314 research outputs found
Towards Argument-Aware Abstractive Summarization of Long Legal Opinions with Summary Reranking
We propose a simple approach for the abstractive summarization of long legal
opinions that considers the argument structure of the document. Legal opinions
often contain complex and nuanced argumentation, making it challenging to
generate a concise summary that accurately captures the main points of the
legal opinion. Our approach involves using argument role information to
generate multiple candidate summaries, then reranking these candidates based on
alignment with the document's argument structure. We demonstrate the
effectiveness of our approach on a dataset of long legal opinions and show that
it outperforms several strong baselines
CCharPPI web server: computational characterization of proteinâprotein interactions from structure
The atomic structures of proteinâprotein interactions are central to understanding their role in biological systems, and a wide variety of biophysical functions and potentials have been developed for their characterization and the construction of predictive models. These tools are scattered across a multitude of stand-alone programs, and are often available only as model parameters requiring reimplementation. This acts as a significant barrier to their widespread adoption. CCharPPI integrates many of these tools into a single web server. It calculates up to 108 parameters, including models of electrostatics, desolvation and hydrogen bonding, as well as interface packing and complementarity scores, empirical potentials at various resolutions, docking potentials and composite scoring functions.The research leading to these results has received funding from the People Programme (Marie Curie Actions) of the European Unions Seventh Framework Programme (FP7/2007-
2013) under REA grant agreement PIEF-GA-2012-327899 and grant BIO2013-48213-R from Spanish Ministry of Economy and
Competitiveness.Peer ReviewedPostprint (published version
Structured lexical similarity via convolution Kernels on dependency trees
A central topic in natural language process-ing is the design of lexical and syntactic fea-tures suitable for the target application. In this paper, we study convolution dependency tree kernels for automatic engineering of syntactic and semantic patterns exploiting lexical simi-larities. We define efficient and powerful ker-nels for measuring the similarity between de-pendency structures, whose surface forms of the lexical nodes are in part or completely dif-ferent. The experiments with such kernels for question classification show an unprecedented results, e.g. 41 % of error reduction of the for-mer state-of-the-art. Additionally, semantic role classification confirms the benefit of se-mantic smoothing for dependency kernels.
Learning Structural Kernels for Natural Language Processing
Structural kernels are a flexible learning
paradigm that has been widely used in Natural
Language Processing. However, the problem
of model selection in kernel-based methods
is usually overlooked. Previous approaches
mostly rely on setting default values for kernel
hyperparameters or using grid search,
which is slow and coarse-grained. In contrast,
Bayesian methods allow efficient model
selection by maximizing the evidence on the
training data through gradient-based methods.
In this paper we show how to perform this
in the context of structural kernels by using
Gaussian Processes. Experimental results on
tree kernels show that this procedure results
in better prediction performance compared to
hyperparameter optimization via grid search.
The framework proposed in this paper can be
adapted to other structures besides trees, e.g.,
strings and graphs, thereby extending the utility
of kernel-based methods
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Scoring functions for protein docking and drug design
textPredicting the structure of complexes formed by two interacting proteins is an important problem in computation structural biology. Proteins perform many of their functions by binding to other proteins. The structure of protein-protein complexes provides atomic details about protein function and biochemical pathways, and can help in designing drugs that inhibit binding. Docking computationally models the structure of protein-protein complexes, given three-dimensional structures of the individual chains. Protein docking methods have two phases. In the first phase, a comprehensive, coarse search is performed for optimally docked models. In the second refinement and reranking phase, the models from the first phase are refined and reranked, with the expectation of extracting a small set of accurate models from the pool of thousands of models obtained from the first phase. In this thesis, new algorithms are developed for the refinement and reranking phase of docking. New scoring functions, or potentials, that rank models are developed. These potentials are learnt using large-scale machine learning methods based on mathematical programming. The procedure for learning these potentials involves examining hundreds of thousands of correct and incorrect models. In this thesis, hierarchical constraints were introduced into the learning algorithm. First, an atomic potential was developed using this learning procedure. A refinement procedure involving side-chain remodeling and conjugate gradient-based minimization was introduced. The refinement procedure combined with the atomic potential was shown to improve docking accuracy significantly. Second, a hydrogen bond potential, was developed. Molecular dynamics-based sampling combined with the hydrogen bond potential improved docking predictions. Third, mathematical programming compared favorably to SVMs and neural networks in terms of accuracy, training and test time for the task of designing potentials to rank docking models. The methods described in this thesis are implemented in the docking package DOCK/PIERR. DOCK/PIERR was shown to be among the best automated docking methods in community wide assessments. Finally, DOCK/PIERR was extended to predict membrane protein complexes. A membrane-based score was added to the reranking phase, and shown to improve the accuracy of docking. This docking algorithm for membrane proteins was used to study the dimers of amyloid precursor protein, implicated in Alzheimer's disease.R. DOCK/PIERR was shown to be among the best automated docking methods in community wide assessments. Finally, DOCK/PIERR was extended to predict membrane protein complexes. A membrane-based score was added to the reranking phase, and shown to improve the accuracy of docking. This docking algorithm for membrane proteins was used to study the dimers of amyloid precursor protein, implicated in Alzheimerâs disease.Computer Science
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