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<p> </p>
<p
style="font-weight: normal; line-height: 100%; margin-bottom: 0.35cm"><font
face="FreeSans, sans-serif"><span style="font-variant: normal"><font
color="#000000"><span style="text-decoration: none"><font
size="2" style="font-size: 11pt"><span
style="font-style: normal"><b><span
style="background: transparent"><u>Please feel
free to share this offer for a PHD position at
IGMM in Montpellier</u><br>
<br>
Project:</span></b></span></font></span></font></span><span
style="font-variant: normal"><font color="#000000"><span
style="text-decoration: none"><span
style="background: transparent">
</span></span></font></span><span
style="font-variant: normal"><font color="#000000"><span
style="text-decoration: none"><font size="2"
style="font-size: 11pt"><span style="font-style: normal"><span
style="background: transparent">DNA
large language models for end to end genome
interpretation</span></span></font></span></font></span></font></p>
<p
style="font-weight: normal; line-height: 100%; margin-bottom: 0.35cm">
<font face="FreeSans, sans-serif"><u><span
style="font-variant: normal"><font color="#000000"><span
style="text-decoration: none"><font size="2"
style="font-size: 11pt"><span
style="font-style: normal"><b><span
style="background: transparent">Motivation</span></b></span></font></span></font></span></u></font></p>
<p
style="font-weight: normal; line-height: 100%; margin-bottom: 0.35cm">
<font face="FreeSans, sans-serif"><span
style="font-variant: normal"><font color="#000000"><span
style="text-decoration: none"><font size="2"
style="font-size: 11pt"><span style="font-style: normal"><span
style="background: transparent">Interpreting
the genome means modeling the relationship between
genotype and
phenotype, which is the fundamental goal of biology.
Achieving this
would revolutionize genetics, medicine, and
agro-tech. In clinical
genetics, it could lead to personalized treatments
tailored to each
patient's genome, enabling precision medicine. </span></span></font></span></font></span></font></p>
<p
style="font-weight: normal; line-height: 100%; margin-bottom: 0.35cm">
<font face="FreeSans, sans-serif"><u><span
style="font-variant: normal"><font color="#000000"><span
style="text-decoration: none"><font size="2"
style="font-size: 11pt"><span
style="font-style: normal"><b><span
style="background: transparent">Objectives</span></b></span></font></span></font></span></u></font></p>
<p
style="font-weight: normal; line-height: 100%; margin-bottom: 0.35cm">
<font face="FreeSans, sans-serif"><span
style="font-variant: normal"><font color="#000000"><span
style="text-decoration: none"><font size="2"
style="font-size: 11pt"><span style="font-style: normal"><span
style="background: transparent">This
project fuses quantitative genetics with
bioinformatics and
cutting-edge Artificial Intelligence, using the
latest Deep Learning
Large Language Models for DNA to advance our ability
to predict the
phenotypes deriving from the observed genotypes.
This project is
based on the previous work of Dr. Raimondi on Genome
Interpretation
(GI) for the prediction of clinically relevant
phenotypes in humans. </span></span></font></span></font></span></font></p>
<p
style="font-variant: normal; font-style: normal; font-weight: normal; line-height: 100%; margin-bottom: 0.35cm; text-decoration: none">
<font color="#000000"><font face="FreeSans, sans-serif"><font
size="2" style="font-size: 11pt"><span
style="background: transparent">Dr.
Raimondi previous works focused on encoding
Whole-Exome/Whole-Genome
Sequencing (WES/WGS) data into compact, machine-readable
features,
while reducing overfitting caused by high-dimensional
genomic data.
