AI and biology

Timings (Europe/CET)	Speaker
12:00 – 13:30	Registration and light refreshments
13:45 – 17:15	Session 1: Challenging the state of the art Chairs: Anna Kreshuk and Mohammed AlQuraishi
13:30 – 13:45	Opening remarks
13:45 – 14:15	Question everything: A critical reflection of medical imaging AI Lena Maier-Hein – German Cancer Research Center, Germany
14:15 – 14:30	GROVER: Building a language model of the human genome Melissa Sanabria – Dresden University of Technology, Germany
14:30 – 14:45	Deep mutational scanning of entire human protein interaction domain families Guillaume Diss (Virtual speaker) – Friedrich Miescher Institute for Biomedical Research, Germany
14:45 – 15:15	Coffee break and meet the speakers of day one Lena Maier-Hein, Michael Bronstein, Mihaela van der Schaar
15:15 – 15:45	To be presented on-site Michael Bronstein – University of Oxford, UK
15:45 – 16:00	Protein engineering using transformer-based energy landscape approximation Evgenii Lobzaev – University of Edinburgh, UK
16:00 – 16:15	AI-based biomarker identification and profiling in heterogeneous prostate tumors Kathleen Marchal – Ghent University/IMEC, Belgium
16:15 – 16:45	Beyond Causality: Discovering and Analyzing the Governing Equations of Medicine Mihaela van der Schaar – University of Cambridge, UK
16:45 – 17:15	Flash talks for poster session 1: Anna Poetsch (41), Bernard Ciraulo (55), Ava Khamseh (87), Christian Kolter (93), Dan Liu (103), Niklas Schmacke (143), Ron Schwessinger (145), Konstantina Tzavella (157)
17:15 – 18:45	Poster session 1 (odd numbers)
18:45 – 20:15	Dinner in canteen
20:15 – 22:00	After dinner drinks in the ATC Foyer
20:15	Conference shuttle bus to all stops downtown including ISG
21:00	Conference shuttle bus to all stops downtown including ISG
22:00	Conference shuttle bus to all stops downtown including ISG

Timings (Europe/CET)	Speaker
08:45 – 9:00	Arrival and coffee
09:00 – 12:00	Session 2: cross-domain, cross-modality learning Chairs: Jong Chul Ye and Uwe Ohler
09:00 – 09:30	Learning a foundational representation of the cellular niche Fabian Theis – Helmholtz Munich, Germany
09:30 – 09:45	SpaceTree: Deciphering Tumor Microenvironments by joint modeling of cell states and genotype-phenotype relationships in spatial omics data Olga Lazareva – EMBL/DKFZ, Germany
09:45 – 10:00	Accurately predicting single-cell drug responses of progressed melanoma patients Gabriele Gut – University Hospital Zürich, Switzerland
10:00 – 10:30	Coffee break and meet the Editors Gemma K. Alderton, Deputy Editor, Insights, Science George Caputa, Senior Editor, Nature Research Rituparna Chakrabarti, Senior Scientific Editor, iScience Qian Cheng, Associate Editor (Computational Biology), Nature Communications Mike Fletcher, Senior Editor, Nature Genetics Sara Osman, Associate Editor, Nature Structural & Molecular Biology Maria Polychronidou, Senior Editor, Molecular Systems Biology Arunima Singh, Senior Editor, Nature Methods
10:30 – 11:00	Machine learning for reconstructing protein structure and dynamics from cryo-EM images Ellen Zhong – Princeton University, USA
11:00 – 11:15	AI based protein stability prediction from sequences and structures and its application to the engineering of plastic-degrading enzymes Ania Di Pede – Mattatelli, Institute of Marine Sciences – ICM-CSIC Barcelona, Spain
11:15 – 11:30	Regression on latent spaces predicts multi-condition single-cell gene expression Constantin Ahlmann-Eltze – EMBL Heidelberg, Germany
11:30 – 12:00	To be presented on-site Sami Kaski – Aalto University and University of Helsinki, Finland
12:00 – 13:30	Lunch
13:30 – 16:00	Session 3: Explainable AI and its role in science Chairs: Leopold Parts and Alex Rives
13:30 – 14:00	Causal Representation Learning and Optimal Design of Interventions Caroline Uhler – Broad Institute of MIT and Harvard, USA
14:00 – 14:15	Learning and visualizing the morphological differences between synapses of different types Diane Adjavon – HHMI – Janelia, USA
14:15 – 14:30	MoCHI: mechanistic AI models from deep mutational scanning data Andre Faure – ALLOX, Spain
14:30 – 15:00	Coffee break and meet the speakers of day two Fabian Theis, Ellen Zhong, Sami Kaski, Caroline Uhler, Trey Ideker
15:00 – 15:30	Assembling a Digital Tumor Cell Trey Ideker – University of California, San Diego, USA
15:30 – 15:45	Variational autoencoder for design of synthetic viral vector serotypes Michael Garton (Virtual speaker) – University of Toronto, Canada
15:45 – 16:00	Comprehensive characterization of human druggable pockets through novel binding site descriptors built upon inverse docking Arnau Comajuncosa-Creus – IRB Barcelona, Spain
16:00	Free evening – downtown Heidelberg
16:15	Conference shuttle bus to all stops downtown including ISG

