Modeling electronic health record data using a knowledge-graph-embedded topic model
Yuesong Zou
Ahmad Pesaranghader
Aman Verma
David Buckeridge
Yue Li
The rapid growth of electronic health record (EHR) datasets opens up promising opportunities to understand human diseases in a systematic wa… (voir plus)y. However, effective extraction of clinical knowledge from the EHR data has been hindered by its sparsity and noisy information. We present KG-ETM, an end-to-end knowledge graph-based multimodal embedded topic model. KG-ETM distills latent disease topics from EHR data by learning the embedding from the medical knowledge graphs. We applied KG-ETM to a large-scale EHR dataset consisting of over 1 million patients. We evaluated its performance based on EHR reconstruction and drug imputation. KG-ETM demonstrated superior performance over the alternative methods on both tasks. Moreover, our model learned clinically meaningful graph-informed embedding of the EHR codes. In additional, our model is also able to discover interpretable and accurate patient representations for patient stratification and drug recommendations.
2022-06-03
ArXiv (prépublication)
doi.org
arxiv.org
Vendor-neutral sequences and fully transparent workflows improve inter-vendor reproducibility of quantitative MRI
Agah Karakuzu
Labonny Biswas
Julien Cohen-Adad
Nikola Stikov
Purpose We developed an end-to-end workflow that starts with a vendor-neutral acquisition and tested the hypothesis that vendor-neutral sequ… (voir plus)ences decrease inter-vendor variability of T1, MTR and MTsat measurements. Methods We developed and deployed a vendor-neutral 3D spoiled gradient-echo (SPGR) sequence on three clinical scanners by two MRI vendors. We then acquired T1 maps on the ISMRM-NIST system phantom, as well as T1, MTR and MTsat maps in three healthy participants. We performed hierarchical shift function analysis in vivo to characterize the differences between scanners when the vendor-neutral sequence is used instead of commercial vendor implementations. Inter-vendor deviations were compared for statistical significance to test the hypothesis. Results In the phantom, the vendor-neutral sequence reduced inter-vendor differences from 8 - 19.4% to 0.2 - 5% with an overall accuracy improvement, reducing ground truth T1 deviations from 7 - 11% to 0.2 - 4%. In vivo we found that the variability between vendors is significantly reduced (p = 0.015) for all maps (T1, MTR and MTsat) using the vendor-neutral sequence. Conclusion We conclude that vendor-neutral workflows are feasible and compatible with clinical MRI scanners. The significant reduction of inter-vendor variability using vendor-neutral sequences has important implications for qMRI research and for the reliability of multicenter clinical trials.
2022-06-03
Magnetic Resonance in Medicine (publié)
doi.org
Genetic correlates of phenotypic heterogeneity in autism
Varun Warrier
Xinhe Zhang
Patrick Reed
Alexandra Havdahl
Tyler M. Moore
Freddy Cliquet
Claire Leblond
Thomas Rolland
Anders Rosengren
Antonia San Jose Hannah Daisy Jessica Jessica Claire Bethany Eva Tony Declan Rosemary Jack Jessica Nicola Meng-Chuan Gwilym Amber Emily Hisham Julia Sara Ambrosino Sarai Yvonne Tabitha Miriam Alyssia Iris Maarten Anna Ver Loren Nico Sarah Larry Carsten Annika Daniel Ineke Yvette Maartje Elzbieta Elodie Kristiina Rouslan Guillaume Yang-Min Thomas Caceres
Antonia San Jose Hannah Daisy Jessica Jessica Claire Betha Caceres Hayward Crawley Faulkner Sabet Ellis Oakle
Antonia San José Cáceres
Hannah Hayward
Daisy Crawley
Jessica Faulkner
Jessica Sabet
Claire Ellis
Beth Oakley
Eva Loth
Tony Charman … (voir 67 de plus)
Declan Murphy
Rosemary Holt
Jack Waldman
Jessica Upadhyay
Nicola Gunby
Meng-Chuan Lai
Gwilym Renouf
Amber N. V. Ruigrok
Emily Taylor
Hisham Ziauddeen
Julia Deakin
Sara Ambrosino di Bruttopilo
Sarai van Dijk
Yvonne Rijks
Tabitha Koops
Miriam Douma
Alyssia Spaan
Iris Selten
Maarten Steffers
Anna Ver Loren van Themaat
Nico Bast
Sarah Baumeister
Larry O’Dwyer
Carsten Bours
Annika Rausch
Daniel von Rhein
Ineke Cornelissen
Yvette de Bruin
Maartje Graauwmans
Elzbieta Kostrzewa
Elodie Cauvet
Kristiina Tammimies
Rouslan Sitnikow
Guillaume Dumas
Yang-Min Kim
Thomas Bourgeron
David M. Jonas Thomas Preben Bo Ole Merete Hougaard
David M. Hougaard
Jonas Bybjerg-Grauholm
Thomas Werge
Preben Bo Mortensen
Ole Mors
Merete Nordentoft
Dwaipayan Armandina Carrie Isabelle Tracey Paula Alex Graham J. Alexander E. P. Lidia V. Tal Madeline A. Deepak P. Jonathan Adhya
