Substituting clinical features using synthetic medical phrases: Medical text data augmentation techniques.

Biomedical natural language processing (NLP) has an important role in extracting consequential information in medical discharge notes. Detecting meaningful features from unstructured notes is a challenging task in medical document classification. The domain specific phrases and different synonyms within the medical documents make it hard to analyze them. Analyzing clinical notes becomes more challenging for short documents like abstract texts. All of these can result in poor classification performance, especially when there is a shortage of the clinical data in real life. Two new approaches (an ontology-guided approach and a combined ontology-based with dictionary-based approach) are suggested for augmenting medical data to enrich training data. Three different deep learning approaches are used to evaluate the classification performance of the proposed methods. The obtained results show that the proposed methods improved the classification accuracy in clinical notes classification.

Understanding patient complaint characteristics using contextual clinical BERT embeddings.

In clinical conversational applications, extracted entities tend to capture the main subject of a patient's complaint, namely symptoms or diseases. However, they mostly fail to recognize the characterizations of a complaint such as the time, the onset, and the severity. For example, if the input is "I have a headache and it is extreme", state-of-the-art models only recognize the main symptom entity - headache, but ignore the severity factor of extreme, that characterises headache. In this paper, we design a two-fold approach to detect the characterizations of entities like symptoms presented by general users in contexts where they would describe their symptoms to a clinician. We use Word2Vec and BERT models to encode clinical text given by the patients. We transform the output and re-frame the task as a multi-label classification problem. Finally, we combine the processed encodings with the Linear Discriminant Analysis (LDA) algorithm to classify the characterizations of the main entity. Experimental results demonstrate that our method achieves 40-50% improvement in the accuracy over the state-of-the-art models.

Inverse similarity and reliable negative samples for drug side-effect prediction.

BACKGROUND: In silico prediction of potential drug side-effects is of crucial importance for drug development, since wet experimental identification of drug side-effects is expensive and time-consuming. Existing computational methods mainly focus on leveraging validated drug side-effect relations for the prediction. The performance is severely impeded by the lack of reliable negative training data. Thus, a method to select reliable negative samples becomes vital in the performance improvement. METHODS: Most of the existing computational prediction methods are essentially based on the assumption that similar drugs are inclined to share the same side-effects, which has given rise to remarkable performance. It is also rational to assume an inverse proposition that dissimilar drugs are less likely to share the same side-effects. Based on this inverse similarity hypothesis, we proposed a novel method to select highly-reliable negative samples for side-effect prediction. The first step of our method is to build a drug similarity integration framework to measure the similarity between drugs from different perspectives. This step integrates drug chemical structures, drug target proteins, drug substituents, and drug therapeutic information as features into a unified framework. Then, a similarity score between each candidate negative drug and validated positive drugs is calculated using the similarity integration framework. Those candidate negative drugs with lower similarity scores are preferentially selected as negative samples. Finally, both the validated positive drugs and the selected highly-reliable negative samples are used for predictions. RESULTS: The performance of the proposed method was evaluated on simulative side-effect prediction of 917 DrugBank drugs, comparing with four machine-learning algorithms. Extensive experiments show that the drug similarity integration framework has superior capability in capturing drug features, achieving much better performance than those based on a single type of drug property. Besides, the four machine-learning algorithms achieved significant improvement in macro-averaging F1-score (e.g., SVM from 0.655 to 0.898), macro-averaging precision (e.g., RBF from 0.592 to 0.828) and macro-averaging recall (e.g., KNN from 0.651 to 0.772) complimentarily attributed to the highly-reliable negative samples selected by the proposed method. CONCLUSIONS: The results suggest that the inverse similarity hypothesis and the integration of different drug properties are valuable for side-effect prediction. The selection of highly-reliable negative samples can also make significant contributions to the performance improvement.

Quro: Facilitating User Symptom Check Using a Personalised Chatbot-Oriented Dialogue System.

