With the exponential growth of information on the internet, users have been relying on search engines for finding the precise documents. However, user queries are often short. The inherent ambiguity of short queries imposes great challenges for search engines to understand user intent. Query suggestion is one key technique for search engines to augment user queries so that they can better understand user intent. In the past, query suggestions have been relying on either term-frequency--based methods with little semantic understanding of the query, or word-embedding--based methods with little personalization efforts. Here, we present a sequence-to-sequence-model--based query suggestion framework that is capable of modeling structured, personalized features and unstructured query texts naturally. This capability opens up the opportunity to better understand query semantics and user intent at the same time. As the largest professional network, LinkedIn has the advantage of utilizing a rich amount of accurate member profile information to personalize query suggestions. We applied this framework in the LinkedIn production traffic and showed that personalized query suggestions significantly improved member search experience as measured by key business metrics at LinkedIn.

When learning a hidden Markov model (HMM), sequential observations can often be complemented by real-valued summary response variables generated from the path of hidden states. Such settings arise in numerous domains, including many applications in biology, like motif discovery and genome annotation. In this paper, we present a flexible framework for jointly modeling both latent sequence features and the functional mapping that relates the summary response variables to the hidden state sequence. The algorithm is compatible with a rich set of mapping functions. Results show that the availability of additional continuous response variables can simultaneously improve the annotation of the sequential observations and yield good prediction performance in both synthetic data and real-world datasets.

MOTIVATION: Transcriptional regulation is directly enacted by the interactions between DNA and many proteins, including transcription factors (TFs), nucleosomes and polymerases. A critical step in deciphering transcriptional regulation is to infer, and eventually predict, the precise locations of these interactions, along with their strength and frequency. While recent datasets yield great insight into these interactions, individual data sources often provide only partial information regarding one aspect of the complete interaction landscape. For example, chromatin immunoprecipitation (ChIP) reveals the binding positions of a protein, but only for one protein at a time. In contrast, nucleases like MNase and DNase can be used to reveal binding positions for many different proteins at once, but cannot easily determine the identities of those proteins. Currently, few statistical frameworks jointly model these different data sources to reveal an accurate, holistic view of the in vivo protein-DNA interaction landscape. RESULTS: Here, we develop a novel statistical framework that integrates different sources of experimental information within a thermodynamic model of competitive binding to jointly learn a holistic view of the in vivo protein-DNA interaction landscape. We show that our framework learns an interaction landscape with increased accuracy, explaining multiple sets of data in accordance with thermodynamic principles of competitive DNA binding. The resulting model of genomic occupancy provides a precise mechanistic vantage point from which to explore the role of protein-DNA interactions in transcriptional regulation. AVAILABILITY AND IMPLEMENTATION: The C source code for compete and Python source code for MCMC-based inference are available at http://www.cs.duke.edu/∼amink. CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.