The immense growth in the volume of research literature and experimental data in the field of molecular biology calls for efficient automatic methods to capture and store information. In recent years, several groups have worked on specific problems in this area, such as automated selection of articles pertinent to molecular biology, or automated extraction of information using natural-language processing, information visualization, and generation of specialized knowledge bases for molecular biology. GeneWays is an integrated system that combines several such subtasks. It analyzes interactions between molecular substances, drawing on multiple sources of information to infer a consensus view of molecular networks. GeneWays is designed as an open platform, allowing researchers to query, review, and critique stored information.

We present an automated system for assigning protein, gene, or mRNA class labels to biological terms in free text. Three machine learning algorithms and several extended ways for defining contextual features for disambiguation are examined, and a fully unsupervised manner for obtaining training examples is proposed. We train and evaluate our system over a collection of 9 million words of molecular biology journal articles, obtaining accuracy rates up to 85%.

A Natural Language Generation system produces text using as input semantic data. One of its very first tasks is to decide which pieces of information to convey in the output. This task, called Content Selection, is quite domain dependent, requiring considerable re-engineering to transport the system from one scenario to another. In this paper, we present a method to acquire content selection rules automatically from a corpus of text and associated semantics. Our proposed technique was evaluated by comparing its output with information selected by human authors in unseen texts, where we were able to filter half the input data set without loss of recall.

The final stage in the IBM DeepQA pipeline involves ranking all candidate answers according to their evidence scores and judging the likelihood that each candidate answer is correct. In DeepQA, this is done using a machine learning framework that is phase-based, providing capabilities for manipulating the data and applying machine learning in successive applications. We show how this design can be used to implement solutions to particular challenges that arise in applying machine learning for evidence-based hypothesis evaluation. Our approach facilitates an agile development environment for DeepQA; evidence scoring strategies can be easily introduced, revised, and reconfigured without the need for error-prone manual effort to determine how to combine the various evidence scores. We describe the framework, explain the challenges, and evaluate the gain over a baseline machine learning approach.

In a language generation system, a content planner embodies one or more "plans" that are usually hand-crafted, sometimes through manual analysis of target text. In this paper, we present a system that we developed to automatically learn elements of a plan and the ordering constraints among them. As training data, we use semantically annotated transcripts of domain experts performing the task our system is designed to mimic. Given the large degree of variation in the spoken language of the transcripts, we developed a novel algorithm to find parallels between transcripts based on techniques used in computational genomics. Our proposed methodology was evaluated two-fold: the learning and generalization capabilities were quantitatively evaluated using cross validation obtaining a level of accuracy of 89%. A qualitative evaluation is also provided.