Foundation Models for Fungal Genomes
An introduction to DNA and protein foundation models and their early, still-unproven applications to fungal genome interpretation.
Program identification
- 1.1Program name
- Foundation Models for Fungal Genomes
- 1.2Type of qualification
- Course
- 1.3Provider / endorsing institution
- Fungaris – International Institute of Mycology, School of Digital Mycology: AI, Genomics & Data. A Fungaris program of its own, not endorsed by a university.
- 1.4Mode of study
- Online, with live sessions in a small group, recordings and a virtual campus.
- 1.5Duration (hours / ECTS credits)
- 3 months (12 weeks) · 72 hours in total · 6 modules of 12 hours · 12 live sessions of 2 hours. ECTS credits: not applicable (Fungaris own program, not an official university degree).
- 1.6Language
- English
- 1.7Start and end dates / intake
- Next intake: January 11, 2027 to April 2, 2027. Enrollment closes on January 4, 2027. Following intake: March 8, 2027. How intakes work →
Overview
2.1Program description
Foundation Models for Fungal Genomes is an introduction to DNA and protein language models and their early applications to fungi. You follow the path from classic sequence models to large pretrained models, study the architectures and training strategies of genomic language models, and examine how they are used to predict regulatory elements and gene function. A key theme is that fungal genomes are underrepresented in training data, which affects performance in ways that must be measured.
Foundation models are attracting great interest in biology, but applications to fungal genomes remain largely unproven. Researchers need to separate promising results from overreach and know how to test models fairly. The course suits computational biologists and machine learning researchers comfortable with Python and basic deep learning. For the final project you fine-tune or evaluate a pretrained model on a fungal task, compare it with a simpler baseline and write a short critical report on what the results show.
2.2Why it matters / what need it meets
It meets a practical need: applied, up-to-date knowledge in digital mycology, useful in areas such as academic research, biotechnology, AI and software for life sciences, agricultural genomics.
Mycology is moving fast and good practical training is still scarce. This program gives you a structured path, taught live by people who work in the field, so you can apply what you learn with judgment and safety.
Objectives and competences
3.1General objective
To finish the program able to apply its content professionally and with judgment. In short:
An introduction to DNA and protein foundation models and their early, still-unproven applications to fungal genome interpretation.
3.2Specific objectives
- Build the foundations: From sequence models to foundation models; Genomic language models: architectures and training.
- Put them into practice: Predicting regulation and gene function; Fungal genomes as an underrepresented domain.
- Apply everything to a real case: Fine-tuning, evaluation and benchmarks; Research directions and limitations.
- Complete a final project reviewed by your instructor.
3.3Competences you will gain
- Explain how genomic and protein foundation models are trained.
- Assess training-data bias affecting fungal genome applications.
- Fine-tune or probe a pretrained model on a fungal task.
- Design fair benchmarks with simple baselines for comparison.
- Report model results with appropriate caution and context.
Student profile
4.1Who it is for (entry profile)
Computational biologists and ml researchers.
4.2Entry requirements
Solid Python skills and basic knowledge of deep learning and genomics are expected, ideally from previous courses or professional experience.
4.3Career paths (exit profile)
- Computational biologist exploring genomic AI
- Machine learning researcher in life sciences
- Bioinformatics scientist in biotech R&D
- Doctoral or postdoctoral researcher in genomic AI
- Technical evaluator of AI tools for genomics
Outcomes depend on your experience and on your local market.
Study plan
5.1Overall structure (modules and workload)
| Module | Title | Phase | Topics | Hours |
|---|---|---|---|---|
| 01 | From sequence models to foundation models | Foundations | 3 | 12 |
| 02 | Genomic language models: architectures and training | Foundations | 3 | 12 |
| 03 | Predicting regulation and gene function | Practice | 3 | 12 |
| 04 | Fungal genomes as an underrepresented domain | Practice | 3 | 12 |
| 05 | Fine-tuning, evaluation and benchmarks | Application & project | 3 | 12 |
| 06 | Research directions and limitations | Application & project | 3 | 12 |
| Total | 72 |
6 modules × 12 hours = 72 hours: 24 hours of live sessions, and the rest for campus study, exercises and the final project.
5.2Content by module
Hover or tap a module to follow the path from the first session to the final project. Open a module to see the topics it covers.