Automated conversational agents built with medical applications in mind, have the potential to reduce healthcare readmissions and improve accessibility to medical knowledge. In this work, we demonstrate the development and evaluation of an automated chatbot for triage and conditions assessment, based on user inputs in natural language. The implemented bot engages patients in conversation about symptoms experienced and provides a personalized pre-synopsis based on their symptoms and profile. Our chatbot system was able to predict user conditions correctly based on two sets of patient test cases with an average precision of 0.82. Our implementation demonstrates that a medical chatbot can help with automatic triage and pre-assessment of patients with simple symptom analysis and a conversational approach without the use of cumbersome form-based data entry.

Septic shock prediction for ICU patients via coupled HMM walking on sequential contrast patterns.

BACKGROUND AND OBJECTIVE: Critical care patient events like sepsis or septic shock in intensive care units (ICUs) are dangerous complications which can cause multiple organ failures and eventual death. Preventive prediction of such events will allow clinicians to stage effective interventions for averting these critical complications. METHODS: It is widely understood that physiological conditions of patients on variables such as blood pressure and heart rate are suggestive to gradual changes over a certain period of time, prior to the occurrence of a septic shock. This work investigates the performance of a novel machine learning approach for the early prediction of septic shock. The approach combines highly informative sequential patterns extracted from multiple physiological variables and captures the interactions among these patterns via coupled hidden Markov models (CHMM). In particular, the patterns are extracted from three non-invasive waveform measurements: the mean arterial pressure levels, the heart rates and respiratory rates of septic shock patients from a large clinical ICU dataset called MIMIC-II. EVALUATION AND RESULTS: For baseline estimations, SVM and HMM models on the continuous time series data for the given patients, using MAP (mean arterial pressure), HR (heart rate), and RR (respiratory rate) are employed. Single channel patterns based HMM (SCP-HMM) and multi-channel patterns based coupled HMM (MCP-HMM) are compared against baseline models using 5-fold cross validation accuracies over multiple rounds. Particularly, the results of MCP-HMM are statistically significant having a p-value of 0.0014, in comparison to baseline models. Our experiments demonstrate a strong competitive accuracy in the prediction of septic shock, especially when the interactions between the multiple variables are coupled by the learning model. CONCLUSIONS: It can be concluded that the novelty of the approach, stems from the integration of sequence-based physiological pattern markers with the sequential CHMM model to learn dynamic physiological behavior, as well as from the coupling of such patterns to build powerful risk stratification models for septic shock patients.

Hypotension Risk Prediction via Sequential Contrast Patterns of ICU Blood Pressure.

Acute hypotension is a significant risk factor for in-hospital mortality at intensive care units. Prolonged hypotension can cause tissue hypoperfusion, leading to cellular dysfunction and severe injuries to multiple organs. Prompt medical interventions are thus extremely important for dealing with acute hypotensive episodes (AHE). Population level prognostic scoring systems for risk stratification of patients are suboptimal in such scenarios. However, the design of an efficient risk prediction system can significantly help in the identification of critical care patients, who are at risk of developing an AHE within a future time span. Toward this objective, a pattern mining algorithm is employed to extract informative sequential contrast patterns from hemodynamic data, for the prediction of hypotensive episodes. The hypotensive and normotensive patient groups are extracted from the MIMIC-II critical care research database, following an appropriate clinical inclusion criteria. The proposed method consists of a data preprocessing step to convert the blood pressure time series into symbolic sequences, using a symbolic aggregate approximation algorithm. Then, distinguishing subsequences are identified using the sequential contrast mining algorithm. These subsequences are used to predict the occurrence of an AHE in a future time window separated by a user-defined gap interval. Results indicate that the method performs well in terms of the prediction performance as well as in the generation of sequential patterns of clinical significance. Hence, the novelty of sequential patterns is in their usefulness as potential physiological biomarkers for building optimal patient risk stratification systems and for further clinical investigation of interesting patterns in critical care patients.

