Comparative experiments on learning information extractors for proteins and their interactions

OBJECTIVE

Automatically extracting information from biomedical text holds the promise of easily consolidating large amounts of biological knowledge in computer-accessible form. This strategy is particularly attractive for extracting data relevant to genes of the human genome from the 11 million abstracts in Medline. However, extraction efforts have been frustrated by the lack of conventions for describing human genes and proteins. We have developed and evaluated a variety of learned information extraction systems for identifying human protein names in Medline abstracts and subsequently extracting information on interactions between the proteins.

METHODS AND MATERIAL

We used a variety of machine learning methods to automatically develop information extraction systems for extracting information on gene/protein name, function and interactions from Medline abstracts. We present cross-validated results on identifying human proteins and their interactions by training and testing on a set of approximately 1000 manually-annotated Medline abstracts that discuss human genes/proteins.

RESULTS

We demonstrate that machine learning approaches using support vector machines and maximum entropy are able to identify human proteins with higher accuracy than several previous approaches. We also demonstrate that various rule induction methods are able to identify protein interactions with higher precision than manually-developed rules.

CONCLUSION

Our results show that it is promising to use machine learning to automatically build systems for extracting information from biomedical text. The results also give a broad picture of the relative strengths of a wide variety of methods when tested on a reasonably large human-annotated corpus.

Mining knowledge from text using information extraction

An important approach to text mining involves the use of natural-language information extraction. Information extraction (IE) distills structured data or knowledge from unstructured text by identifying references to named entities as well as stated relationships between such entities. IE systems can be used to directly extricate abstract knowledge from a text corpus, or to extract concrete data from a set of documents which can then be further analyzed with traditional data-mining techniques to discover more general patterns. We discuss methods and implemented systems for both of these approaches and summarize results on mining real text corpora of biomedical abstracts, job announcements, and product descriptions. We also discuss challenges that arise when employing current information extraction technology to discover knowledge in text.

Using LSTMs to learn physiological models of blood glucose behavior

For people with type 1 diabetes, good blood glucose control is essential to keeping serious disease complications at bay. This entails carefully monitoring blood glucose levels and taking corrective steps whenever they are too high or too low. If blood glucose levels could be accurately predicted, patients could take proactive steps to prevent blood glucose excursions from occurring. However, accurate predictions require complex physiological models of blood glucose behavior. Factors such as insulin boluses, carbohydrate intake, and exercise influence blood glucose in ways that are difficult to capture through manually engineered equations. In this paper, we describe a recursive neural network (RNN) approach that uses long short-term memory (LSTM) units to learn a physiological model of blood glucose. When trained on raw data from real patients, the LSTM networks (LSTMs) obtain results that are competitive with a previous state-of-the-art model based on manually engineered physiological equations. The RNN approach can incorporate arbitrary physiological parameters without the need for sophisticated manual engineering, thus holding the promise of further improvements in prediction accuracy.

LSTMs and Neural Attention Models for Blood Glucose Prediction: Comparative Experiments on Real and Synthetic Data

We have shown in previous work that LSTM networks are effective at predicting blood glucose levels in patients with type I diabetes, outperforming human experts and an SVR model trained with features computed by manually engineered physiological models. In this paper we present the results of a much larger set of experiments on real and synthetic datasets in what-if, agnostic, and inertial scenarios. Experiments on a more recent real-patient dataset, which we are releasing to the research community, demonstrate that LSTMs are robust to noise and can easily incorporate additional features, such as skin temperature, heart rate and skin conductance, without any change in the architecture. A neural attention module that we designed specifically for time series prediction improves prediction performance on synthetic data; however, the improvements do not transfer to real data. Conversely, using time of day as an additional input feature consistently improves the LSTM performance on real data but not on synthetic data. These and other differences show that behavior on synthetic data cannot be assumed to always transfer to real data, highlighting the importance of evaluating physiological models on data from real patients.

