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1. SchemaDrill: Interactive Semi-Structured Schema Design

   https://doi.org/10.1145/3209900.3209908  

   Spoth, William ; Xie, Ting ; Kennedy, Oliver ; Yang, Ying ; Hammerschmidt, Beda ; Liu, Zhen Hua ; Gawlick, Dieter ( January 2018 , Proceedings of the Workshop on Human-In-the-Loop Data Analytics)

   Ad-hoc data models like JSON make it easy to evolve schemas and to multiplex different data-types into a single stream. This flexibility makes JSON great for generating data, but also makes it much harder to query, ingest into a database, and index. In this paper, we explore the first step of JSON data loading: schema design. Specifically, we consider the challenge of designing schemas for existing JSON datasets as an interactive problem. We present SchemaDrill, a roll-up/drill-down style interface for exploring collections of JSON records. SchemaDrill helps users to visualize the collection, identify relevant fragments, and map it down into one or more flat, relational schemas. We describe and evaluate two key components of SchemaDrill: (1) A summary schema representation that significantly reduces the complexity of JSON schemas without a meaningful reduction in information content, and (2) A collection of schema visualizations that help users to qualitatively survey variability amongst different schemas in the collection. 

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2. Adaptive Schema Databases

   Spoth, W. ; Arab, B. S. ; Chan, E. S. ; Gawlick, D. ; Ghoneimy, A. ; Glavic, B. ; Hammerschmidt, B. ; Kennedy, O. ; Lee, S. ; Liu, Z. H. ; et al ( January 2017 , CIDR 2017, 8th Biennial Conference on Innovative Data Systems Research, Chaminade, CA, USA, January 8-11, 2017, Online Proceedings)

   The rigid schemas of classical relational databases help users in specifying queries and inform the storage organization of data. However, the advantages of schemas come at a high upfront cost through schema and ETL process design. In this work, we propose a new paradigm where the database system takes a more active role in schema development and data integration. We refer to this approach as adaptive schema databases (ASDs). An ASD ingests semi-structured or unstructured data directly using a pluggable combination of extraction and data integration techniques. Over time it discovers and adapts schemas for the ingested data using information provided by data integration and information extraction techniques, as well as from queries and user-feedback. In contrast to relational databases, ASDs maintain multiple schema workspaces that represent individualized views over the data, which are fine-tuned to the needs of a particular user or group of users. A novel aspect of ASDs is that probabilistic database techniques are used to encode ambiguity in automatically generated data extraction workflows and in generated schemas. ASDs can provide users with context-dependent feedback on the quality of a schema, both in terms of its ability to satisfy a user's queries, and the quality of the resulting answers. We outline our vision for ASDs, and present a proof of concept implementation as part of the Mimir probabilistic data curation system. 

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3. Building and steering binned template fits with cabinetry

   https://doi.org/10.1051/epjconf/202125103067  

   Cranmer, Kyle ; Held, Alexander ( January 2021 , EPJ Web of Conferences)

   Biscarat, C. ; Campana, S. ; Hegner, B. ; Roiser, S. ; Rovelli, C.I. ; Stewart, G.A. (Ed.)

   The cabinetry library provides a Python-based solution for building and steering binned template fits. It tightly integrates with the pythonic High Energy Physics ecosystem, and in particular with pyhf for statistical inference. cabinetry uses a declarative approach for building statistical models, with a JSON schema describing possible configuration choices. Model building instructions can additionally be provided via custom code, which is automatically executed when applicable at key steps of the workflow. The library implements interfaces for performing maximum likelihood fitting, upper parameter limit determination, and discovery significance calculation. cabinetry also provides a range of utilities to study and disseminate fit results. These include visualizations of the fit model and data, visualizations of template histograms and fit results, ranking of nuisance parameters by their impact, a goodness-of-fit calculation, and likelihood scans. The library takes a modular approach, allowing users to include some or all of its functionality in their workflow. 

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4. Software Environments in Binder Containers

   https://doi.org/10.5281/zenodo.4891790  

   Shaffer, Tim ; Chard, Kyle ; Thain, Douglas ( January 2021 , Zenodo)

   Binder is a publicly accessible online service for executing interactive notebooks based on Git repositories. Binder dynamically builds and deploys containers following a recipe stored in the repository, then gives the user a browser-based notebook interface. The Binder group periodically releases a log of container launches from the public Binder service. Archives of launch records are available here. These records do not include identifiable information like IP addresses, but do give the source repo being launched along with some other metadata. The main content of this dataset is in the binder.sqlite file. This SQLite database includes launch records from 2018-11-03 to 2021-06-06 in the events table, which has the following schema.

