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
A Python library created to assist programmers with complex mathematical functions

libmaths libmaths was created not only as a learning experience for me, but as a way to make mathematical models in seconds for Python users using mat

Simple 73 Oct 02, 2022
Using PyTorch Perform intent classification using three different models to see which one is better for this task

Using PyTorch Perform intent classification using three different models to see which one is better for this task

Yoel Graumann 1 Feb 14, 2022
Text and code for the forthcoming second edition of Think Bayes, by Allen Downey.

Think Bayes 2 by Allen B. Downey The HTML version of this book is here. Think Bayes is an introduction to Bayesian statistics using computational meth

Allen Downey 1.5k Jan 08, 2023
Source code for deep symbolic optimization.

Update July 10, 2021: This repository now supports an additional symbolic optimization task: learning symbolic policies for reinforcement learning. Th

Brenden Petersen 290 Dec 25, 2022
LLVIP: A Visible-infrared Paired Dataset for Low-light Vision

LLVIP: A Visible-infrared Paired Dataset for Low-light Vision Project | Arxiv | Abstract It is very challenging for various visual tasks such as image

CVSM Group - email: <a href=[email protected]"> 377 Jan 07, 2023
A mini-course offered to Undergrad chemistry students

The best way to use this material is by forking it by click the Fork button at the top, right corner. Then you will get your own copy to play with! Th

Raghu 19 Dec 19, 2022
Get the partition that a file belongs and the percentage of space that consumes

tinos_eisai_sy Get the partition that a file belongs and the percentage of space that consumes (works only with OSes that use the df command) tinos_ei

Konstantinos Patronas 6 Jan 24, 2022
Pytorch implementation of Hinton's Dynamic Routing Between Capsules

pytorch-capsule A Pytorch implementation of Hinton's "Dynamic Routing Between Capsules". https://arxiv.org/pdf/1710.09829.pdf Thanks to @naturomics fo

Tim Omernick 625 Oct 27, 2022
Pytorch-3dunet - 3D U-Net model for volumetric semantic segmentation written in pytorch

pytorch-3dunet PyTorch implementation 3D U-Net and its variants: Standard 3D U-Net based on 3D U-Net: Learning Dense Volumetric Segmentation from Spar

Adrian Wolny 1.3k Dec 28, 2022
ICRA 2021 "Towards Precise and Efficient Image Guided Depth Completion"

PENet: Precise and Efficient Depth Completion This repo is the PyTorch implementation of our paper to appear in ICRA2021 on "Towards Precise and Effic

232 Dec 25, 2022
SpeechNAS Better Trade off between Latency and Accuracy for Large Scale Speaker Verification

SpeechNAS Better Trade off between Latency and Accuracy for Large Scale Speaker Verification

Wentao Zhu 24 May 20, 2022
Mitsuba 2: A Retargetable Forward and Inverse Renderer

Mitsuba Renderer 2 Documentation Mitsuba 2 is a research-oriented rendering system written in portable C++17. It consists of a small set of core libra

Mitsuba Physically Based Renderer 2k Jan 07, 2023
Official repository for the NeurIPS 2021 paper Get Fooled for the Right Reason: Improving Adversarial Robustness through a Teacher-guided curriculum Learning Approach

Get Fooled for the Right Reason Official repository for the NeurIPS 2021 paper Get Fooled for the Right Reason: Improving Adversarial Robustness throu

Sowrya Gali 1 Apr 25, 2022
Code for "Contextual Non-Local Alignment over Full-Scale Representation for Text-Based Person Search"

Contextual Non-Local Alignment over Full-Scale Representation for Text-Based Person Search This is an implementation for our paper Contextual Non-Loca

Tencent YouTu Research 50 Dec 03, 2022
Official Pytorch and JAX implementation of "Efficient-VDVAE: Less is more"

The Official Pytorch and JAX implementation of "Efficient-VDVAE: Less is more" Arxiv preprint Louay Hazami   ·   Rayhane Mama   ·   Ragavan Thurairatn

Rayhane Mama 144 Dec 23, 2022
Relative Positional Encoding for Transformers with Linear Complexity

Stochastic Positional Encoding (SPE) This is the source code repository for the ICML 2021 paper Relative Positional Encoding for Transformers with Lin

Antoine Liutkus 48 Nov 16, 2022
Realtime_Multi-Person_Pose_Estimation

Introduction Multi Person PoseEstimation By PyTorch Results Require Pytorch Installation git submodule init && git submodule update Demo Download conv

tensorboy 1.3k Jan 05, 2023
CVPR2020 Counterfactual Samples Synthesizing for Robust VQA

CVPR2020 Counterfactual Samples Synthesizing for Robust VQA This repo contains code for our paper "Counterfactual Samples Synthesizing for Robust Visu

72 Dec 22, 2022
EFENet: Reference-based Video Super-Resolution with Enhanced Flow Estimation

EFENet EFENet: Reference-based Video Super-Resolution with Enhanced Flow Estimation Code is a bit messy now. I woud clean up soon. For training the EF

Yaping Zhao 19 Nov 05, 2022