Timings (Europe/CET)	Speaker
08:45 – 09:00	Arrival and coffee
09:00 – 12:15	Session 4: from algorithms to biology Chairs: Ellen Zhong and Florian Jug
09:00 – 09:30	The convergence of genomics, imaging and AI for understanding life Ewan Birney – EMBL-EBI Hinxton, Cambridge UK
09:30 – 09:45	Modeling regulatory networks with single cell expression data Uwe Ohler – Max Delbrück Center for Molecular Medicine and Humboldt University of Berlin, Germany
09:45 – 10:00	Pre-trained molecular representations can aid antimicrobial discovery Roberto Olayo – Institute for Statistics, LMU München, Germany
10:00 – 10:30	Coffee break
10:30 – 11:00	Enabling discovery by in-cell structural biology: challenges in cryo-electron tomography data mining and integration Julia Mahamid – EMBL Heidelberg, Germany Not available on demand
11:00 – 11:15	Integration of variant annotations using deep set networks boosts rare variant association genetics Eva Holtkamp – Technical University of Munich, Germany
11:15 – 11:30	Exploiting time to phenotype cell morphology Julian Pietsch – Max Planck Institute for Terrestrial Microbiology, Germany
11:30 – 12:15	Panel discussion: From algorithms to biology Moderator: Emma Lundberg
12:15 – 13:45	Lunch
13:45 – 16:45	Session 5: connections to the wider AI field Chairs: Oliver Stegle and Samuel Kaski
13:45 – 14:15	Towards a Complete Structural Map of the Human Proteome Using AlphaFold Arne Elofsson – SciLifeLab, Sweden
14:15 – 14:30	Towards transformer-based tracking in live-cell microscopy Benjamin Galusser – EPFL, Switzerland
14:30 – 14:45	Can AI predict how human cells interpret dinosaur DNA? Leopold Parts – The Wellcome Trust Sanger Institute, UK
14:45 – 15:15	Coffee break and meet the speakers of day three Ewan Birney, Julia Mahamid, Arne Elofsson, Alex Rives, Jong Chul Ye
15:15 – 15:45	Language Modeling at the Scale of Evolution Alex Rives – EvolutionaryScale, USA Not available on demand
15:45 – 16:00	BioCypher and BioChatter: open frameworks for AI-ready biomedical knowledge graphs and their integration with current Large Language Models Sebastian Lobentanzer – Heidelberg University and Heidelberg University Hospital, Germany
16:00 – 16:30	Enlarging the Capability of Diffusion Models for Inverse Problems in Imaging Jong Chul Ye – Korea Advanced Institute of Science and Technology (KAIST), Korea
16:30 – 16:45	PeTriBERT : Augmenting BERT with tridimensional encoding for inverse protein folding and design Baldwin Dumortier – CNRS, France
16:45 – 17:15	Flash talks for poster session 2: Cedric Allier (42). Noah Bruderer (52), Adele de Hoffer (58), Albert Dominguez Mantes (62), Lucas Farndale (64), Lucien Hinderling (76), Grzegorz Kudla (96), Xiaomei Li (100), Paulyna Magaña (106), Abdelrahman Mahmoud (108), Roman Bushuiev (138), Yuxin Shen (148)
17:15 – 18:45	Poster session 2 (even numbers)
18:45 – 21:00	Conference dinner
21:00 – 00:00	Party with The Chaotics band
20:30	Conference shuttle bus to all stops downtown including ISG
21:30	Conference shuttle bus to all stops downtown including ISG
22:30	Conference shuttle bus to all stops downtown including ISG
23:59	Conference shuttle bus to all stops downtown including ISG