- Motifs, HMMs and early neural models
- Self-supervised pretraining
- What makes a model foundational
- Transformer and state-space architectures
- Tokenization of DNA
- Training data and compute
- Promoters and regulatory elements
- Variant effect prediction
- Gene function annotation
- Taxonomic bias in training sets
- Effects on fungal performance
- Building fungal-specific datasets
- Fine-tuning strategies
- Choosing fair baselines
- Benchmark design
- Promising applications
- Current limitations
- Responsible reporting of results
5.3Company placement
This program does not include a company placement. Practice is built into every module through exercises, case studies and the final project.
5.4Final project
A fine-tuning or evaluation study of a foundation model on a fungal genomic task, compared with a baseline.
Methodology
6.1How it is taught
- Live online sessions, usually weekly, with a working professional and a small group.
- Recordings of every session, so you can catch up if work or time zones get in the way.
- Exercises and real case studies in every module.
- Tutoring: your instructor answers questions and gives feedback on your exercises and project.
6.2Platform and resources
A Moodle virtual campus with session recordings, readings, exercises and forums for each module. You need a computer, an up-to-date browser and a stable connection; a webcam and microphone are recommended.
Technical requirements →6.3Estimated weekly workload
About 6 hours a week for 12 weeks: one 2-hour live session on a weekday evening, plus study and exercises on the campus at your own pace.
Assessment
7.1Assessment system and weighting
Progress is assessed through participation in live sessions, notebook exercises in each module and a final project reviewed by the instructor.
7.2Requirements to pass
- Complete every module, by attending the live sessions or watching the recordings.
- Hand in the module exercises.
- Have your final project approved by your instructor.
Teaching team
8.1Academic direction
At Fungaris, the Digital Mycology school coordinates the content and quality of this program. The academic director of each intake is named in the intake guide.
8.2Faculty
Taught by professionals who work in the field. The instructor for each intake is confirmed before the start.
Meet our faculty →Certificate
9.1Certificate awarded
Course Certificate
On completing the program and its project, Fungaris issues a Course Certificate. Fungaris certificates are the institute's own. Whether an employer, school or authority recognizes them depends on that organization and on local rules in each country.
9.2Issuing body / recognition
Issued by Fungaris (operated by Nexora Generation, S.L.) as a digital certificate. It is a Fungaris certificate of its own: it is not an official university degree and does not award ECTS credits.
About our certificates →Admission and enrollment
10.1Admission process (steps)
- Send your request through the form or write to admissions.
- Admissions reviews your profile and confirms the start date, the session schedule and the fee.
- You secure your place with full payment or a 40% reservation.
- You receive your campus access and welcome guide before the first session.
10.2Documents required
- A valid identity document.
- Contact and billing details (personal or company).
10.3Deadlines
Enrollment for the intake starting on January 11, 2027 is open until January 4, 2027, or until the group is full (maximum 20 students).
10.4Fee and payment options
Fee: $450
- Full payment before the start: $360 (20% reduction).
- 40% reservation ($180) and 3 monthly installments of $90.
10.5Grants, discounts and funding
Discounts: 10% for Fungaris alumni and 15% for groups of three or more people from the same organization. Discounts cannot be combined with each other or with the full-payment reduction.
Your employer can pay for the program and receive the invoice in the company name. Whether a public or employer training budget can cover the fee depends on your country, so check with them.
10.6Cancellation policy
The conditions for canceling, withdrawing or moving to a later intake are explained in our cancellation policy and in your enrollment confirmation. Nothing there limits your rights under the consumer law that applies to you.
Cancellation and refunds →Additional information
11.1Frequently asked questions
Do I need experience to study Foundation Models for Fungal Genomes?
Solid Python skills and basic knowledge of deep learning and genomics are expected, ideally from previous courses or professional experience.
How is Foundation Models for Fungal Genomes taught?
Live online, in 6 modules with a working professional, a small group and a final project.
How am I assessed?
Progress is assessed through participation in live sessions, notebook exercises in each module and a final project reviewed by the instructor.
What is the final project?
A fine-tuning or evaluation study of a foundation model on a fungal genomic task, compared with a baseline.
What certificate do I get?
On completing the program and its project, Fungaris issues a Course Certificate. Fungaris certificates are the institute's own. Whether an employer, school or authority recognizes them depends on that organization and on local rules in each country.
What can I study after Foundation Models for Fungal Genomes?
The natural next step is Diploma in Fungal Bioinformatics.
11.2Alumni testimonials
We only publish verified testimonials from real students. This program does not have any published yet; they will appear here once its first intakes finish.
11.3Admissions contact
Write to info@fungaris.institute or use the contact form. Admissions answers in your language.
Keep branching.
Join the next intake.
Pay in full with a 20% reduction, or reserve your place with 40% and pay the rest in monthly installments. All prices are stated in US dollars (USD).