Establishing Strong Baselines for TripClick Health Retrieval; ECIR 2022

Overview

TripClick Baselines with Improved Training Data

Welcome 🙌 to the hub-repo of our paper:

Establishing Strong Baselines for TripClick Health Retrieval Sebastian Hofstätter, Sophia Althammer, Mete Sertkan and Allan Hanbury

https://arxiv.org/abs/2201.00365

tl;dr We create strong re-ranking and dense retrieval baselines (BERTCAT, BERTDOT, ColBERT, and TK) for TripClick (health ad-hoc retrieval). We improve the – originally too noisy – training data with a simple negative sampling policy. We achieve large gains over BM25 in the re-ranking and retrieval setting on TripClick, which were not achieved with the original baselines. We publish the improved training files for everyone to use.

If you have any questions, suggestions, or want to collaborate please don't hesitate to get in contact with us via Twitter or mail to [email protected]

Please cite our work as:

@misc{hofstaetter2022tripclick,
      title={Establishing Strong Baselines for TripClick Health Retrieval}, 
      author={Sebastian Hofst{\"a}tter and Sophia Althammer and Mete Sertkan and Allan Hanbury},
      year={2022},
      eprint={2201.00365},
      archivePrefix={arXiv},
      primaryClass={cs.IR}
}

Training Files

We publish the improved training files without the text content instead using the ids from TripClick (with permission from the TripClick owners); for the text content please get the full TripClick dataset from the TripClick Github page.

Our training files have the format query_id pos_passage_id neg_passage_id (with tab separation) and are available as a HuggingFace dataset: https://huggingface.co/datasets/sebastian-hofstaetter/tripclick-training

Source Code

The full source-code for our paper is here, as part of our matchmaker library: https://github.com/sebastian-hofstaetter/matchmaker

We provide getting started guides for training re-ranking and retrieval models, as well as a range of evaluation setups.

Pre-Trained Models

Unfortunately, the license of TripClick does not allow us to publish the trained models.

TripClick Baselines Results

For more information and commentary on the results, please see our ECIR paper.

BM25 Top200 Re-Ranking

Model BERT Instance HEAD TORSO TAIL
nDCG MRR nDCG MRR nDCG MRR
Original Baselines
BM25 -- .140 .276 .206 .283 .267 .258
ConvKNRM -- .198 .420 .243 .347 .271 .265
TK -- .208 .434 .272 .381 .295 .280
Our Improved Baselines
TK -- .232 .472 .300 .390 .345 .319
ColBERT SciBERT .270 .556 .326 .426 .374 .347
PubMedBERT-Abstract .278 .557 .340 .431 .387 .361
BERT_CAT DistilBERT .272 .556 .333 .427 .381 .355
BERT-Base .287 .579 .349 .453 .396 .366
SciBERT .294 .595 .360 .459 .408 .377
PubMedBERT-Full .298 .582 .365 .462 .412 .381
PubMedBERT-Abstract .296 .587 .359 .456 .409 .380
Ensemble (Last 3 BERT_CAT) .303 .601 .370 .472 .420 .392

Dense Retrieval Results

Model BERT Instance Head(DCTR)
[email protected] [email protected] [email protected] [email protected] [email protected] [email protected]
Original Baselines
BM25 -- 31% .140 .276 .499 .621 .834
Our Improved Baselines
BERT_DOT DistilBERT 39% .236 .512 .550 .648 .813
SciBERT 41% .243 .530 .562 .640 .793
PubMedBERT 40% .235 .509 .582 .673 .828
Owner
Sebastian Hofstätter
PhD student; working on machine learning and information retrieval
Sebastian Hofstätter
Disagreement-Regularized Imitation Learning

Due to a normalization bug the expert trajectories have lower performance than the rl_baseline_zoo reported experts. Please see the following link in

Kianté Brantley 25 Apr 28, 2022
Election Exit Poll Prediction and U.S.A Presidential Speech Analysis using Machine Learning

Machine_Learning Election Exit Poll Prediction and U.S.A Presidential Speech Analysis using Machine Learning This project is based on 2 case-studies:

Avnika Mehta 1 Jan 27, 2022
X-VLM: Multi-Grained Vision Language Pre-Training

X-VLM: learning multi-grained vision language alignments Multi-Grained Vision Language Pre-Training: Aligning Texts with Visual Concepts. Yan Zeng, Xi

Yan Zeng 286 Dec 23, 2022
Аналитика доходности инвестиционного портфеля в Тинькофф брокере

Аналитика доходности инвестиционного портфеля Тиньков Видео на YouTube Для работы скрипта нужно установить три переменных окружения: export TINKOFF_TO

Alexey Goloburdin 64 Dec 17, 2022
Joint Channel and Weight Pruning for Model Acceleration on Mobile Devices