However, to limit complexity, we had to rely on coarse
gene-level
summaries, such as mutational burden per gene, which
sacrificed
fine-grained genetic detail.</span></font></font></font></p>
<p
style="font-variant: normal; font-style: normal; font-weight: normal; line-height: 100%; margin-bottom: 0.35cm; text-decoration: none">
<font color="#000000"><font face="FreeSans, sans-serif"><font
size="2" style="font-size: 11pt"><span
style="background: transparent">The
goal of this project is to move beyond these gene-centric
encodings
by building neural network architectures that operate
directly at the
nucleotide level. To achieve this, we propose integrating
pre-trained
DNA LLMs as unsupervised feature extractors within GI
models. These
models, trained using self-supervised learning on entire
genomes,
capture rich patterns of DNA dependencies and can produce
information-dense latent representations.</span></font></font></font></p>
<p
style="font-variant: normal; font-style: normal; font-weight: normal; line-height: 100%; margin-bottom: 0.35cm; text-decoration: none">
<font color="#000000"><font face="FreeSans, sans-serif"><font
size="2" style="font-size: 11pt"><span
style="background: transparent">DNA
LLMs have shown strong performance in various functional
genomics
tasks, such as identifying regulatory elements and variant
effects.
This project will evaluate whether their latent
representations can
improve phenotype prediction. The new DNA LLM methods will
be
prototyped on A.thaliana, which is a well known model
organism. Later
developments will be translated to the disease risk
prediction of
Inflammatory Bowel Disease (IBD). Unlike DNA LLM research,
this work
applies LLMs to the interpretation of individual-level
WES/WGS data
for disease risk, marking a novel use of these models in
human
genetic prediction.</span></font></font></font></p>
<p
style="font-weight: normal; line-height: 100%; margin-bottom: 0.35cm">
<font face="FreeSans, sans-serif"><u><span
style="font-variant: normal"><font color="#000000"><span
style="text-decoration: none"><font size="2"
style="font-size: 11pt"><span
style="font-style: normal"><b><span
style="background: transparent">Candidate
profile</span></b></span></font></span></font></span></u></font></p>
<p
style="font-weight: normal; line-height: 100%; margin-bottom: 0.35cm">
<font face="FreeSans, sans-serif"><span
style="font-variant: normal"><font color="#000000"><span
style="text-decoration: none"><font size="2"
style="font-size: 11pt"><span style="font-style: normal"><span
style="background: transparent">We
are looking for a </span></span></font></span></font></span><span
style="font-variant: normal"><font color="#000000"><span
style="text-decoration: none"><font size="2"
style="font-size: 11pt"><span style="font-style: normal"><b><span
style="background: transparent">motivated</span></b></span></font></span></font></span><span
style="font-variant: normal"><font color="#000000"><span
style="text-decoration: none"><span
style="background: transparent">
</span></span></font></span><span
style="font-variant: normal"><font color="#000000"><span
style="text-decoration: none"><font size="2"
style="font-size: 11pt"><span style="font-style: normal"><span
style="background: transparent">and
</span></span></font></span></font></span><span
style="font-variant: normal"><font color="#000000"><span
style="text-decoration: none"><font size="2"
style="font-size: 11pt"><span style="font-style: normal"><b><span
style="background: transparent">curious</span></b></span></font></span></font></span><span
style="font-variant: normal"><font color="#000000"><span
style="text-decoration: none"><span
style="background: transparent">
</span></span></font></span><span
style="font-variant: normal"><font color="#000000"><span
style="text-decoration: none"><font size="2"
style="font-size: 11pt"><span style="font-style: normal"><span
style="background: transparent">candidate,
with a strong passion for science and for scientific
discovery
through the use and creation of new data science and
Machine Learning
methods. Bioinformatics and Genome Interpretation
are
multi-disciplinary and rapidly evolving fields.
