1,363 research outputs found
Potential Maximal Clique Algorithms for Perfect Phylogeny Problems
Kloks, Kratsch, and Spinrad showed how treewidth and minimum-fill, NP-hard
combinatorial optimization problems related to minimal triangulations, are
broken into subproblems by block subgraphs defined by minimal separators. These
ideas were expanded on by Bouchitt\'e and Todinca, who used potential maximal
cliques to solve these problems using a dynamic programming approach in time
polynomial in the number of minimal separators of a graph. It is known that
solutions to the perfect phylogeny problem, maximum compatibility problem, and
unique perfect phylogeny problem are characterized by minimal triangulations of
the partition intersection graph. In this paper, we show that techniques
similar to those proposed by Bouchitt\'e and Todinca can be used to solve the
perfect phylogeny problem with missing data, the two- state maximum
compatibility problem with missing data, and the unique perfect phylogeny
problem with missing data in time polynomial in the number of minimal
separators of the partition intersection graph
Unique Perfect Phylogeny Characterizations via Uniquely Representable Chordal Graphs
The perfect phylogeny problem is a classic problem in computational biology,
where we seek an unrooted phylogeny that is compatible with a set of
qualitative characters. Such a tree exists precisely when an intersection graph
associated with the character set, called the partition intersection graph, can
be triangulated using a restricted set of fill edges. Semple and Steel used the
partition intersection graph to characterize when a character set has a unique
perfect phylogeny. Bordewich, Huber, and Semple showed how to use the partition
intersection graph to find a maximum compatible set of characters. In this
paper, we build on these results, characterizing when a unique perfect
phylogeny exists for a subset of partial characters. Our characterization is
stated in terms of minimal triangulations of the partition intersection graph
that are uniquely representable, also known as ur-chordal graphs. Our
characterization is motivated by the structure of ur-chordal graphs, and the
fact that the block structure of minimal triangulations is mirrored in the
graph that has been triangulated
Semantic Entity Retrieval Toolkit
Unsupervised learning of low-dimensional, semantic representations of words
and entities has recently gained attention. In this paper we describe the
Semantic Entity Retrieval Toolkit (SERT) that provides implementations of our
previously published entity representation models. The toolkit provides a
unified interface to different representation learning algorithms, fine-grained
parsing configuration and can be used transparently with GPUs. In addition,
users can easily modify existing models or implement their own models in the
framework. After model training, SERT can be used to rank entities according to
a textual query and extract the learned entity/word representation for use in
downstream algorithms, such as clustering or recommendation.Comment: SIGIR 2017 Workshop on Neural Information Retrieval (Neu-IR'17). 201
Pyndri: a Python Interface to the Indri Search Engine
We introduce pyndri, a Python interface to the Indri search engine. Pyndri
allows to access Indri indexes from Python at two levels: (1) dictionary and
tokenized document collection, (2) evaluating queries on the index. We hope
that with the release of pyndri, we will stimulate reproducible, open and
fast-paced IR research.Comment: ECIR2017. Proceedings of the 39th European Conference on Information
Retrieval. 2017. The final publication will be available at Springe
Lexical Query Modeling in Session Search
Lexical query modeling has been the leading paradigm for session search. In
this paper, we analyze TREC session query logs and compare the performance of
different lexical matching approaches for session search. Naive methods based
on term frequency weighing perform on par with specialized session models. In
addition, we investigate the viability of lexical query models in the setting
of session search. We give important insights into the potential and
limitations of lexical query modeling for session search and propose future
directions for the field of session search.Comment: ICTIR2016, Proceedings of the 2nd ACM International Conference on the
Theory of Information Retrieval. 201
Neural Vector Spaces for Unsupervised Information Retrieval
We propose the Neural Vector Space Model (NVSM), a method that learns
representations of documents in an unsupervised manner for news article
retrieval. In the NVSM paradigm, we learn low-dimensional representations of
words and documents from scratch using gradient descent and rank documents
according to their similarity with query representations that are composed from
word representations. We show that NVSM performs better at document ranking
than existing latent semantic vector space methods. The addition of NVSM to a
mixture of lexical language models and a state-of-the-art baseline vector space
model yields a statistically significant increase in retrieval effectiveness.
Consequently, NVSM adds a complementary relevance signal. Next to semantic
matching, we find that NVSM performs well in cases where lexical matching is
needed.
NVSM learns a notion of term specificity directly from the document
collection without feature engineering. We also show that NVSM learns
regularities related to Luhn significance. Finally, we give advice on how to
deploy NVSM in situations where model selection (e.g., cross-validation) is
infeasible. We find that an unsupervised ensemble of multiple models trained
with different hyperparameter values performs better than a single
cross-validated model. Therefore, NVSM can safely be used for ranking documents
without supervised relevance judgments.Comment: TOIS 201
Structural Regularities in Text-based Entity Vector Spaces
Entity retrieval is the task of finding entities such as people or products
in response to a query, based solely on the textual documents they are
associated with. Recent semantic entity retrieval algorithms represent queries
and experts in finite-dimensional vector spaces, where both are constructed
from text sequences.
We investigate entity vector spaces and the degree to which they capture
structural regularities. Such vector spaces are constructed in an unsupervised
manner without explicit information about structural aspects. For concreteness,
we address these questions for a specific type of entity: experts in the
context of expert finding. We discover how clusterings of experts correspond to
committees in organizations, the ability of expert representations to encode
the co-author graph, and the degree to which they encode academic rank. We
compare latent, continuous representations created using methods based on
distributional semantics (LSI), topic models (LDA) and neural networks
(word2vec, doc2vec, SERT). Vector spaces created using neural methods, such as
doc2vec and SERT, systematically perform better at clustering than LSI, LDA and
word2vec. When it comes to encoding entity relations, SERT performs best.Comment: ICTIR2017. Proceedings of the 3rd ACM International Conference on the
Theory of Information Retrieval. 201
- …