Joint Channel and Weight Pruning for Model Acceleration on Mobile Devices Abstract For practical deep neural network design on mobile devices, it is e

11 Dec 30, 2022
Clustergram - Visualization and diagnostics for cluster analysis in Python

Clustergram Visualization and diagnostics for cluster analysis Clustergram is a diagram proposed by Matthias Schonlau in his paper The clustergram: A

Martin Fleischmann 96 Dec 26, 2022
Differentiable molecular simulation of proteins with a coarse-grained potential

Differentiable molecular simulation of proteins with a coarse-grained potential This repository contains the learned potential, simulation scripts and

UCL Bioinformatics Group 44 Dec 10, 2022
This was initially the repo for the project of [email protected] of Asaf Mazar, Millad Kassaie and Georgios Chochlakis named "Powered by the Will? Exploring Lay Theories of Behavior Change through Social Media"

Subreddit Analysis This repo includes tools for Subreddit analysis, originally developed for our class project of PSYC 626 in USC, titled "Powered by

Georgios Chochlakis 1 Dec 17, 2021
The PyTorch re-implement of a 3D CNN Tracker to extract coronary artery centerlines with state-of-the-art (SOTA) performance. (paper: 'Coronary artery centerline extraction in cardiac CT angiography using a CNN-based orientation classifier')

The PyTorch re-implement of a 3D CNN Tracker to extract coronary artery centerlines with state-of-the-art (SOTA) performance. (paper: 'Coronary artery centerline extraction in cardiac CT angiography

James 135 Dec 23, 2022
The implemention of Video Depth Estimation by Fusing Flow-to-Depth Proposals

Flow-to-depth (FDNet) video-depth-estimation This is the implementation of paper Video Depth Estimation by Fusing Flow-to-Depth Proposals Jiaxin Xie,

32 Jun 14, 2022
Single cell current best practices tutorial case study for the paper:Luecken and Theis, "Current best practices in single-cell RNA-seq analysis: a tutorial"

Scripts for "Current best-practices in single-cell RNA-seq: a tutorial" This repository is complementary to the publication: M.D. Luecken, F.J. Theis,

Theis Lab 968 Dec 28, 2022
[ICML 2021] DouZero: Mastering DouDizhu with Self-Play Deep Reinforcement Learning | 斗地主AI

[ICML 2021] DouZero: Mastering DouDizhu with Self-Play Deep Reinforcement Learning DouZero is a reinforcement learning framework for DouDizhu (斗地主), t

Kwai Inc. 3.1k Jan 04, 2023
ArtEmis: Affective Language for Art

ArtEmis: Affective Language for Art Created by Panos Achlioptas, Maks Ovsjanikov, Kilichbek Haydarov, Mohamed Elhoseiny, Leonidas J. Guibas Introducti

Panos 268 Dec 12, 2022
Introduction to Statistics and Basics of Mathematics for Data Science - The Hacker's Way

HackerMath for Machine Learning “Study hard what interests you the most in the most undisciplined, irreverent and original manner possible.” ― Richard

Amit Kapoor 1.4k Dec 22, 2022
Robust Video Matting in PyTorch, TensorFlow, TensorFlow.js, ONNX, CoreML!

Robust Video Matting (RVM) English | 中文 Official repository for the paper Robust High-Resolution Video Matting with Temporal Guidance. RVM is specific

flow-dev 2 Aug 21, 2022
Implementation of H-Transformer-1D, Hierarchical Attention for Sequence Learning using 🤗 transformers

hierarchical-transformer-1d Implementation of H-Transformer-1D, Hierarchical Attention for Sequence Learning using 🤗 transformers In Progress!! 2021.

MyungHoon Jin 7 Nov 06, 2022
Deconfounding Temporal Autoencoder: Estimating Treatment Effects over Time Using Noisy Proxies

Deconfounding Temporal Autoencoder (DTA) This is a repository for the paper "Deconfounding Temporal Autoencoder: Estimating Treatment Effects over Tim

Milan Kuzmanovic 3 Feb 04, 2022
Educational API for 3D Vision using pose to control carton.

Educational API for 3D Vision using pose to control carton.

41 Jul 10, 2022
DNA-RECON { Automatic Web Reconnaissance Tool }

ABOUT TOOL : DNA-RECON is an automatic web reconnaissance tool written in python. This tool made for reconnaissance and information gathering with an

NIKUNJ BHATT 25 Aug 11, 2021
scikit-learn inspired API for CRFsuite

sklearn-crfsuite sklearn-crfsuite is a thin CRFsuite (python-crfsuite) wrapper which provides interface simlar to scikit-learn. sklearn_crfsuite.CRF i

417 Dec 20, 2022