Emerging Applications for Intelligent Diabetes Management

Diabetes management is a difficult task for patients, who must monitor and control their blood glucose levels in order to avoid serious diabetic complications. It is a difficult task for physicians, who must manually interpret large volumes of blood glucose data to tailor therapy to the needs of each patient. This paper describes three emerging applications that employ AI to ease this task: (1) case-based decision support for diabetes management; (2) machine learning classification of blood glucose plots; and (3) support vector regression for blood glucose prediction. The first application provides decision support by detecting blood glucose control problems and recommending therapeutic adjustments to correct them. The second provides an automated screen for excessive glycemic variability. The third aims to build a hypoglycemia predictor that could alert patients to dangerously low blood glucose levels in time to take preventive action. All are products of the 4 Diabetes Support SystemTM project, which uses AI to promote the health and wellbeing of people with type 1 diabetes. These emerging applications could potentially benefit 20 million patients who are at risk for devastating complications, thereby improving quality of life and reducing health care cost expenditures.

Set cover-based methods for motif selection

Motivation

De novo motif discovery algorithms find statistically over-represented sequence motifs that may function as transcription factor binding sites. Current methods often report large numbers of motifs, making it difficult to perform further analyses and experimental validation. The motif selection problem seeks to identify a minimal set of putative regulatory motifs that characterize sequences of interest (e.g. ChIP-Seq binding regions).

Results

In this study, the motif selection problem is mapped to variants of the set cover problem that are solved via tabu search and by relaxed integer linear programing (RILP). The algorithms are employed to analyze 349 ChIP-Seq experiments from the ENCODE project, yielding a small number of high-quality motifs that represent putative binding sites of primary factors and cofactors. Specifically, when compared with the motifs reported by Kheradpour and Kellis, the set cover-based algorithms produced motif sets covering 35% more peaks for 11 TFs and identified 4 more putative cofactors for 6 TFs. Moreover, a systematic evaluation using nested cross-validation revealed that the RILP algorithm selected fewer motifs and was able to cover 6% more peaks and 3% fewer background regions, which reduced the error rate by 7%.

Availability and implementation

The source code of the algorithms and all the datasets are available at https://github.com/YichaoOU/Set_cover_tools.

Supplementary information

Supplementary data are available at Bioinformatics online.

The OhioT1DM Dataset for Blood Glucose Level Prediction: Update 2020

This paper documents the OhioT1DM Dataset, which was developed to promote and facilitate research in blood glucose level prediction. It contains eight weeks' worth of continuous glucose monitoring, insulin, physiological sensor, and self-reported life-event data for each of 12 people with type 1 diabetes. An associated graphical software tool allows researchers to visualize the integrated data. The paper details the contents and format of the dataset and tells interested researchers how to obtain it. The OhioT1DM Dataset was first released in 2018 for the first Blood Glucose Level Prediction (BGLP) Challenge. At that time, the dataset was half its current size, containing data for only six people with type 1 diabetes. Data for an additional six people is being released in 2020 for the second BGLP Challenge. This paper subsumes and supersedes the paper which documented the original dataset.

A Semantic Parsing Pipeline for Context-Dependent Question Answering over Temporally Structured Data

We propose a new setting for question answering in which users can query the system using both natural language and direct interactions within a graphical user interface that displays multiple time series associated with an entity of interest. The user interacts with the interface in order to understand the entity's state and behavior, entailing sequences of actions and questions whose answers may depend on previous factual or navigational interactions. We describe a pipeline implementation where spoken questions are first transcribed into text which is then semantically parsed into logical forms that can be used to automatically extract the answer from the underlying database. The speech recognition module is implemented by adapting a pre-trained LSTM-based architecture to the user's speech, whereas for the semantic parsing component we introduce an LSTM-based encoder-decoder architecture that models context dependency through copying mechanisms and multiple levels of attention over inputs and previous outputs. When evaluated separately, with and without data augmentation, both models are shown to substantially outperform several strong baselines. Furthermore, the full pipeline evaluation shows only a small degradation in semantic parsing accuracy, demonstrating that the semantic parser is robust to mistakes in the speech recognition output. The new question answering paradigm proposed in this paper has the potential to improve the presentation and navigation of the large amounts of sensor data and life events that are generated in many areas of medicine.