Therefore, the
candidate is expected to 1) be eager to continuously
</span></span></font></span></font></span><span
style="font-variant: normal"><font color="#000000"><span
style="text-decoration: none"><font size="2"
style="font-size: 11pt"><span style="font-style: normal"><b><span
style="background: transparent">learn</span></b></span></font></span></font></span><span
style="font-variant: normal"><font color="#000000"><span
style="text-decoration: none"><span
style="background: transparent">
</span></span></font></span><span
style="font-variant: normal"><font color="#000000"><span
style="text-decoration: none"><font size="2"
style="font-size: 11pt"><span style="font-style: normal"><span
style="background: transparent">new
skills, methods and concepts, and 2) to </span></span></font></span></font></span><span
style="font-variant: normal"><font color="#000000"><span
style="text-decoration: none"><font size="2"
style="font-size: 11pt"><span style="font-style: normal"><b><span
style="background: transparent">enjoy</span></b></span></font></span></font></span><span
style="font-variant: normal"><font color="#000000"><span
style="text-decoration: none"><span
style="background: transparent">
</span></span></font></span><span
style="font-variant: normal"><font color="#000000"><span
style="text-decoration: none"><font size="2"
style="font-size: 11pt"><span style="font-style: normal"><span
style="background: transparent">finding
new solutions in the face of new and unforeseen
difficulties.</span></span></font></span></font></span></font></p>
<p
style="font-weight: normal; line-height: 100%; margin-bottom: 0.35cm">
<font face="FreeSans, sans-serif"><span
style="font-variant: normal"><font color="#000000"><span
style="text-decoration: none"><font size="2"
style="font-size: 11pt"><span style="font-style: normal"><span
style="background: transparent">The
ideal candidate has </span></span></font></span></font></span><span
style="font-variant: normal"><font color="#000000"><span
style="text-decoration: none"><font size="2"
style="font-size: 11pt"><span style="font-style: normal"><b><span
style="background: transparent">very
good</span></b></span></font></span></font></span><span
style="font-variant: normal"><font color="#000000"><span
style="text-decoration: none"><span
style="background: transparent">
</span></span></font></span><span
style="font-variant: normal"><font color="#000000"><span
style="text-decoration: none"><font size="2"
style="font-size: 11pt"><span style="font-style: normal"><span
style="background: transparent">1)
python programming skills, 2) understanding of </span></span></font></span></font></span><span
style="font-variant: normal"><font color="#000000"><span
style="text-decoration: none"><font size="2"
style="font-size: 11pt"><span style="font-style: normal"><b><span
style="background: transparent">the
mathematical foundations and principles</span></b></span></font></span></font></span><span
style="font-variant: normal"><font color="#000000"><span
style="text-decoration: none"><span
style="background: transparent">
</span></span></font></span><span
style="font-variant: normal"><font color="#000000"><span
style="text-decoration: none"><font size="2"
style="font-size: 11pt"><span style="font-style: normal"><span
style="background: transparent">of
Machine Learning, Linear Algebra (vectorial and
matricial operations,
optimization), with a particular focus on </span></span></font></span></font></span><span
style="font-variant: normal"><font color="#000000"><span
style="text-decoration: none"><font size="2"
style="font-size: 11pt"><span style="font-style: normal"><b><span
style="background: transparent">Neural
Networks</span></b></span></font></span></font></span><span
style="font-variant: normal"><font color="#000000"><span
style="text-decoration: none"><font size="2"
style="font-size: 11pt"><span style="font-style: normal"><span
style="background: transparent">,
3) </span></span></font></span></font></span><span
style="font-variant: normal"><font color="#000000"><span
style="text-decoration: none"><font size="2"
style="font-size: 11pt"><span style="font-style: normal"><b><span
style="background: transparent">problem
solving</span></b></span></font></span></font></span><span
style="font-variant: normal"><font color="#000000"><span