Timings (Europe/CET)	Speaker
08:45 – 09:00	Arrival and coffee
09:00 – 13:00	Session 6: generative modeling from drug design to synthetic images Chairs: Wolfgang Huber and Arne Eloffson
09:00 – 09:30	From Content-Aware Denoising to Semantic Unmixing of Microscopy Data – how AI is and will transform scientific image data analysis in the life sciences Florian Jug – Human Technopole, Italy
09:30 – 09:45	Controllable generative modelling – lessons from protein design Kieran Didi – University of Cambridge, UK
09:45 – 10:15	Some thoughts on machine learning-based protein engineering Jennifer Listgarten – University of California, Berkeley, USA
10:15 – 10:45	Coffee Break and Meet the speakers of day four Florian Jug, Jennifer Listgarten, Mohammed AlQuraishi
10:45 – 11:45	Panel discussion: Industry vs Academia Moderators: Wolfgang Huber and Oliver Stegle
11:45 – 12:00	Seedling: a scoring and generation framework for protein-ligand co-folding William McCorkindale – Charm Therapeutics, UK
12:00 – 12:30	To be presented on-site Mohammed AlQuraishi – Columbia University, USA
12:30 – 12:45	Efficient and accurate sequence generation with small-scale protein language models Yaiza Serrano – Nostrum Biodiscovery, Spain
12:45 – 13:00	Closing Remarks and Poster Prize Announcements
13:00	Packed lunch and departure
13:20	Conference shuttle bus to all stops downtown including ISG
13:20	Conference shuttle bus to Frankfurt Am Main International Airport

On-site registration fees include admission, conference materials, meals and coffee breaks. Participants are expected to book and pay their own accommodation and travel expenses.

Virtual registration fees include access to all of the talks (live streamed and on-demand) and the facility to submit questions.

On-site Academia	€725
On-site PhD Student	€625
On-site Industry	€925
On-site Journal Editors*	€300
Virtual Academia	€225
Virtual PhD Student	€175
Virtual Industry	€275

* Editors from scientific journals are allowed to attend at a reduced rate, but asked to contribute to the conference in return by taking part in ‘meet the editors’ sessions or other planned activities within the programme.

A letter to support your visa application will be issued, on request, once payment of the registration fee is confirmed. We recommend that you book your visa appointment as soon as possible, to avoid any delay with your visa application.

Accredited journalists may be eligible to register for complimentary press registration. Registrants may be required to provide accreditation or equivalent proof of press membership after registration. Please contact Charlotte Courtney for more information. Please note that we do not offer complimentary registrations for editors of scientific journals.

Confirmation and payment

Registration will be on a first come, first served basis. Your place can only be confirmed after payment of the registration fee. If you are added to our waiting list, please consider taking advantage of our offerings to participate virtually.

On-site participants: Types of payments accepted are international bank transfers and credit card payments. 

Virtual participants: We are only able to accept card payments. In exceptional cases we can accept bank transfers. Please contact events@embl.de for details.

Abstract submission

Only participants registering to attend the on-site event are eligible to submit an abstract. Abstracts will not be accepted from virtual participants.

After registration you can submit your abstract via a separate link that will be provided in the email confirmation. Alternatively, you can access the link on the confirmation page directly after registering. The same login credentials are used for both processes.

Please note:

Abstract body: The limit of 2000 characters refers to manually typed text and excludes spaces. If an error occurs try using a different web browser (preferably Google Chrome or Mozilla Firefox).

If you copy-paste the text into the form, hidden formatting might still be included which may cause the text to exceed the 2,000 character limit resulting in an error message. We recommend you clear all formatting before pasting in the text.

If you have special symbols in your text, make sure you are using Unicode characters, otherwise these will not be recognised.

