Way of the Geophysicist https://the-geophysicist.com Machine Learning Research and Education in Geoscience Fri, 18 Oct 2019 12:03:37 +0000 en-US hourly 1 https://wordpress.org/?v=5.2.4 https://the-geophysicist.com/wp-content/uploads/2015/09/cropped-favicon-32x32.png Way of the Geophysicist https://the-geophysicist.com 32 32 Machine Learning in Geoscience with FORCE! – Friday Faves https://the-geophysicist.com/machine-learning-in-geoscience-with-force-friday-faves?utm_source=rss&utm_medium=rss&utm_campaign=machine-learning-in-geoscience-with-force-friday-faves https://the-geophysicist.com/machine-learning-in-geoscience-with-force-friday-faves#respond Fri, 18 Oct 2019 10:40:32 +0000 https://the-geophysicist.com/?p=2378

This week was a rough one. This is Friday Faves, I try to show you the cool stuff. The week was dominated by fraud and plagiarism, but we’re not about that today. Let’s look at the cool stuff that came out of Stavanger and the US and an awesome tool for open science instead! First […]

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This week was a rough one. This is Friday Faves, I try to show you the cool stuff. The week was dominated by fraud and plagiarism, but we’re not about that today. Let’s look at the cool stuff that came out of Stavanger and the US and an awesome tool for open science instead!

First All Female Space Walk

If you’re early, this is the live stream!

Open Science

Making Science open is often possible, but journals will obviously not send you to a free and open version of the same paper. So of course there is a browser extension that will show a little green ribbon on the side, if it automagically finds an open version. It will only show up when looking at scientific articles too. Get it here:

https://unpaywall.org/

FORCE Symposium videos

This year’s videos and presentations of the FORCE Machine Learning are online. Find the full playlist here with the presentations also available. Here’s one example

FORCE Hackathon

With the FORCE Symposium, there was also a hackathon organized in part by Matt Hall at Agile. His write up is here and (I know this is cheating) the video, which is in the playlist from before:

Matt Hall presents the project round-up of Force ML

Responsible AI

Our professional societies are luckily not just getting in on the AI hype, but creating space to discuss how to responsibly introduce AI into Earth Science:

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The 99%, an amazing new GAN and noble Lithium– Friday Faves https://the-geophysicist.com/the-99-an-amazing-new-gan-and-noble-lithium-friday-faves?utm_source=rss&utm_medium=rss&utm_campaign=the-99-an-amazing-new-gan-and-noble-lithium-friday-faves https://the-geophysicist.com/the-99-an-amazing-new-gan-and-noble-lithium-friday-faves#respond Fri, 11 Oct 2019 12:55:19 +0000 https://the-geophysicist.com/?p=2365

This week in the Friday Faves we have a cheeky Tweet, a new GAN that might find some amazing applications in geophysics and the Nobel Prize for chemistry. 99% Let’s start out with some wisdom of the creator of Keras: VSCode Universe now with Jupyter My editor of choice is VSCode with the Python extension. […]

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This week in the Friday Faves we have a cheeky Tweet, a new GAN that might find some amazing applications in geophysics and the Nobel Prize for chemistry.

99%

Let’s start out with some wisdom of the creator of Keras:

VSCode Universe now with Jupyter

My editor of choice is VSCode with the Python extension. Finally, they added native Jupyter support. Read the announcement and then some.

WaveForms in a GAN

In a story that only the internet can write, Marco Pasini experimented with an unpaired GAN architecture. This has been done by pix2pix before, which brought me many hackathon projects and even the first application of GANs in geophysics ever. But those are image-based. MelGAN is waveform-based on different length tracks!

I love the idea of combining siamese networks to stabilize the unpaired training, but read for yourself, because the reddit community /r/machinelearning encouraged Pasini to write up a paper!

Considering the trajectory of pix2pix, which led us to almost believable DeepFakes today, it will be exciting to see what this brings in the future. Moreover, waveform transfer may solve some technological problems of matching vintage oil-based streamer seismic data sets to modern 4D acquisitions.

