topics' quality, we perform and contrast two types of evaluation, considering an extensive repository of Brazilian curricula vitae: (1) an offline evaluation, in which we exploit a traditional metric (NPMI) to measure the quality of several data representations strategies including (i) TFIDF, (ii) TFIDF with Bi-grams, (iii) Cluwords, and (iv) CluWords with Bi-grams; and (2) an online evaluation through an A/B test where researchers evaluate their own built profiles. We also perform an online assessment of SAP user interface through a usability test following the SUS methodology. Our experiments indicate that the CluWords with Bi-grams is the best solution and the SAP interface is very useful. We also observed essential differences in the online and offline assessments, indicating that using both together is very important for a comprehensive quality evaluation. Such type of study is scarce in the literature and our findings open space for new lines of investigation in the Topic Modeling area.

Social Determinants in Self-Protective Behavior Related to COVID-19: Association Rule-Mining Study.

BACKGROUND: Human behavior is crucial in health outcomes. Particularly, individual behavior is a determinant of the success of measures to overcome critical conditions, such as a pandemic. In addition to intrinsic public health challenges associated with COVID-19, in many countries, some individuals decided not to get vaccinated, streets were crowded, parties were happening, and businesses struggling to survive were partially open, despite lockdown or stay-at-home instructions. These behaviors contrast with the instructions for potential benefits associated with social distancing, use of masks, and vaccination to manage collective and individual risks. OBJECTIVE: Considering that human behavior is a result of individuals' social and economic conditions, we investigated the social and working characteristics associated with reports of appropriate protective behavior in Brazil. METHODS: We analyzed data from a large web survey of individuals reporting their behavior during the pandemic. We selected 3 common self-care measures: use of protective masks, distancing by at least 1 m when out of the house, and handwashing or use of alcohol, combined with assessment of the social context of respondents. We measured the frequency of the use of these self-protective measures. Using a frequent pattern-mining perspective, we generated association rules from a set of answers to questions that co-occur with at least a given frequency, identifying the pattern of characteristics of the groups divided according to protective behavior reports. RESULTS: The rationale was to identify a pool of working and social characteristics that might have better adhesion to behaviors and self-care measures, showing these are more socially determined than previously thought. We identified common patterns of socioeconomic and working determinants of compliance with protective self-care measures. Data mining showed that social determinants might be important to shape behavior in different stages of the pandemic. CONCLUSIONS: Identification of context determinants might be helpful to identify unexpected facilitators and constraints to fully follow public policies. The context of diseases contributes to psychological and physical health outcomes, and context understanding might change the approach to a disease. Hidden social determinants might change protective behavior, and social determinants of protective behavior related to COVID-19 are related to work and economic conditions. TRIAL REGISTRATION: Not applicable.

Counterfactual inference with latent variable and its application in mental health care.

This paper deals with the problem of modeling counterfactual reasoning in scenarios where, apart from the observed endogenous variables, we have a latent variable that affects the outcomes and, consequently, the results of counterfactuals queries. This is a common setup in healthcare problems, including mental health. We propose a new framework where the aforementioned problem is modeled as a multivariate regression and the counterfactual model accounts for both observed and a latent variable, where the latter represents what we call the patient individuality factor ( φ ). In mental health, focusing on individuals is paramount, as past experiences can change how people see or deal with situations, but individuality cannot be directly measured. To the best of our knowledge, this is the first counterfactual approach that considers both observational and latent variables to provide deterministic answers to counterfactual queries, such as: what if I change the social support of a patient, to what extent can I change his/her anxiety? The framework combines concepts from deep representation learning and causal inference to infer the value of φ and capture both non-linear and multiplicative effects of causal variables. Experiments are performed with both synthetic and real-world datasets, where we predict how changes in people's actions may lead to different outcomes in terms of symptoms of mental illness and quality of life. Results show the model learns the individually factor with errors lower than 0.05 and answers counterfactual queries that are supported by the medical literature. The model has the potential to recommend small changes in people's lives that may completely change their relationship with mental illness.

Deep neural network-estimated electrocardiographic age as a mortality predictor.