Title: The title should not exceed 20 words. Only the first word of the title should start with a capital letter and the rest should be lowercase.

Authors and affiliations: Please fill in the author’s details as requested in the online form. The compulsory fields are: First Name, Last Name, Organisation Name (Affiliation or Company), Country and Email.

Kindly mark only one author in the role of First Author and please don’t forget to indicate who will be the Presenter.

Please enter your co-authors correctly via the system by adding accounts together with their organisation/institute. Do not copy-paste them into the body of the abstract text, as they will not be indexed in the abstract book.

Presentation types: When submitting your abstract, you can apply for an oral or poster presentation. A selection process will take place with the results announced 2-3 weeks after the abstract submission deadline.

For detailed instructions on how to submit a conference abstract, follow the instructions provided in this video.

Please check our FAQs pages for further information on how to submit an abstract.

Financial assistance

Limited financial assistance is provided by the EMBL Advanced Training Centre Corporate Partnership Programme and EMBO in the form of registration fee waivers, travel grants and childcare grants. 

Your place in the meeting is only confirmed by paying the registration fee, which is mandatory even when receiving a fee waiver.

Registration fee waiver

The fee waiver will cover the registration sum that you have paid to attend the course or conference.

Travel grant

The travel grant will cover the cost of travel to an on-site event (airfare, train, bus, taxi, accommodation, visa, and/or registration fees*) and is provided up to specified caps which are normally as follows:

–up to €400 for participants travelling to an EMBL Conference or EMBO|EMBL Symposium from within Europe.

–up to €1000 for participants travelling to an EMBL Conference or EMBO|EMBL Symposium from outside Europe.

–up to €500 for any participant travelling to an EMBO Workshop.

–up to €1000 for any participant working in Chile, India, Singapore or Taiwan travelling to an EMBO Workshop.

–up to €700 for any participant working in Croatia, Czech Republic, Estonia, Greece, Hungary, Italy, Lithuania, Luxembourg, Poland, Slovenia, and Turkey travelling to an EMBO Workshop.

*Registration fees are only covered for EMBO Workshops

The organisers may reduce the grant cap to accommodate more participants. Recipients will be notified of their travel cap amount when they are informed of the outcome of their application. Original receipts must be provided with your signature for all costs incurred within two months of completion of travel. Scanned copies cannot be accepted.

Childcare grant

There is the possibility to apply for a childcare grant to offset child care costs incurred by participants, speakers and organisers when attending a conference. Eligible costs include (but are not limited to) fees for a baby-sitter or child-care facility and travel costs for a caregiver. Please note that priority will be given to early stage researchers. In order to apply for this grant, you must be registered by the abstract submission deadline. There is a limited amount of funding available for the childcare grants and funds will be distributed amongst eligible applicants.

Application

On-site participants

You may apply for financial assistance when submitting your abstract. In your application you will be asked to answer questions regarding why your lab cannot fund your attendance and how your attendance will make a difference to your career. Application for financial support will not affect the outcome of your registration application.

Virtual participants

If you are attending virtually, you can apply for financial assistance in the submission portal by the abstract deadline. Read the instructions on how to apply for financial assistance. Only submissions for financial assistance will be accepted. Presentation abstracts cannot be submitted here and will be declined. 

In your application you will be asked to summarise your current work,  answer questions regarding why your lab cannot fund your attendance, and how your attendance will make a difference to your career. Application for financial support will not affect the outcome of your registration application.

Selection

The scientific organisers will select the recipients of all financial assistance during the abstract selection process. Results will be announced approximately 6 – 8 weeks before the event start date, however for some events this may be delayed. Selection results do not impact your admission to the meeting. Selection is based on scientific merit, your current work or study location, the reasons for needing financial support, and the impact this event will have on your career.

Reimbursement

Costs will be reimbursed after the meeting only once a reimbursement form and original receipts (from travel costs) have been received.

Further details

View our list of external funding opportunities and information on attending a conference as an event reporter.

For further information about financial assistance please refer to the FAQ page.

Accommodation is not included in the conference registration fee.

The hotels below have rooms on hold for participants until Monday 12th February 2024, in some cases at special rates. Please email the hotel directly, quoting the booking code EES24-01 to confirm the exact price of the room.