Pytorch 1.3 is out!

On another note. Just a week after Tensorflow 2.0 finally dropped their big revamp, PyTorch bring mobile support, quantization and other nice tools for researchers.

Nobel Prize goes to Lithium Batteries

You’re probably reading this on a device run by Lithium-Ion batteries. Why does this warrant a Nobel Prize? If you get it wrong you get the Samsung Galaxy Note 7. If you get it right, you get computers more powerful than the machines that sent humanity to the moon, in our pockets running for a day and charging in below an hour.

In a world that is slowly edging toward de-carbonization, energy storage is the biggest problem to tackle. Learn something about Lithium batteries and take a look inside:

Chemists reacting to announcement of Nobel Prize

Nobel Press Release: “They created a rechargeable world

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The Hidden Cost on Mental Health of Living Abroad https://the-geophysicist.com/the-hidden-cost-on-health-of-living-abroad?utm_source=rss&utm_medium=rss&utm_campaign=the-hidden-cost-on-health-of-living-abroad https://the-geophysicist.com/the-hidden-cost-on-health-of-living-abroad#respond Thu, 10 Oct 2019 19:20:53 +0000 https://the-geophysicist.com/?p=2353 International Boundaries by Jim Witkowski on Unsplash

It is World Mental Health Day. People are sharing valuable resources and personal stories on Twitter and Instagram. Usually, I miss these days, but it just so happens that I have a story or two when it comes to mental health. When I finished my studies I found a job in the happiest (or so) […]

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International Boundaries by Jim Witkowski on Unsplash

It is World Mental Health Day. People are sharing valuable resources and personal stories on Twitter and Instagram. Usually, I miss these days, but it just so happens that I have a story or two when it comes to mental health.

When I finished my studies I found a job in the happiest (or so) country in the world: Denmark. I got a Ph.D. position here which gives me great opportunities, one of which was spending a year at Heriot-Watt University in Scotland, UK. Before this turns into too much of a humblebrag, back to the facts:

I’m a EU citizen, that means, Denmark provides universal health care without much hassle for me. However, it’s important to note, that you get assigned to a Doctor’s office. My first Doctor was a very nice older Dane. As it goes for most well-educated Danes, his English was flawless when I came to his office. I needed a refill for my prescription of anti-depressants. The pills that kept me alive ever since I experienced Burnout in university.

The doctor was very nice and renewed my prescription without a hassle. Nevertheless, he gave me some advice to eat well, stay hydrated and try working out. Advice I’m used to when general practitioners hear, I have depression. Good advice, which is why I followed it for years already by that point. Well-meaning advice is common when it comes to mental health.

Have you tried eating healthy and working out?

Scotland, in the UK, has a very similar system. You get assigned to a Doctor’s office and as an EU citizen (for now) you are insured. This is great, right? In the United States you’d already be in debt by this point. But this positive experience with the nice Dane stopped when I had to move. You get assigned to a new Doctor in a new place. The new Doctor suggested to work out and eat better, I don’t need the medication.

The only way to get a diagnosis would be to go to a specialist like a psychiatrist. Any country I have ever lived, psychiatrists and psychologists have waiting lists for months, sometimes years. Moreover, following the law of the market, they are in high demand. Psychiatrists don’t need a good website. The practice phone doesn’t even have to be in English. Would you like to ask your new native colleagues to translate the phone message of the psychiatrist’s office for you? I didn’t either.

Here are some of the possible side effects of quitting anti-depressants cold turkey because you’re at the whim of a new doctor:

  • anxiety
  • nightmares
  • trouble sleeping
  • depression and mood swings
  • nausea
  • abdominal cramping
  • flu-like symptoms
  • headache
  • sweating

The benefit of healthcare and insurance might not mean you will get mental health care abroad.

In a modern world, where you have to move to the job, you get to sample a lot of assigned doctors. This is not an isolated case, especially general practitioners can be reluctant renewing existing prescriptions, but are generous with their helpful advice. Both Denmark and Scotland have beautiful nature for leisurely walks after all.