Predicting short-term ICU outcomes using a sequential contrast motif based classification framework.

Critical ICU events like acute hypotension and septic shock are dangerous complications, leading to multiple organ failures and eventual death. Previously, pattern mining algorithms have been employed for extracting interesting rules in various clinical domains. However, the extracted rules are directly investigated by clinicians for diagnosing a disease. Towards this purpose, there is a need to develop advanced prediction models which integrate dynamic patterns to learn a patient's physiological condition. In this study, a sequential contrast patterns-based classification framework is presented for detecting critical patient events, like hypotension and septic shock. Initially, a set of sequential patterns are obtained by using a contrast mining algorithm. Later, these patterns undergo post-processing, for conversion to two novel representations-(1) frequency-based feature space and (2) ordered sequences of patterns, which conserve positional information of a pattern in a time series sequence. Each of these representations are automatically used for developing classification models using SVM and HMM methods. Our results on hypotension and septic shock datasets from a large scale ICU database demonstrate better predictive capabilities, when sequential patterns are used as features.

Using sequential patterns as features for classification models to make accurate predictions on ICU events.

Pattern mining algorithms have previously been utilized to extract informative rules in various clinical contexts. However, the number of generated patterns are numerous. In most cases, the extracted rules are directly investigated by clinicians for understanding disease diagnoses. The elicitation of important patterns for clinical investigation places a significant demand for precision and interpretability. Hence, it is essential to obtain a set of informative interpretable patterns for building advanced learning models about a patient's physiological condition, specially in critical care units. In this study, a two stage sequential contrast patterns based classification framework is presented, which is used to detect critical patient events like hypotension. In the first stage, we obtain a set of sequential patterns by using a contrast mining algorithm. These sequential patterns undergo post-processing, for conversion to binary valued and frequency based features for developing a classification model, in the second stage. Our results on eight critical care datasets demonstrate better predictive capabilities, when sequential patterns are used as features.

Risk prediction for acute hypotensive patients by using gap constrained sequential contrast patterns.

The development of acute hypotension in a critical care patient causes decreased tissue perfusion, which can lead to multiple organ failures. Existing systems that employ population level prognostic scores to stratify the risks of critical care patients based on hypotensive episodes are suboptimal in predicting impending critical conditions, or in directing an effective goal-oriented therapy. In this work, we propose a sequential pattern mining approach which target novel and informative sequential contrast patterns for the detection of hypotension episodes. Our results demonstrate the competitiveness of the approach, in terms of both prediction performance as well as knowledge interpretability. Hence, sequential patterns-based computational biomarkers can help comprehend unusual episodes in critical care patients ahead of time for early warning systems. Sequential patterns can thus aid in the development of a powerful critical care knowledge discovery framework for facilitating novel patient treatment plans.

Hybrid biogeography based simultaneous feature selection and MHC class I peptide binding prediction using support vector machines and random forests.

Accurate detection of peptides binding to specific Major Histocompatibility Complex Class I (MHC-I) molecules is extremely important for understanding the underlying process of the immune system, as well as for effective vaccine design and developing immunotherapies. Development of learning algorithms and their application for binding predictions have thus speeded up the state-of-the-art in immunological research, in a cost-effective manner. In this work, we propose the application of a hybrid filter-wrapper algorithm employing concepts from the recently developed biogeography based optimization algorithm, in conjunction with SVM and Random Forests for identification of MHC-I binding peptides. In the process, we demonstrate the effectiveness of this evolutionary technique, coupled with weighted heuristics, for the construction of improved prediction models. The experiments have been carried out for the CoEPrA competition datasets (accessible online at: http://www.coepra.org) and the results show a marked improvement over the winner results in some situations and comparably good with regard to others .We thus hope to initiate further research on the application of this new bio-inspired methodology for immunological research.