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1. Multi-Task Learning For Document Ranking And Query Suggestion

   Wasi Uddin Ahmad, Kai-Wei Chang (April 2018, Sixth International Conference on Learning Representations)

   We propose a multi-task learning framework to jointly learn document ranking and query suggestion for web search. It consists of two major components, a document ranker and a query recommender. Document ranker combines current query and session information and compares the combined representation with document representation to rank the documents. Query recommender tracks users’ query reformulation sequence considering all previous in-session queries using a sequence to sequence approach. As both tasks are driven by the users’ underlying search intent, we perform joint learning of these two components through session recurrence, which encodes search context and intent. Extensive comparisons against state-of-the-art document ranking and query suggestion algorithms are performed on the public AOL search log, and the promising results endorse the effectiveness of the joint learning framework. 

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2. Intent-aware Query Obfuscation for Privacy Protection in Personalized Web Search

   Ahmad, Wasi and (April 2018, Sixth International Conference on Learning Representations)

   We propose a multi-task learning framework to jointly learn document ranking and query suggestion for web search. It consists of two major components, a document ranker and a query recommender. Document ranker combines current query and session information and compares the combined representation with document representation to rank the documents. Query recommender tracks users’ query reformulation sequence considering all previous in-session queries using a sequence to sequence approach. As both tasks are driven by the users’ underlying search intent, we perform joint learning of these two components through session recurrence, which encodes search context and intent. Extensive comparisons against state-of-the-art document ranking and query suggestion algorithms are performed on the public AOL search log, and the promising results endorse the effectiveness of the joint learning framework. 

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3. Patterns of Gender-Specializing Query Reformulation

   Raj, Amifa; Mitra, Bhaksar; Ekstrand, Michael D.; Craswell, Nick (July 2023, Proceedings of the 46th International ACM SIGIR Conference on Research and Development in Information Retrieval (SIGIR ’23))

   Users of search systems often reformulate their queries by adding query terms to reflect their evolving information need or to more precisely express their information need when the system fails to surface relevant content. Analyzing these query reformulations can inform us about both system and user behavior. In this work, we study a special category of query reformulations that involve specifying demographic group attributes, such as gender, as part of the reformulated query (e.g., “olympic 2021 soccer results” → “olympic 2021 women‘s soccer results”). There are many ways a query, the search results, and a demographic attribute such as gender may relate, leading us to hypothesize different causes for these reformulation patterns, such as under-representation on the original result page or based on the linguistic theory of markedness. This paper reports on an observational study of gender-specializing query reformulations—their contexts and effects—as a lens on the relationship between system results and gender, based on large-scale search log data from Bing. We find that these reformulations sometimes correct for and other times reinforce gender representation on the original result page, but typically yield better access to the ultimately-selected results. The prevalence of these reformulations—and which gender they skew towards—differ by topical context. However, we do not find evidence that either group under-representation or markedness alone adequately explains these reformulations. We hope that future research will use such reformulations as a probe for deeper investigation into gender (and other demographic) representation on the search result page. 

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4. PPIT: an R package for inferring microbial taxonomy from nifH sequences

   https://doi.org/10.1093/bioinformatics/btab100  

   Kapili, Bennett J; Dekas, Anne E (February 2021, Bioinformatics)

   Birol, Inanc (Ed.)

   Abstract Motivation Linking microbial community members to their ecological functions is a central goal of environmental microbiology. When assigned taxonomy, amplicon sequences of metabolic marker genes can suggest such links, thereby offering an overview of the phylogenetic structure underpinning particular ecosystem functions. However, inferring microbial taxonomy from metabolic marker gene sequences remains a challenge, particularly for the frequently sequenced nitrogen fixation marker gene, nitrogenase reductase (nifH). Horizontal gene transfer in recent nifH evolutionary history can confound taxonomic inferences drawn from the pairwise identity methods used in existing software. Other methods for inferring taxonomy are not standardized and require manual inspection that is difficult to scale. Results We present Phylogenetic Placement for Inferring Taxonomy (PPIT), an R package that infers microbial taxonomy from nifH amplicons using both phylogenetic and sequence identity approaches. After users place query sequences on a reference nifH gene tree provided by PPIT (n = 6317 full-length nifH sequences), PPIT searches the phylogenetic neighborhood of each query sequence and attempts to infer microbial taxonomy. An inference is drawn only if references in the phylogenetic neighborhood are: (1) taxonomically consistent and (2) share sufficient pairwise identity with the query, thereby avoiding erroneous inferences due to known horizontal gene transfer events. We find that PPIT returns a higher proportion of correct taxonomic inferences than BLAST-based approaches at the cost of fewer total inferences. We demonstrate PPIT on deep-sea sediment and find that Deltaproteobacteria are the most abundant potential diazotrophs. Using this dataset we show that emending PPIT inferences based on visual inspection of query sequence placement can achieve taxonomic inferences for nearly all sequences in a query set. We additionally discuss how users can apply PPIT to the analysis of other marker genes. Availability PPIT is freely available to non-commercial users at https://github.com/bkapili/ppit. Installation includes a vignette that demonstrates package use and reproduces the nifH amplicon analysis discussed here. The raw nifH amplicon sequence data have been deposited in the GenBank, EMBL, and DDBJ databases under BioProject number PRJEB37167. Supplementary information Supplementary data are available at Bioinformatics online. 

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5. BioModME for building and simulating dynamic computational models of complex biological systems

   https://doi.org/10.1093/bioadv/vbae023  

   Womack, Justin A.; Shah, Viren; Audi, Said H.; Terhune, Scott S.; Dash, Ranjan K.; Lengauer, ed., Thomas (February 2024, Bioinformatics Advances)

   Abstract SummaryMolecular mechanisms of biological functions and disease processes are exceptionally complex, and our ability to interrogate and understand relationships is becoming increasingly dependent on the use of computational modeling. We have developed “BioModME,” a standalone R-based web application package, providing an intuitive and comprehensive graphical user interface to help investigators build, solve, visualize, and analyze computational models of complex biological systems. Some important features of the application package include multi-region system modeling, custom reaction rate laws and equations, unit conversion, model parameter estimation utilizing experimental data, and import and export of model information in the Systems Biology Matkup Language format. The users can also export models to MATLAB, R, and Python languages and the equations to LaTeX and Mathematical Markup Language formats. Other important features include an online model development platform, multi-modality visualization tool, and efficient numerical solvers for differential-algebraic equations and optimization. Availability and implementationAll relevant software information including documentation and tutorials can be found at https://mcw.marquette.edu/biomedical-engineering/computational-systems-biology-lab/biomodme.php. Deployed software can be accessed at https://biomodme.ctsi.mcw.edu/. Source code is freely available for download at https://github.com/MCWComputationalBiologyLab/BioModME. 

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