Psychotherapy and Others

Does Psychotherapy work? Do pills help?

Unfortunately, it does not stop there. Nowadays, it is still very rare for therapy to be covered by any insurance. There may be alternatives, even if you’re “just down” for a couple of weeks. It doesn’t need to be the hospital or psych ward.

Is there hope?

Podcast that always makes me smile.

Sometimes universities may provide a psychological service, some therapists might cut you a deal if they can, but it is at a cost. While in theory, Betterhelp and Talkspace sound really good, they never worked for me. It was text-only expensive chatting with a therapist that had enough other clients to deal with. Maybe it’s a cultural problem, seeing that all therapists on those platforms are US-based.

These days, although possibly a cliché, support groups may help you. Sometimes having someone that goes through something similar, helps more than the seemingly all-knowing therapist with their helpful tips.

Personally, I have worked through many problems in therapy. Medication has helped me wade through the mess that is a Master’s thesis. And today, my friends, healthy habits, and making sure I’m in a positive environment, have made me weather any storm to date. In fact, I’m handing in my Ph.D. thesis soon.

My hope for us is to reduce the stigma. My hope for you is that you get the help you need, whether you moved abroad or not.

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TF2, Physics in GCNs and Aftershocks – Friday Faves https://the-geophysicist.com/tf2-physics-in-gcns-and-aftershocks-friday-faves?utm_source=rss&utm_medium=rss&utm_campaign=tf2-physics-in-gcns-and-aftershocks-friday-faves https://the-geophysicist.com/tf2-physics-in-gcns-and-aftershocks-friday-faves#respond Fri, 04 Oct 2019 10:37:53 +0000 https://the-geophysicist.com/?p=2337

In this week’s Friday Faves, we have Tensorflow 2 dropping and a beautiful bonus, next level physics-based ML, and a problem with a Harvard deep learning paper. Tensorflow 2 for Researchers Tensorflow 2.0 dropped this week and it has Eager Execution (read “normal behaviour”) per default and the Keras API per default. If you’re familiar […]

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In this week’s Friday Faves, we have Tensorflow 2 dropping and a beautiful bonus, next level physics-based ML, and a problem with a Harvard deep learning paper.

Tensorflow 2 for Researchers

Tensorflow 2.0 dropped this week and it has Eager Execution (read “normal behaviour”) per default and the Keras API per default.

If you’re familiar with PyTorch, you’ll wonder “that’s news?” but you can now use one of three, which for PyTorch users will be another “that’s news?”

Depending on how reproducible and complicated your model gets, you’ll need to make that choice. I have personally yet to use Subclassing, but I hear good things. Specifically, good things by François Chollet, the creator of Keras and Google employee. He compiled a truly amazing thread for researchers:

If you’re too busy, you can go straight to the Google Colab. But I really recommend looking at the thread, there are some gems in there.

Physics-based DeepMind

If you’ve been around any geophysics or machine learning conference, you have seen the hype of physics-based machine learning. And personally, I really like the interesting combinations of known methods with neural networks. So DeepMind swoops in and combines some interesting concepts, namely Hamiltonian physics, graph neural networks and a sprinkling of Runge Kutta.

The Aftershock to the Aftershock AI

Earlier 2019 Google and Harvard published a paper in Nature, predicting aftershock patterns with a deep neural network. It did not take long for people to poke holes in the paper. It did not take long for the Harvard scientists to respond indignantly. It did, however, take a bit to get the following preprint published in Nature Matters Arising:

One neuron versus deep learning in aftershock prediction

https://arxiv.org/abs/1904.01983 and the Nature paper is available here: https://www.nature.com/articles/s41586-019-1582-8.epdf

It shows the problems of Deep Learning being terribly publishable, but basic data science principle not being followed, aka: did you try a simpler model?