Dwaipayan Armandina Carrie Isabelle Tracey Paula Alex Graham Adhya Alamanza Allison Garvey Parsons Smith Tsompa
Dwaipayan Adhya
Armandina Alamanza
Carrie Allison
Isabelle Garvey
Tracey Parsons
Paula Smith
Alex Tsompanidis
Graham J. Burton
Alexander E. P. Heazell
Lidia V. Gabis
Tal Biron-Shental
Madeline A. Lancaster
Deepak P. Srivastava
Jonathan Mill
David H. Rowitch
Matthew E. Hurles
Daniel H. Geschwind
Anders D. Børglum
Elise B. Robinson
Jakob Grove
Hilary C. Martin
Simon Baron-Cohen
2022-06-02
Nature Genetics (publié)
doi.org
Monocular Robot Navigation with Self-Supervised Pretrained Vision Transformers
Miguel Saavedra-Ruiz
Sacha Morin
Liam Paull
In this work, we consider the problem of learning a perception model for monocular robot navigation using few annotated images. Using a Visi… (voir plus)on Transformer (ViT) pretrained with a label-free self-supervised method, we successfully train a coarse image segmentation model for the Duckietown environment using 70 training images. Our model performs coarse image segmentation at the
2022-06-02
2022 19th Conference on Robots and Vision (CRV) (publié)
doi.org
arxiv.org
Using Representation Expressiveness and Learnability to Evaluate Self-Supervised Learning Methods
Yuchen Lu
Zhen Liu
Aristide Baratin
Romain Laroche
Aaron Courville
Alessandro Sordoni
2022-06-02
ArXiv (prépublication)
arxiv.org
arxiv.org
Using Representation Expressiveness and Learnability to Evaluate Self-Supervised Learning Methods
Yuchen Lu
Zhen Liu
Aristide Baratin
Romain Laroche
Aaron Courville
Alessandro Sordoni
2022-06-02
ArXiv (prépublication)
arxiv.org
arxiv.org
Ageism and Artificial Intelligence: Protocol for a Scoping Review
Charlene H Chu
Kathleen Leslie
Jiamin Shi
Rune Nyrup
Andria Bianchi
Shehroz S Khan
Samira Abbasgholizadeh-Rahimi
Alexandra Lyn
Amanda Grenier
Background Artificial intelligence (AI) has emerged as a major driver of technological development in the 21st century, yet little attention… (voir plus) has been paid to algorithmic biases toward older adults. Objective This paper documents the search strategy and process for a scoping review exploring how age-related bias is encoded or amplified in AI systems as well as the corresponding legal and ethical implications. Methods The scoping review follows a 6-stage methodology framework developed by Arksey and O’Malley. The search strategy has been established in 6 databases. We will investigate the legal implications of ageism in AI by searching grey literature databases, targeted websites, and popular search engines and using an iterative search strategy. Studies meet the inclusion criteria if they are in English, peer-reviewed, available electronically in full text, and meet one of the following two additional criteria: (1) include “bias” related to AI in any application (eg, facial recognition) and (2) discuss bias related to the concept of old age or ageism. At least two reviewers will independently conduct the title, abstract, and full-text screening. Search results will be reported using the PRISMA-ScR (Preferred Reporting Items for Systematic Reviews and Meta-Analyses Extension for Scoping Reviews) reporting guideline. We will chart data on a structured form and conduct a thematic analysis to highlight the societal, legal, and ethical implications reported in the literature. Results The database searches resulted in 7595 records when the searches were piloted in November 2021. The scoping review will be completed by December 2022. Conclusions The findings will provide interdisciplinary insights into the extent of age-related bias in AI systems. The results will contribute foundational knowledge that can encourage multisectoral cooperation to ensure that AI is developed and deployed in a manner consistent with ethical values and human rights legislation as it relates to an older and aging population. We will publish the review findings in peer-reviewed journals and disseminate the key results with stakeholders via workshops and webinars. Trial Registration OSF Registries AMG5P; https://osf.io/amg5p International Registered Report Identifier (IRRID) DERR1-10.2196/33211
2022-06-01
JMIR Research Protocols (publié)
doi.org
Aligning artificial intelligence with climate change mitigation
Lynn H. Kaack
Priya L. Donti
Emma Strubell
George Yoshito Kamiya
Felix Creutzig
David Rolnick
2022-06-01
Nature Climate Change (publié)
doi.org
Brain-spinal cord interaction in long-term motor sequence learning in human: An fMRI study
Ali Khatibi
Shahabeddin Vahdat
Ovidiu Lungu
Jürgen Finsterbusch