The electrocardiogram (ECG) is the most commonly used exam for the evaluation of cardiovascular diseases. Here we propose that the age predicted by artificial intelligence (AI) from the raw ECG (ECG-age) can be a measure of cardiovascular health. A deep neural network is trained to predict a patient's age from the 12-lead ECG in the CODE study cohort (n = 1,558,415 patients). On a 15% hold-out split, patients with ECG-age more than 8 years greater than the chronological age have a higher mortality rate (hazard ratio (HR) 1.79, p < 0.001), whereas those with ECG-age more than 8 years smaller, have a lower mortality rate (HR 0.78, p < 0.001). Similar results are obtained in the external cohorts ELSA-Brasil (n = 14,236) and SaMi-Trop (n = 1,631). Moreover, even for apparent normal ECGs, the predicted ECG-age gap from the chronological age remains a statistically significant risk predictor. These results show that the AI-enabled analysis of the ECG can add prognostic information.

Towards automatic diagnosis of rheumatic heart disease on echocardiographic exams through video-based deep learning.

OBJECTIVE: Rheumatic heart disease (RHD) affects an estimated 39 million people worldwide and is the most common acquired heart disease in children and young adults. Echocardiograms are the gold standard for diagnosis of RHD, but there is a shortage of skilled experts to allow widespread screenings for early detection and prevention of the disease progress. We propose an automated RHD diagnosis system that can help bridge this gap. MATERIALS AND METHODS: Experiments were conducted on a dataset with 11 646 echocardiography videos from 912 exams, obtained during screenings in underdeveloped areas of Brazil and Uganda. We address the challenges of RHD identification with a 3D convolutional neural network (C3D), comparing its performance with a 2D convolutional neural network (VGG16) that is commonly used in the echocardiogram literature. We also propose a supervised aggregation technique to combine video predictions into a single exam diagnosis. RESULTS: The proposed approach obtained an accuracy of 72.77% for exam diagnosis. The results for the C3D were significantly better than the ones obtained by the VGG16 network for videos, showing the importance of considering the temporal information during the diagnostic. The proposed aggregation model showed significantly better accuracy than the majority voting strategy and also appears to be capable of capturing underlying biases in the neural network output distribution, balancing them for a more correct diagnosis. CONCLUSION: Automatic diagnosis of echo-detected RHD is feasible and, with further research, has the potential to reduce the workload of experts, enabling the implementation of more widespread screening programs worldwide.

Pilot study GLIM criteria for categorization of a malnutrition diagnosis of patients undergoing elective gastrointestinal operations: A pilot study of applicability and validation.

OBJECTIVES: The Global Leadership Initiative on Malnutrition (GLIM) was proposed to provide a common malnutrition diagnostic framework. The aims of this study were to evaluate the applicability and validity of the GLIM and use machine-learning techniques to help provide the best malnutrition-related variables/combinations to predict complications in patients undergoing gastrointestinal (GI) surgeries. METHOD: This was a prospective cohort study enrolling surgical patients with GI diseases. Malnutrition prevalence was classified by the GLIM, subjective global assessment (SGA), and various anthropometric parameters. The various combination of the phenotypic criteria generated 10 different models. Sensibility (SE) and specificity (SP) were calculated using SGA as the reference criterion. Machine-learning approaches were used to predict complications. P < 0.05 was set as statistically significant. RESULTS: We evaluated 206 patients. Half of the patients were malnourished according SGA, and 16.5% had postoperative complications. The prevalence of malnutrition using GLIM varied from 10.7% to 41.3% among the whole population, 11.7% and 43.6% in the elderly, from 0 to 24% in overweight non-obese and from 0 to 19.6% in obese patients. SE and SP values varied between 61.2% and 100% and 55.3% and 98.1%, respectively, for the general population. Machine-learning models indicated that midarm circumference, one of the GLIM models, and midarm muscle area were the most relevant criteria to predict complications. CONCLUSIONS: The various GLIM combinations provided different rates of malnutrition according to the population. Machine-learning techniques supported the use of common single variables and one GLIM model to predict postoperative complications.