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GIS, Fossils and Loads of Data – Friday Faves https://the-geophysicist.com/gis-fossils-and-loads-of-data-friday-faves?utm_source=rss&utm_medium=rss&utm_campaign=gis-fossils-and-loads-of-data-friday-faves https://the-geophysicist.com/gis-fossils-and-loads-of-data-friday-faves#respond Fri, 27 Sep 2019 12:00:05 +0000 https://the-geophysicist.com/?p=2274

This week, we have loads of geoscience-y favourites. Between great Jupyter widgets, augmented reality and a huge new dataset to play with, in the Friday Faves. Geoscience and Python Martin Renou gave a fantastic talk about Jupyter Voila at EuroScipy. He tweeted out their newest developments in iPyLeaflet, which brings GIS capabilities to Jupyter. Once […]

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This week, we have loads of geoscience-y favourites. Between great Jupyter widgets, augmented reality and a huge new dataset to play with, in the Friday Faves.

Geoscience and Python

Martin Renou gave a fantastic talk about Jupyter Voila at EuroScipy. He tweeted out their newest developments in iPyLeaflet, which brings GIS capabilities to Jupyter.

Velocities with iPyLeaflet

Once you got that done, you might even build a Dashboard using Voila after. Check out the full Blog post here, it’s awe-inspiring. So many possibilities, I thought should be much harder to do!

Geoscience and Augmented Reality

In this amazing Tweet, the University of Wyoming built a killer application for Paleontology, combining AR and 3D models for education.

What’s more?

You can print them yourself! And get the Apps here:

Get Fossil App on Google Play
Get Fossil App on Apple App Store

Machine Learning in Geoscience

GeoProvider (http://geoprovider.no/) has sponsored the preparation of a new dataset of 1240 Norwegian wells was made available CC-BY 4.0.

The dataset includes core porosity, permeability and lithology, available on Google Drive. The data are licensed CC-BY 4.0. The dataset contains 270000 individual core plug measurements, 6500m of depth referenced core images and digitized core log descriptions. A I first heard about a new dataset via Peter Borman on Software Underground.

Announcement of Geoprovider Dataset

Brendon Hall has further popularized the dataset:

I can’t wait to read the roll up from the event, to see what people came up with this year.

Machine Learning for Code

Everyone knows, searching for code is at the core of getting software done.

But it turns out, searching code is a really hard problem. So GitHub teamed up with Microsoft Research Cambridge to provide 2 million code-comment pairs (out of 6 million total) to train a new machine learning solution to make coding a bit less of a hassle.

The Blog Post is here: https://github.blog/
The Github Repo is here: https://github.com/github/CodeSearchNet
The Leaderboard is provided by Weights & Biases with the submission instructions here.

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Hide & Seek – Friday Faves https://the-geophysicist.com/hide-seek-friday-faves?utm_source=rss&utm_medium=rss&utm_campaign=hide-seek-friday-faves https://the-geophysicist.com/hide-seek-friday-faves#respond Fri, 20 Sep 2019 12:00:08 +0000 https://the-geophysicist.com/?p=2255

This week was a special week, as the SEG Annual Meeting 2019 in San Antonio was in full progress and the FORCE hackathon in Stavanger with an accompanying Symposium is in full progress. Here are my highlights of the week, that I’d like to share with you. Geoscience I talked to some contacts that visited […]

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This week was a special week, as the SEG Annual Meeting 2019 in San Antonio was in full progress and the FORCE hackathon in Stavanger with an accompanying Symposium is in full progress. Here are my highlights of the week, that I’d like to share with you.

Geoscience

I talked to some contacts that visited SEG. GANs seem to be in full force. Physics-based ML is really hot. Generalization, benchmarks and meaningful metrics in geoscience are a problem holding the industry and research back. Satyakee Sen has written a nice summary on LinkedIn that deserves more eyes:

Interesting Post by Satyakee Sen
https://www.linkedin.com/posts/satyakeesen_seg19-activity-6580557209682395137-ScTH

In the context of physics-based ML, you may also enjoy one of my more recent preprints here: https://arxiv.org/abs/1904.02254

Machine Learning

Say what you will about OpenAI (for example the irony of the “Open”), the following video describing how agents learn the game hide & seek through reinforcement learning is both adorable and informative:

Gadget

I organize both my life and my Ph.D. in an app called Notion. I happily paid for it, but they recently made Notion available to educators and students for free. Notion did, in fact, replace Evernote for me, after they upped their prices to an unreasonable amount.