style="text-decoration: none"><span
style="background: transparent">
</span></span></font></span><span
style="font-variant: normal"><font color="#000000"><span
style="text-decoration: none"><font size="2"
style="font-size: 11pt"><span style="font-style: normal"><span
style="background: transparent">skills,
4) familiarity with GNU/Linux environment and 5)
ability to
</span></span></font></span></font></span><span
style="font-variant: normal"><font color="#000000"><span
style="text-decoration: none"><font size="2"
style="font-size: 11pt"><span style="font-style: normal"><b><span
style="background: transparent">multi-task</span></b></span></font></span></font></span><span
style="font-variant: normal"><font color="#000000"><span
style="text-decoration: none"><span
style="background: transparent">
</span></span></font></span><span
style="font-variant: normal"><font color="#000000"><span
style="text-decoration: none"><font size="2"
style="font-size: 11pt"><span style="font-style: normal"><span
style="background: transparent">across
different projects. A good understanding of the
basic concepts of
Bioinformatics is not necessary but welcome. The
project will be
based on the development of </span></span></font></span></font></span><span
style="font-variant: normal"><font color="#000000"><span
style="text-decoration: none"><font size="2"
style="font-size: 11pt"><span style="font-style: normal"><b><span
style="background: transparent">un-orthodox
Neural Network</span></b></span></font></span></font></span><span
style="font-variant: normal"><font color="#000000"><span
style="text-decoration: none"><span
style="background: transparent">
</span></span></font></span><span
style="font-variant: normal"><font color="#000000"><span
style="text-decoration: none"><font size="2"
style="font-size: 11pt"><span style="font-style: normal"><span
style="background: transparent">models
with </span></span></font></span></font></span><span
style="font-variant: normal"><font color="#000000"><span
style="text-decoration: none"><font size="2"
style="font-size: 11pt"><span style="font-style: normal"><b><span
style="background: transparent">Pytorch</span></b></span></font></span></font></span><span
style="font-variant: normal"><font color="#000000"><span
style="text-decoration: none"><font size="2"
style="font-size: 11pt"><span style="font-style: normal"><span
style="background: transparent">.</span></span></font></span></font></span></font></p>
<p
style="font-weight: normal; line-height: 100%; margin-bottom: 0.35cm">
<font face="FreeSans, sans-serif"><span
style="font-variant: normal"><font color="#000000"><span
style="text-decoration: none"><font size="2"
style="font-size: 11pt"><span style="font-style: normal"><span
style="background: transparent">B2
level of English is </span></span></font></span></font></span><span
style="font-variant: normal"><font color="#000000"><span
style="text-decoration: none"><font size="2"
style="font-size: 11pt"><span style="font-style: normal"><b><span
style="background: transparent">required</span></b></span></font></span></font></span><span
style="font-variant: normal"><font color="#000000"><span
style="text-decoration: none"><font size="2"
style="font-size: 11pt"><span style="font-style: normal"><span
style="background: transparent">.</span></span></font></span></font></span></font></p>
<p
style="font-variant: normal; font-style: normal; font-weight: normal; line-height: 100%; margin-bottom: 0.35cm; text-decoration: none">
<font color="#000000"><font face="FreeSans, sans-serif"><font
size="2" style="font-size: 11pt"><span
style="background: transparent">The
offer provides an initial 6-month contract, with
possibility of
renewal to 2 years. This project can be extended to 3
years and
offers the opportunity to obtain a PhD.</span></font></font></font></p>
<p
style="font-weight: normal; line-height: 100%; margin-bottom: 0.35cm">
<font face="FreeSans, sans-serif"><span
style="font-variant: normal"><font color="#000000"><span
style="text-decoration: none"><font size="2"
style="font-size: 11pt"><span style="font-style: normal"><u><b><span
style="background: transparent">Research
environment</span></b></u></span></font></span></font></span><span
style="font-variant: normal"><font color="#000000"><span