Author Correction: Automatic diagnosis of the 12-lead ECG using a deep neural network.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Automatic diagnosis of the 12-lead ECG using a deep neural network.

The role of automatic electrocardiogram (ECG) analysis in clinical practice is limited by the accuracy of existing models. Deep Neural Networks (DNNs) are models composed of stacked transformations that learn tasks by examples. This technology has recently achieved striking success in a variety of task and there are great expectations on how it might improve clinical practice. Here we present a DNN model trained in a dataset with more than 2 million labeled exams analyzed by the Telehealth Network of Minas Gerais and collected under the scope of the CODE (Clinical Outcomes in Digital Electrocardiology) study. The DNN outperform cardiology resident medical doctors in recognizing 6 types of abnormalities in 12-lead ECG recordings, with F1 scores above 80% and specificity over 99%. These results indicate ECG analysis based on DNNs, previously studied in a single-lead setup, generalizes well to 12-lead exams, taking the technology closer to the standard clinical practice.

Where did I get dengue? Detecting spatial clusters of infection risk with social network data.

Typical spatial disease surveillance systems associate a single address to each disease case reported, usually the residence address. Social network data offers a unique opportunity to obtain information on the spatial movements of individuals as well as their disease status as cases or controls. This provides information to identify visit locations with high risk of infection, even in regions where no one lives such as parks and entertainment zones. We develop two probability models to characterize the high-risk regions. We use a large Twitter dataset from Brazilian users to search for spatial clusters through analysis of the tweets' locations and textual content. We apply our models to both real-world and simulated data, demonstrating the advantage of our models as compared to the usual spatial scan statistic for this type of data.

Performance evaluation of GPU parallelization, space-time adaptive algorithms, and their combination for simulating cardiac electrophysiology.

The use of computer models as a tool for the study and understanding of the complex phenomena of cardiac electrophysiology has attained increased importance nowadays. At the same time, the increased complexity of the biophysical processes translates into complex computational and mathematical models. To speed up cardiac simulations and to allow more precise and realistic uses, 2 different techniques have been traditionally exploited: parallel computing and sophisticated numerical methods. In this work, we combine a modern parallel computing technique based on multicore and graphics processing units (GPUs) and a sophisticated numerical method based on a new space-time adaptive algorithm. We evaluate each technique alone and in different combinations: multicore and GPU, multicore and GPU and space adaptivity, multicore and GPU and space adaptivity and time adaptivity. All the techniques and combinations were evaluated under different scenarios: 3D simulations on slabs, 3D simulations on a ventricular mouse mesh, ie, complex geometry, sinus-rhythm, and arrhythmic conditions. Our results suggest that multicore and GPU accelerate the simulations by an approximate factor of 33×, whereas the speedups attained by the space-time adaptive algorithms were approximately 48. Nevertheless, by combining all the techniques, we obtained speedups that ranged between 165 and 498. The tested methods were able to reduce the execution time of a simulation by more than 498× for a complex cellular model in a slab geometry and by 165× in a realistic heart geometry simulating spiral waves. The proposed methods will allow faster and more realistic simulations in a feasible time with no significant loss of accuracy.

Dengue prediction by the web: Tweets are a useful tool for estimating and forecasting Dengue at country and city level.