If you sign up through my link, you’ll get an extra 5$ in credit, and I’ll get a small kickback as well: https://www.notion.so/

I already had an account and had to change my email to my student email. The official Notion announcement explains how to join the Educators plan.

Check the full announcement here: https://www.notion.so/notion/Notion-for-students-teachers-adc631df15ee4ab9a7a33dd50f4c16fe

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The Only Moat worthy for a Geologists Lair https://the-geophysicist.com/the-only-moat-worthy-for-a-geologists-lair?utm_source=rss&utm_medium=rss&utm_campaign=the-only-moat-worthy-for-a-geologists-lair https://the-geophysicist.com/the-only-moat-worthy-for-a-geologists-lair#respond Mon, 02 Sep 2019 10:39:44 +0000 https://the-geophysicist.com/?p=2247

Did you ever wonder how to protect your lair once you turn to the dark side? (Listen up Elon) Randal Munroe of xkcd fame collaborated with Minute Physics to solve this problem. How to build a Lava Moat: It’s a collaboration to promote the new book “How To: Absurd Scientific Advice for Common Real-World Problems“. […]

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Did you ever wonder how to protect your lair once you turn to the dark side? (Listen up Elon)

Randal Munroe of xkcd fame collaborated with Minute Physics to solve this problem. How to build a Lava Moat:

It’s a collaboration to promote the new book “How To: Absurd Scientific Advice for Common Real-World Problems“. Since “What If” and “Thing Explainer” I expect this book to, once again, be fantastically absurd but scientifically accurate.

xkcd: Geologist https://xkcd.com/1198/

If you don’t know xkcd yet, get on over there and lose a couple of hours. It’s a webcomic about all sorts nerdery included geoscience! The comic has gained such a following that fans submitted Munroe’s name for an Asteroid.

xkcd: Seismic Waves https://xkcd.com/723/

So go ahead, watch the awesome video, sink some time into xkcd, then go on and enjoy the books!

Get “How To” on Amazon

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How do we thrive in the AI industrial revolution? https://the-geophysicist.com/how-do-we-thrive-in-the-ai-industrial-revolution?utm_source=rss&utm_medium=rss&utm_campaign=how-do-we-thrive-in-the-ai-industrial-revolution https://the-geophysicist.com/how-do-we-thrive-in-the-ai-industrial-revolution#respond Fri, 26 Jul 2019 19:28:11 +0000 http://the-geophysicist.com/?p=2232

Our world is changing and skilled workers are being replaced by intelligent systems. Where do the strengths of humans lie? Working in ML and taking the stage, whenever anyone lets me, I am no stranger to the question: What is AI good at? What are humans good at? So I was invited to give a […]

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Our world is changing and skilled workers are being replaced by intelligent systems. Where do the strengths of humans lie?

Working in ML and taking the stage, whenever anyone lets me, I am no stranger to the question:

What is AI good at?

What are humans good at?

So I was invited to give a talk on exactly that topic. Here are the recordings. Unfortunately, I made a blunder in the recording and couldn’t record better audio. Let me know if you’re interested in me diving further into this matter.

That’s it for AI, how do humans stack up?

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Kaggle Days Two – Googling in San Francisco https://the-geophysicist.com/kaggle-days-two?utm_source=rss&utm_medium=rss&utm_campaign=kaggle-days-two Tue, 18 Jun 2019 08:24:07 +0000 http://the-geophysicist.com/?p=2223 Kaggle Days SF Group Photo

Have you met our Lord and Saviour AutoML? Day two of the Kaggle Days was, what it had to be, a competition. Very interesting to be in a room with Grandmasters, Pros and then there’s me. But the real struggle was for everyone to compete with the AutoML solutions by Google and H2O.ai. One of […]

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Kaggle Days SF Group Photo

Have you met our Lord and Saviour AutoML?