style="text-decoration: none"><u><span
style="background: transparent">
</span></u></span></font></span></font>
</p>
<p
style="font-weight: normal; line-height: 100%; margin-bottom: 0.35cm">
<font face="FreeSans, sans-serif"><span
style="font-variant: normal"><font color="#000000"><span
style="text-decoration: none"><font size="2"
style="font-size: 11pt"><span style="font-style: normal"><span
style="background: transparent">The
recruited person will join the “AI for Genome
Interpretation”
team led by Dr. Daniele Raimondi at IGMM. The work
will be conducted
in an international (English-speaking) and
interdisciplinary
environment. </span></span></font></span></font></span></font></p>
<p
style="font-variant: normal; font-style: normal; font-weight: normal; line-height: 100%; margin-bottom: 0.35cm; text-decoration: none">
<font color="#000000"><font face="FreeSans, sans-serif"><font
size="2" style="font-size: 11pt"><span
style="background: transparent">The
Institute of Molecular Genetics of Montpellier (IGMM) is a
joint
research unit affiliated with the CNRS and the University
of
Montpellier. It comprises around 200 members, organized
into 18
research groups, 9 shared support services and 9
technological and
scientific platforms.</span></font></font></font></p>
<p
style="font-variant: normal; font-style: normal; font-weight: normal; line-height: 100%; margin-bottom: 0.35cm; text-decoration: none">
<font color="#000000"><font face="FreeSans, sans-serif"><font
size="2" style="font-size: 11pt"><span
style="background: transparent">IGMM
is a multidisciplinary institute whose research has both
fundamental
and translational impact in molecular and cellular biology
at the
international level.</span></font></font></font></p>
<p style="line-height: 100%"><a
name="docs-internal-guid-b209c73f-7fff-de56-8ffe-0248c058f5d0"></a>
<font face="FreeSans, sans-serif"><br>
<span style="font-variant: normal"><font color="#000000"><span
style="text-decoration: none"><font size="2"
style="font-size: 11pt"><span style="font-style: normal"><u><b><span
style="background: transparent">Qualifications</span></b></u></span></font></span></font></span></font></p>
<p
style="font-weight: normal; line-height: 100%; margin-bottom: 0.35cm">
<font face="FreeSans, sans-serif"><span
style="font-variant: normal"><font color="#000000"><span
style="text-decoration: none"><font size="2"
style="font-size: 11pt"><span style="font-style: normal"><span
style="background: transparent">The
ideal candidate has </span></span></font></span></font></span><span
style="font-variant: normal"><font color="#000000"><span
style="text-decoration: none"><font size="2"
style="font-size: 11pt"><span style="font-style: normal"><b><span
style="background: transparent">very
good</span></b></span></font></span></font></span><span
style="font-variant: normal"><font color="#000000"><span
style="text-decoration: none"><span
style="background: transparent">
</span></span></font></span><span
style="font-variant: normal"><font color="#000000"><span
style="text-decoration: none"><font size="2"
style="font-size: 11pt"><span style="font-style: normal"><span
style="background: transparent">1)
python programming skills, 2) understanding of </span></span></font></span></font></span><span
style="font-variant: normal"><font color="#000000"><span
style="text-decoration: none"><font size="2"
style="font-size: 11pt"><span style="font-style: normal"><b><span
style="background: transparent">the
mathematical foundations and principles</span></b></span></font></span></font></span><span
style="font-variant: normal"><font color="#000000"><span
style="text-decoration: none"><span
style="background: transparent">
</span></span></font></span><span
style="font-variant: normal"><font color="#000000"><span
style="text-decoration: none"><font size="2"
style="font-size: 11pt"><span style="font-style: normal"><span
style="background: transparent">of
Machine Learning, Linear Algebra (vectorial and
matricial operations,
optimization), with a particular focus on </span></span></font></span></font></span><span
style="font-variant: normal"><font color="#000000"><span
style="text-decoration: none"><font size="2"
style="font-size: 11pt"><span style="font-style: normal"><b><span
style="background: transparent">Neural