Christian Büchel
Julien Cohen-Adad
V. Marchand-Pauvert
Julien Doyon
2022-06-01
NeuroImage (publié)
doi.org
Conjugate Adder Net (CAddNet) - a Space-Efficient Approximate CNN
Lulan Shen
Maryam Ziaeefard
Brett Meyer
Warren Gross
James J. Clark
The AdderNet was recently developed as a way to implement deep neural networks without needing multiplication operations to combine weights … (voir plus)and inputs. Instead, absolute values of the difference between weights and inputs are used, greatly reducing the gate-level implementation complexity. Training of AdderNets is challenging, however, and the loss curves during training tend to fluctuate significantly. In this paper we propose the Conjugate Adder Network, or CAddNet, which uses the difference between the absolute values of conjugate pairs of inputs and the weights. We show that this can be implemented simply via a single minimum operation, resulting in a roughly 50% reduction in logic gate complexity as compared with AdderNets. The CAddNet method also stabilizes training as compared with AdderNets, yielding training curves similar to standard CNNs.
2022-06-01
2022 IEEE/CVF Conference on Computer Vision and Pattern Recognition Workshops (CVPRW) (publié)
doi.org
Efficient Fine-Tuning of BERT Models on the Edge
Danilo Vucetic
Mohammadreza Tayaranian
Maryam Ziaeefard
James J. Clark
Brett Meyer
Warren Gross
Resource-constrained devices are increasingly the deployment targets of machine learning applications. Static models, however, do not always… (voir plus) suffice for dynamic environments. On-device training of models allows for quick adaptability to new scenarios. With the increasing size of deep neural networks, as noted with the likes of BERT and other natural language processing models, comes increased resource requirements, namely memory, computation, energy, and time. Furthermore, training is far more resource intensive than inference. Resource-constrained on-device learning is thus doubly difficult, especially with large BERT-like models. By reducing the memory usage of fine-tuning, pre-trained BERT models can become efficient enough to fine-tune on resource-constrained devices. We propose Freeze And ReconFigure (FAR), a memory-efficient training regime for BERT-like models that reduces the memory usage of activation maps during fine-tuning by avoiding unnecessary parameter updates. FAR reduces fine-tuning time on the DistilBERT model and CoLA dataset by 30 %, and time spent on memory operations by 47%. More broadly, reductions in metric performance on the GLUE and SQuAD datasets are around 1% on average.
2022-06-01
2022 IEEE International Symposium on Circuits and Systems (ISCAS) (publié)
doi.org
arxiv.org
High-Throughput and Energy-Efficient VLSI Architecture for Ordered Reliability Bits GRAND
Syed Mohsin Abbas
Thibaud Tonnellier
Furkan Ercan
Marwan Jalaleddine
Warren Gross
Ultrareliable low-latency communication (URLLC), a major 5G new-radio (NR) use case, is the key enabler for applications with strict reliabi… (voir plus)lity and latency requirements. These applications necessitate the use of short-length and high-rate channel codes. Guessing random additive noise decoding (GRAND) is a recently proposed maximum likelihood (ML) decoding technique for these short-length and high-rate codes. Rather than decoding the received vector, GRAND tries to infer the noise that corrupted the transmitted codeword during transmission through the communication channel. As a result, GRAND can decode any code, structured or unstructured. GRAND has hard-input as well as soft-input variants. Among these variants, ordered reliability bits GRAND (ORBGRAND) is a soft-input variant that outperforms hard-input GRAND and is suitable for parallel hardware implementation. This work reports the first hardware architecture for ORBGRAND, which achieves an average throughput of up to 42.5 Gb/s for a code length of 128 at a target frame error rate (FER) of 10−7. Furthermore, the proposed hardware can be used to decode any code as long as the length and rate constraints are met. In comparison to the GRAND with ABandonment (GRANDAB), a hard-input variant of GRAND, the proposed architecture enhances decoding performance by at least 2 dB. When compared to the state-of-the-art fast dynamic successive cancellation flip decoder (Fast-DSCF) using a 5G polar code (PC) (128, 105), the proposed ORBGRAND VLSI implementation has
2022-06-01
IEEE Transactions on Very Large Scale Integration (VLSI) Systems (publié)
doi.org
arxiv.org