Day two of the Kaggle Days was, what it had to be, a competition. Very interesting to be in a room with Grandmasters, Pros and then there’s me. But the real struggle was for everyone to compete with the AutoML solutions by Google and H2O.ai.

One of the, if not the main author behind Google’s implementation was on stage and I even got to chat with him about their approach, which is exactly what I came to San Francisco for, rub shoulders with the giants.

However, AutoML was beat by a good ol’ home-grown data science solution, which you can read more about on LinkedIn Write Up of Winning Solution. It was even covered on Wired.

Data Science wasn’t all of it though. The people were amazing. The party was fantastic. Access to Google Next and the Google Next party with Gwen Stefani as main act was surprisingly fun. If it ever comes to your continent, I definitely recommend going.

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Meet me at the EAGE Annual 2019 https://the-geophysicist.com/meet-me-at-the-eage-annual-2019?utm_source=rss&utm_medium=rss&utm_campaign=meet-me-at-the-eage-annual-2019 Thu, 30 May 2019 06:14:52 +0000 http://the-geophysicist.com/?p=2218 Schedule at EAGE Annual 2019

It’s the time of the year. The large applied geoscientists conference is coming up, the EAGE Annual Meeting. This year the EAGE is coming to London. I’ll be there as well and I’ll have a couple of speaking engagements, I’d like to invite you along to. Hackathon and Sprint I love the newly created ritual […]

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Schedule at EAGE Annual 2019

It’s the time of the year. The large applied geoscientists conference is coming up, the EAGE Annual Meeting. This year the EAGE is coming to London. I’ll be there as well and I’ll have a couple of speaking engagements, I’d like to invite you along to.

Hackathon and Sprint

I love the newly created ritual of creating an off-brand hackathon accompanying the EAGE annual event. This year, Agile* stepped down as an organizer, but still stepped up as a sponsor for the London hack.

I am planning to work on two general projects. On June first, there is a global TensorFlow Docs Sprint that I want to spend some time on.

But mainly I would like to work on the subsurface package, we started working on at Transform 2019. It will be a central package at the subsurface geoscience Python stack. So, maybe join in the fun?

Monday Workshop

I’ll present work from my collaboration with ETLP Team at Heriot Watt University on including physics in the neural network architecture. I think Lukas Mosser, Olivier Dubrule, Mark Thompson, and Duncan Irving have put a lot of thought in this event. I’m looking forward to an insightful and inspiring event. Just take a look at the (abridged) description:

📝 The workshop will discuss recently developed applications of ML, and the challenges and opportunities associated with the development of these applications in the petroleum industry. The first half of the workshop will include:

  • Speed Posters
  • Where Artificial Intelligence and DL are going in the industry (digital leaders / major operators)
  • Technical presentations (petroleum companies / academia)

The second half of the workshop will be dedicated to:

  • Recent industry initiatives on data availability, open communities, cloud computing and training
  • Perspectives from outside the industry
  • Structured, themed and interactive exchanges with the audience.

My talk will be focusing on:

Including Physics in Deep Learning

An example from 4D seismic pressure saturation inversion

Geoscience data often have to rely on strong priors in the face of uncertainty. Additionally, we often try to detect or model anomalous sparse data that can appear as an outlier in machine learning models. These are classic examples of imbalanced learning. Approaching these problems can benefit from including prior information from physics models or transforming data to a beneficial domain. We show an example of including physical information in the architecture of a neural network as prior information. We go on to present noise injection at training time to successfully transfer the network from synthetic data to field data.

Check it out on ArXiv and come to the workshop.

Tuesday and Wednesday Career Advice

Someone thought it’s a good idea for me to be on a stage and give career advice. I find this relatively funny, as I’m mainly bumbling my way around science, while being pleasant to work with. If you’d like to hear me speak anyways, come by the EAGE Career Advice Center.

On Tuesday, June 4th at 10:00, I hope to have a conversation on

Non-linear careers: Leveraging social media to build a career that matters

On Wednesday, June 5th around lunchtime at 12:30, we’ll chat around

Making sense of AI for a career in a changing industry

I’ll see you at ExCel in London!

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