Networks</span></b></span></font></span></font></span><span
style="font-variant: normal"><font color="#000000"><span
style="text-decoration: none"><font size="2"
style="font-size: 11pt"><span style="font-style: normal"><span
style="background: transparent">,
3) </span></span></font></span></font></span><span
style="font-variant: normal"><font color="#000000"><span
style="text-decoration: none"><font size="2"
style="font-size: 11pt"><span style="font-style: normal"><b><span
style="background: transparent">problem
solving</span></b></span></font></span></font></span><span
style="font-variant: normal"><font color="#000000"><span
style="text-decoration: none"><span
style="background: transparent">
</span></span></font></span><span
style="font-variant: normal"><font color="#000000"><span
style="text-decoration: none"><font size="2"
style="font-size: 11pt"><span style="font-style: normal"><span
style="background: transparent">skills,
4) familiarity with GNU/Linux environment and 5)
ability to
</span></span></font></span></font></span><span
style="font-variant: normal"><font color="#000000"><span
style="text-decoration: none"><font size="2"
style="font-size: 11pt"><span style="font-style: normal"><b><span
style="background: transparent">multi-task</span></b></span></font></span></font></span><span
style="font-variant: normal"><font color="#000000"><span
style="text-decoration: none"><span
style="background: transparent">
</span></span></font></span><span
style="font-variant: normal"><font color="#000000"><span
style="text-decoration: none"><font size="2"
style="font-size: 11pt"><span style="font-style: normal"><span
style="background: transparent">across
different projects. A good understanding of the
basic concepts of
Bioinformatics is not necessary but welcome. The
project will be
based on the development of </span></span></font></span></font></span><span
style="font-variant: normal"><font color="#000000"><span
style="text-decoration: none"><font size="2"
style="font-size: 11pt"><span style="font-style: normal"><b><span
style="background: transparent">un-orthodox
Neural Network</span></b></span></font></span></font></span><span
style="font-variant: normal"><font color="#000000"><span
style="text-decoration: none"><span
style="background: transparent">
</span></span></font></span><span
style="font-variant: normal"><font color="#000000"><span
style="text-decoration: none"><font size="2"
style="font-size: 11pt"><span style="font-style: normal"><span
style="background: transparent">models
with </span></span></font></span></font></span><span
style="font-variant: normal"><font color="#000000"><span
style="text-decoration: none"><font size="2"
style="font-size: 11pt"><span style="font-style: normal"><b><span
style="background: transparent">Pytorch</span></b></span></font></span></font></span><span
style="font-variant: normal"><font color="#000000"><span
style="text-decoration: none"><font size="2"
style="font-size: 11pt"><span style="font-style: normal"><span
style="background: transparent">.
B2 level of English is required. Familiarity with
scientific
computing and libraries such as numpy, scikit-learn,
scipy, pytorch.</span></span></font></span></font></span></font></p>
<p style="line-height: 100%"><font face="FreeSans, sans-serif"><br>
<span style="font-variant: normal"><font color="#000000"><span
style="text-decoration: none"><font size="2"
style="font-size: 11pt"><span style="font-style: normal"><span
style="font-weight: normal"><span
style="background: transparent"><b>HOW TO
APPLY:</b>
<a class="moz-txt-link-freetext" href="https://umontpellier.nous-recrutons.fr/poste/7sqwj9n4vg-ingenieur-en-calcul-scientifique-ou-ingenieur-en-ingenierie-logicielle-fh/">https://umontpellier.nous-recrutons.fr/poste/7sqwj9n4vg-ingenieur-en-calcul-scientifique-ou-ingenieur-en-ingenierie-logicielle-fh/</a></span></span></span></font></span></font></span></font></p>
<p style="line-height: 100%"><font face="FreeSans, sans-serif"><br>
</font>-- <br>
</p>
<pre class="moz-signature" cols="72">Daniele Raimondi, PhD
Chaire de Professeur Junior CNRS
AI for Genome Interpretation group
Institut de Génétique Moléculaire de Montpellier (IGMM)
1919 Route de Mende
34090 Montpellier, France
-obscurum per obscurius-</pre>
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