Hotel Anlage	Hotel ibis Heidelberg	Premier Inn Heidelberg City
Hotel Bayrischer Hof	ISG Hotel	Staycity Aparthotel Heidelberg
B&B Hotel	Leonardo Hotel Heidelberg City Centre	Steffi’s Hostel Heidelberg
Exzellenz Hotel	Meininger Heidelberg	Hotel Vier Jahreszeiten Heidelberg
Hotel Holländer Hof	Hotel Monpti

Travel information

For travel information, please see here.

If you are travelling to the conference within Germany then you are eligible for the Deutsche Bahn ‘Event Ticket’ (called the ‘Veranstaltungsticket’ in German). This will result in a lower ticket price if your travel distance to Heidelberg is more than 100 km. You need to provide proof of your event attendance when purchasing the ticket.

For more information in English see here or in German see here.

You can book your ticket here.

Conference shuttle buses

Conference shuttle buses are free of charge for participants, and depart from designated bus stops near the hotels to EMBL and back, mornings and evenings.

Here is the conference shuttle bus timetable.

The bus stops for this conference are:

• Staycity Aparthotel (Speyerer Str. 7)
• Kurfürsten-Anlage (Opposite Main Train Station)
• Premier Inn (Kurfürsten-Anlage 23)
• Leonardo Hotel Heidelberg City Center (Bergheimer Str. 63)
• Neckarmünzplatz (Heidelberg Tourist Information)
• Peterskirche (Bus stop)
• ISG Hotel (Im Eichwald 19)

View Conference shuttle bus stops and hotels in a larger map. Please note that not every bus stop will be used for every event.

Further details

Address: EMBL, Meyerhofstraße 1, 69117 Heidelberg, Germany.

For more information about accommodation and travel, please refer to the FAQ page.

Catering

All meals and coffee breaks are included in the registration fee. Our catering staff will prepare a wide variety of vegetarian meals, meat and fish dishes, soups, pasta, fresh fruit and vegetables, as well as a variety of desserts.

Please wear your badge at all times when serving yourself.

No food or drinks are allowed in the auditorium.

Charging lockers

There are lockers available next to the stairs leading down into the Auditorium. You will find some of those equipped with sockets to charge your smartphone/tablet etc.

Electricity and charging station

In most places the electricity is 220 volts AC (50 cycles). An adaptor and a plug that fits the German socket may be needed for your appliances/laptop (i.e. American, Japanese, etc.). A USB charging station for electronic devices is available at the registration desk.

EMBL merchandise

If you are interested in purchasing EMBL merchandise (products presented in the glass display in the registration area), please email the EMBL shop to place an order or get in contact with your Course Organiser.

Kindly note the EMBL shop is only open upon request and all purchases must be made in cash (Euros only).

Health and safety notes

Do not smoke in any EMBL building.
Eating and drinking is prohibited in the Auditorium and all laboratories.
Do not enter any restricted areas or the laboratories unless instructed to do so.

If first aid is required …

• The first aid room is located next to the ATC Registration Desk (room 10- 205).
• Dial the Emergency number 222 from any EMBL internal phone only.
• Where is the accident? What happened? How many injured?
• Emergency number 06221-387 7821 from mobile phones.
• Please report all accidents to the conference officer at the registration desk.

In case of fire …

• Press the nearest fire alarm button or the Emergency number 222 from any internal phone.
• A loud fire alarm will go off if an evacuation is required. On hearing the alarm leave the building immediately following the escape route and fire wardens and head to one of the meeting points
• Do not use the lifts.

Beyond first aid…

Please remember to bring your own medication, if needed, to the conference. Note that the next pharmacy is a 4-minute drive from the EMBL, but for many medications you will be required to see a doctor to get a prescription.

Ensure in advance that your medical insurance will cover you during your visit in the event that you do need to see a doctor while in Heidelberg. In any case, the EMBL Course and Conference Office will assist you to get to the pharmacy and a doctor of your choice if necessary.

Internet

Wi-Fi is available on campus using the EMBL-Events network and the event specific password, which will be provided on site. The eduroam network (secure, worldwide roaming access service developed for the international research and education community) is also available.