BACKGROUND: Infectious diseases are a leading threat to public health. Accurate and timely monitoring of disease risk and progress can reduce their impact. Mentioning a disease in social networks is correlated with physician visits by patients, and can be used to estimate disease activity. Dengue is the fastest growing mosquito-borne viral disease, with an estimated annual incidence of 390 million infections, of which 96 million manifest clinically. Dengue burden is likely to increase in the future owing to trends toward increased urbanization, scarce water supplies and, possibly, environmental change. The epidemiological dynamic of Dengue is complex and difficult to predict, partly due to costly and slow surveillance systems. METHODOLOGY / PRINCIPAL FINDINGS: In this study, we aimed to quantitatively assess the usefulness of data acquired by Twitter for the early detection and monitoring of Dengue epidemics, both at country and city level at a weekly basis. Here, we evaluated and demonstrated the potential of tweets modeling for Dengue estimation and forecast, in comparison with other available web-based data, Google Trends and Wikipedia access logs. Also, we studied the factors that might influence the goodness-of-fit of the model. We built a simple model based on tweets that was able to 'nowcast', i.e. estimate disease numbers in the same week, but also 'forecast' disease in future weeks. At the country level, tweets are strongly associated with Dengue cases, and can estimate present and future Dengue cases until 8 weeks in advance. At city level, tweets are also useful for estimating Dengue activity. Our model can be applied successfully to small and less developed cities, suggesting a robust construction, even though it may be influenced by the incidence of the disease, the activity of Twitter locally, and social factors, including human development index and internet access. CONCLUSIONS: Tweets association with Dengue cases is valuable to assist traditional Dengue surveillance at real-time and low-cost. Tweets are able to successfully nowcast, i.e. estimate Dengue in the present week, but also forecast, i.e. predict Dengue at until 8 weeks in the future, both at country and city level with high estimation capacity.

Factors Associated With Weight Change in Online Weight Management Communities: A Case Study in the LoseIt Reddit Community.

BACKGROUND: Recent research has shown that of the 72% of American Internet users who have looked for health information online, 22% have searched for help to lose or control weight. This demand for information has given rise to many online weight management communities, where users support one another throughout their weight loss process. Whether and how user engagement in online communities relates to weight change is not totally understood. OBJECTIVE: We investigated the activity behavior and analyze the semantic content of the messages of active users in LoseIt (r/loseit), a weight management community of the online social network Reddit. We then explored whether these features are associated with weight loss in this online social network. METHODS: A data collection tool was used to collect English posts, comments, and other public metadata of active users (ie, users with at least one post or comment) on LoseIt from August 2010 to November 2014. Analyses of frequency and intensity of user interaction in the community were performed together with a semantic analysis of the messages, done by a latent Dirichlet allocation method. The association between weight loss and online user activity patterns, the semantics of the messages, and real-world variables was found by a linear regression model using 30-day weight change as the dependent variable. RESULTS: We collected posts and comments of 107,886 unique users. Among these, 101,003 (93.62%) wrote at least one comment and 38,981 (36.13%) wrote at least one post. Median percentage of days online was 3.81 (IQR 9.51). The 10 most-discussed semantic topics on posts were related to healthy food, clothing, calorie counting, workouts, looks, habits, support, and unhealthy food. In the subset of 754 users who had gender, age, and 30-day weight change data available, women were predominant and 92.9% (701/754) lost weight. Female gender, body mass index (BMI) at baseline, high levels of online activity, the number of upvotes received per post, and topics discussed within the community were independently associated with weight change. CONCLUSIONS: Our findings suggest that among active users of a weight management community, self-declaration of higher BMI levels (which may represent greater dissatisfaction with excess weight), high online activity, and engagement in discussions that might provide social support are associated with greater weight loss. These findings have the potential to aid health professionals to assist patients in online interventions by focusing efforts on increasing engagement and/or starting discussions on topics of higher impact on weight change.

Isofunctional Protein Subfamily Detection Using Data Integration and Spectral Clustering.

As increasingly more genomes are sequenced, the vast majority of proteins may only be annotated computationally, given experimental investigation is extremely costly. This highlights the need for computational methods to determine protein functions quickly and reliably. We believe dividing a protein family into subtypes which share specific functions uncommon to the whole family reduces the function annotation problem's complexity. Hence, this work's purpose is to detect isofunctional subfamilies inside a family of unknown function, while identifying differentiating residues. Similarity between protein pairs according to various properties is interpreted as functional similarity evidence. Data are integrated using genetic programming and provided to a spectral clustering algorithm, which creates clusters of similar proteins. The proposed framework was applied to well-known protein families and to a family of unknown function, then compared to ASMC. Results showed our fully automated technique obtained better clusters than ASMC for two families, besides equivalent results for other two, including one whose clusters were manually defined. Clusters produced by our framework showed great correspondence with the known subfamilies, besides being more contrasting than those produced by ASMC. Additionally, for the families whose specificity determining positions are known, such residues were among those our technique considered most important to differentiate a given group. When run with the crotonase and enolase SFLD superfamilies, the results showed great agreement with this gold-standard. Best results consistently involved multiple data types, thus confirming our hypothesis that similarities according to different knowledge domains may be used as functional similarity evidence. Our main contributions are the proposed strategy for selecting and integrating data types, along with the ability to work with noisy and incomplete data; domain knowledge usage for detecting subfamilies in a family with different specificities, thus reducing the complexity of the experimental function characterization problem; and the identification of residues responsible for specificity.