   CREATE TABLE events( version INTEGER, timestamp TEXT, provider TEXT, spec TEXT, origin TEXT, ref TEXT, guessed_ref TEXT ); CREATE INDEX idx_timestamp ON events(timestamp);

   • version indicates the version of the record as assigned by Binder. The origin field became available with version 3, and the ref field with version 4. Older records where this information was not recorded will have the corresponding fields set to null.
   • timestamp is the ISO timestamp of the launch
   • provider gives the type of source repo being launched ("GitHub" is by far the most common). The rest of the explanations assume GitHub, other providers may differ.
   • spec gives the particular branch/release/commit being built. It consists of <github-id>/<repo>/<branch>.
   • origin indicates which backend was used. Each has its own storage, compute, etc. so this info might be important for evaluating caching and performance. Note that only recent records include this field. May be null.
   • ref specifies the git commit that was actually used, rather than the named branch referenced by spec. Note that this was not recorded from the beginning, so only the more recent entries include it. May be null.
   • For records where ref is not available, we attempted to clone the named reference given by spec rather than the specific commit (see below). The guessed_ref field records the commit found at the time of cloning. If the branch was updated since the container was launched, this will not be the exact version that was used, and instead will refer to whatever was available at the time (early 2021). Depending on the application, this might still be useful information. Selecting only records with version 4 (or non-null ref) will exclude these guessed commits. May be null.

   The Binder launch dataset identifies the source repos that were used, but doesn't give any indication of their contents. We crawled GitHub to get the actual specification files in the repos which were fed into repo2docker when preparing the notebook environments, as well as filesystem metadata of the repos. Some repos were deleted/made private at some point, and were thus skipped. This is indicated by the absence of any row for the given commit (or absence of both ref and guessed_ref in the events table). The schema is as follows.

   CREATE TABLE spec_files ( ref TEXT NOT NULL PRIMARY KEY, ls TEXT, runtime BLOB, apt BLOB, conda BLOB, pip BLOB, pipfile BLOB, julia BLOB, r BLOB, nix BLOB, docker BLOB, setup BLOB, postbuild BLOB, start BLOB );

   Here ref corresponds to ref and/or guessed_ref from the events table. For each repo, we collected spec files into the following fields (see the repo2docker docs for details on what these are). The records in the database are simply the verbatim file contents, with no parsing or further processing performed.

   • runtime: runtime.txt
   • apt: apt.txt
   • conda: environment.yml
   • pip: requirements.txt
   • pipfile: Pipfile.lock or Pipfile
   • julia: Project.toml or REQUIRE
   • r: install.R
   • nix: default.nix
   • docker: Dockerfile
   • setup: setup.py
   • postbuild: postBuild
   • start: start

   The ls field gives a metadata listing of the repo contents (excluding the .git directory). This field is JSON encoded with the following structure based on JSON types:

   • Object: filesystem directory. Keys are file names within it. Values are the contents, which can be regular files, symlinks, or subdirectories.
   • String: symlink. The string value gives the link target.
   • Number: regular file. The number value gives the file size in bytes.

   CREATE TABLE clean_specs ( ref TEXT NOT NULL PRIMARY KEY, conda_channels TEXT, conda_packages TEXT, pip_packages TEXT, apt_packages TEXT );

   The clean_specs table provides parsed and validated specifications for some of the specification files (currently Pip, Conda, and APT packages). Each column gives either a JSON encoded list of package requirements, or null. APT packages have been validated using a regex adapted from the repo2docker source. Pip packages have been parsed and normalized using the Requirement class from the pkg_resources package of setuptools. Conda packages have been parsed and normalized using the conda.models.match_spec.MatchSpec class included with the library form of Conda (distinct from the command line tool). Users might want to use these parsers when working with the package data, as the specifications can become fairly complex.

   The missing table gives the repos that were not accessible, and event_logs records which log files have already been added. These tables are used for updating the dataset and should not be of interest to users.

    

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5. Open-Domain Hierarchical Event Schema Induction by Incremental Prompting and Verification

   https://doi.org/10.18653/v1/2023.acl-long.312  

   Li, Sha ; Zhao, Ruining ; Li, Manling ; Ji, Heng ; Callison-Burch, Chris ; Han, Jiawei ( January 2023 , Proceedings of the 61st Annual Meeting of the Association for Computational Linguistics)

   Event schemas are a form of world knowledge about the typical progression of events. Recent methods for event schema induction use information extraction systems to construct a large number of event graph instances from documents, and then learn to generalize the schema from such instances. In contrast, we propose to treat event schemas as a form of commonsense knowledge that can be derived from large language models (LLMs). This new paradigm greatly simplifies the schema induction process and allows us to handle both hierarchical relations and temporal relations between events in a straightforward way. Since event schemas have complex graph structures, we design an incremental prompting and verification method INCPROMPT to break down the construction of a complex event graph into three stages: event skeleton construction, event expansion, and event-event relation verification. Compared to directly using LLMs to generate a linearized graph, INCPROMPT can generate large and complex schemas with 7.2% F1 improvement in temporal relations and 31.0% F1 improvement in hierarchical relations. In addition, compared to the previous state-of-the-art closed-domain schema induction model, human assessors were able to cover ∼10% more events when translating the schemas into coherent stories and rated our schemas 1.3 points higher (on a 5-point scale) in terms of readability. 

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