Lost and found

‘’Lost and Found’’ items are kept at the registration desk until the end of the conference.

Luggage

There are lockers available on-site to store your luggage, which require a 2 EURO coin to operate. There is another luggage room on level E0, which is free to use but remains unlocked during the conference.

Nursing room

There is a nursing room available in the ATC Rooftop Lounge on level A29.

Photography

During the conference, an EMBL Photographer may be taking photos. If you would not like to appear in these, please inform the photographer or a member of the Course and Conference Office.

Printing

We can help to print your boarding pass/train ticket. Please send it to events@embl.de and collect your print-outs at the registration desk.

Room for prayer, yoga and meditation

There is a room for prayer, meditation, and yoga located on level E0 behind the Auditorium. Please be respectful of others using the room.

Sightseeing

A variety of activities in Heidelberg can be found on the website of Heidelberg Marketing.

Travel to and from the venue

During the event, we provide conference shuttle buses to and from EMBL. In addition, there is the public bus 39A that serves the EMBL campus and taxis can be easily booked at any time. Information on the conference shuttle buses can be found on the individual event website and more detailed information on travelling to EMBL can be found on our Travel Information page.

Useful German expressions

Hello	Hallo
Goodbye	Auf Wiedersehen (formal) Tschüss (informal)
Good morning	Guten Morgen
Good afternoon	Guten Tag
Good evening	Guten Abend
Good night	Gute Nacht
I’m sorry	Es tut mir leid
Excuse me…	Entschuldigen Sie
How are you?	Wie gehts?
I’m fine thanks. And you?	Mir geht es gut , danke. Und Dir/Ihnen?
What is your name	Wie heißen Sie? (formal) Wie heißt du? (informal)
My name is..	Ich heiße..
Do you speak English	Sprechen Sie englisch?
I don’t understand	Ich verstehe nicht
Please speak more slowly	Können Sie bitte langsamer sprechen
Thank you	Dankeschön
Where is the toilet?	Wo ist die Toilette?
Please call me a taxi	Bitte rufen Sie mir ein Taxi
How do I get to….?	Wie komme ich zum/zur…..?
A beer/two beers please	Ein Bier/zwei Bier bitte
A glass of red/white wine please	Ein Glas Rot/Weißwein bitte
The menu, please	Die Speisekarte, bitte
Is there a local speciality?	Gibt es eine Spezialität aus dieser Gegend?
I’m vegetarian	Ich bin Vegetarier
It was delicious	Es war hervorragend
The bill, please	Die Rechnung, bitte
I have a headache	Ich habe Kopfschmerzen
I have a sore throat	Ich habe Halsschmerzen
My stomach hurts	Ich habe Magenschmerzen
I’m allergic to	Ich bin allergisch gegen
I need a doctor who speaks English.	Ich brauche einen Arzt, der englisch spricht.

What’s included?

• Access to all the livestreamed talks
• Video library of the recorded talks during the event and for two weeks afterwards. Please note: at the request of individual speakers, some talks are not recorded.
• Facility to submit questions

Please note that only on-site participants are able to submit abstracts and participate in the poster sessions.

Event platform

We are using an event platform for this conference. More information about the platform will be shared ahead of the conference.

Guidelines

• Do not broadcast the conference to unregistered participants.
• You are encouraged to tweet and post about the event. Tweet unless the speaker specifically says otherwise, but be mindful of unpublished data. 
• Please do not capture, transmit or redistribute data presented at the meeting.

Additional information can be found in our Code of Conduct.

Health and well-being

It is important to stay healthy and move around, especially when you are attending an event virtually. We have put together a few coffee break stretches and yoga videos in the conference platform for you to enjoy during the event.

How to ask questions

Please use the Q&A function in the event platform.

If you have any other questions, you can go to the Help Desk in the event platform. Click on ‘more’ on the top menu and click Help Desk. 

Time zone

The programme is planned based on the Europe/Berlin time zone, unless otherwise stated. Please take your time zone into consideration when planning your attendance.

Please find additional information including FAQs, terms and conditions, COVID-19 safety policy and travelling to EMBL on our Information for participants page.

COVID-19 information for on-site events at EMBL Heidelberg can be found in our COVID-19 FAQs.