PDBest: a user-friendly platform for manipulating and enhancing protein structures.

UNLABELLED: PDBest (PDB Enhanced Structures Toolkit) is a user-friendly, freely available platform for acquiring, manipulating and normalizing protein structures in a high-throughput and seamless fashion. With an intuitive graphical interface it allows users with no programming background to download and manipulate their files. The platform also exports protocols, enabling users to easily share PDB searching and filtering criteria, enhancing analysis reproducibility. AVAILABILITY AND IMPLEMENTATION: PDBest installation packages are freely available for several platforms at http://www.pdbest.dcc.ufmg.br CONTACT: wellisson@dcc.ufmg.br, dpires@dcc.ufmg.br, raquelcm@dcc.ufmg.br SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

VERMONT: Visualizing mutations and their effects on protein physicochemical and topological property conservation.

In this paper, we propose an interactive visualization called VERMONT which tackles the problem of visualizing mutations and infers their possible effects on the conservation of physicochemical and topological properties in protein families. More specifically, we visualize a set of structure-based sequence alignments and integrate several structural parameters that should aid biologists in gaining insight into possible consequences of mutations. VERMONT allowed us to identify patterns of position-specific properties as well as exceptions that may help predict whether specific mutations could damage protein function.

ENZYMAP: exploiting protein annotation for modeling and predicting EC number changes in UniProt/Swiss-Prot.

The volume and diversity of biological data are increasing at very high rates. Vast amounts of protein sequences and structures, protein and genetic interactions and phenotype studies have been produced. The majority of data generated by high-throughput devices is automatically annotated because manually annotating them is not possible. Thus, efficient and precise automatic annotation methods are required to ensure the quality and reliability of both the biological data and associated annotations. We proposed ENZYMatic Annotation Predictor (ENZYMAP), a technique to characterize and predict EC number changes based on annotations from UniProt/Swiss-Prot using a supervised learning approach. We evaluated ENZYMAP experimentally, using test data sets from both UniProt/Swiss-Prot and UniProt/TrEMBL, and showed that predicting EC changes using selected types of annotation is possible. Finally, we compared ENZYMAP and DETECT with respect to their predictions and checked both against the UniProt/Swiss-Prot annotations. ENZYMAP was shown to be more accurate than DETECT, coming closer to the actual changes in UniProt/Swiss-Prot. Our proposal is intended to be an automatic complementary method (that can be used together with other techniques like the ones based on protein sequence and structure) that helps to improve the quality and reliability of enzyme annotations over time, suggesting possible corrections, anticipating annotation changes and propagating the implicit knowledge for the whole dataset.

aCSM: noise-free graph-based signatures to large-scale receptor-based ligand prediction.

MOTIVATION: Receptor-ligand interactions are a central phenomenon in most biological systems. They are characterized by molecular recognition, a complex process mainly driven by physicochemical and structural properties of both receptor and ligand. Understanding and predicting these interactions are major steps towards protein ligand prediction, target identification, lead discovery and drug design. RESULTS: We propose a novel graph-based-binding pocket signature called aCSM, which proved to be efficient and effective in handling large-scale protein ligand prediction tasks. We compare our results with those described in the literature and demonstrate that our algorithm overcomes the competitor's techniques. Finally, we predict novel ligands for proteins from Trypanosoma cruzi, the parasite responsible for Chagas disease, and validate them in silico via a docking protocol, showing the applicability of the method in suggesting ligands for pockets in a real-world scenario. AVAILABILITY AND IMPLEMENTATION: Datasets and the source code are available at http://www.dcc.ufmg.br/∼dpires/acsm. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.