A resource-saving collective approach to biomedical semantic role labeling

BACKGROUND: Biomedical semantic role labeling (BioSRL) is a natural language processing technique that identifies the semantic roles of the words or phrases in sentences describing biological processes and expresses them as predicate-argument structures (PAS’s). Currently, a major problem of BioSRL is that most systems label every node in a full parse tree independently; however, some nodes always exhibit dependency. In general SRL, collective approaches based on the Markov logic network (MLN) model have been successful in dealing with this problem. However, in BioSRL such an approach has not been attempted because it would require more training data to recognize the more specialized and diverse terms found in biomedical literature, increasing training time and computational complexity. RESULTS: We first constructed a collective BioSRL system based on MLN. This system, called collective BIOSMILE (CBIOSMILE), is trained on the BioProp corpus. To reduce the resources used in BioSRL training, we employ a tree-pruning filter to remove unlikely nodes from the parse tree and four argument candidate identifiers to retain candidate nodes in the tree. Nodes not recognized by any candidate identifier are discarded. The pruned annotated parse trees are used to train a resource-saving MLN-based system, which is referred to as resource-saving collective BIOSMILE (RCBIOSMILE). Our experimental results show that our proposed CBIOSMILE system outperforms BIOSMILE, which is the top BioSRL system. Furthermore, our proposed RCBIOSMILE maintains the same level of accuracy as CBIOSMILE using 92% less memory and 57% less training time. CONCLUSIONS: This greatly improved efficiency makes RCBIOSMILE potentially suitable for training on much larger BioSRL corpora over more biomedical domains. Compared to real-world biomedical corpora, BioProp is relatively small, containing only 445 MEDLINE abstracts and 30 event triggers. It is not large enough for practical applications, such as pathway construction. We consider it of primary importance to pursue SRL training on large corpora in the future

Improving Data Quality by Leveraging Statistical Relational Learning

Digitally collected data su ↵ ers from many data quality issues, such as duplicate, incorrect, or incomplete data. A common approach for counteracting these issues is to formulate a set of data cleaning rules to identify and repair incorrect, duplicate and missing data. Data cleaning systems must be able to treat data quality rules holistically, to incorporate heterogeneous constraints within a single routine, and to automate data curation. We propose an approach to data cleaning based on statistical relational learning (SRL). We argue that a formalism - Markov logic - is a natural fit for modeling data quality rules. Our approach allows for the usage of probabilistic joint inference over interleaved data cleaning rules to improve data quality. Furthermore, it obliterates the need to specify the order of rule execution. We describe how data quality rules expressed as formulas in first-order logic directly translate into the predictive model in our SRL framework

Improving Data Quality by Leveraging Statistical Relational\ud Learning

Digitally collected data su\ud ↵\ud ers from many data quality issues, such as duplicate, incorrect, or incomplete data. A common\ud approach for counteracting these issues is to formulate a set of data cleaning rules to identify and repair incorrect, duplicate and\ud missing data. Data cleaning systems must be able to treat data quality rules holistically, to incorporate heterogeneous constraints\ud within a single routine, and to automate data curation. We propose an approach to data cleaning based on statistical relational\ud learning (SRL). We argue that a formalism - Markov logic - is a natural fit for modeling data quality rules. Our approach\ud allows for the usage of probabilistic joint inference over interleaved data cleaning rules to improve data quality. Furthermore, it\ud obliterates the need to specify the order of rule execution. We describe how data quality rules expressed as formulas in first-order\ud logic directly translate into the predictive model in our SRL framework

Transforming Graph Representations for Statistical Relational Learning

Relational data representations have become an increasingly important topic due to the recent proliferation of network datasets (e.g., social, biological, information networks) and a corresponding increase in the application of statistical relational learning (SRL) algorithms to these domains. In this article, we examine a range of representation issues for graph-based relational data. Since the choice of relational data representation for the nodes, links, and features can dramatically affect the capabilities of SRL algorithms, we survey approaches and opportunities for relational representation transformation designed to improve the performance of these algorithms. This leads us to introduce an intuitive taxonomy for data representation transformations in relational domains that incorporates link transformation and node transformation as symmetric representation tasks. In particular, the transformation tasks for both nodes and links include (i) predicting their existence, (ii) predicting their label or type, (iii) estimating their weight or importance, and (iv) systematically constructing their relevant features. We motivate our taxonomy through detailed examples and use it to survey and compare competing approaches for each of these tasks. We also discuss general conditions for transforming links, nodes, and features. Finally, we highlight challenges that remain to be addressed

Learning, Probability and Logic: Toward a Unified Approach for Content-Based Music Information Retrieval

Within the last 15 years, the field of Music Information Retrieval (MIR) has made tremendous progress in the development of algorithms for organizing and analyzing the ever-increasing large and varied amount of music and music-related data available digitally. However, the development of content-based methods to enable or ameliorate multimedia retrieval still remains a central challenge. In this perspective paper, we critically look at the problem of automatic chord estimation from audio recordings as a case study of content-based algorithms, and point out several bottlenecks in current approaches: expressiveness and flexibility are obtained to the expense of robustness and vice versa; available multimodal sources of information are little exploited; modeling multi-faceted and strongly interrelated musical information is limited with current architectures; models are typically restricted to short-term analysis that does not account for the hierarchical temporal structure of musical signals. Dealing with music data requires the ability to tackle both uncertainty and complex relational structure at multiple levels of representation. Traditional approaches have generally treated these two aspects separately, probability and learning being the usual way to represent uncertainty in knowledge, while logical representation being the usual way to represent knowledge and complex relational information. We advocate that the identified hurdles of current approaches could be overcome by recent developments in the area of Statistical Relational Artificial Intelligence (StarAI) that unifies probability, logic and (deep) learning. We show that existing approaches used in MIR find powerful extensions and unifications in StarAI, and we explain why we think it is time to consider the new perspectives offered by this promising research field