PhD Position in Computer Science
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We are looking for PhD candidates to join the TACsy (Training Alliance for Computational Systems Chemistry) Marie-Skłodowska-Curie Joint Doctoral Network. This network consists of fifteen (15) highly interlinked PhD projects, of which this particular call is for project DC 1: Efficient Graph Canonicalization and Subgraph Finding Approaches for Typed Attributed Chemical Graphs. The application deadline is 23 October 2023. The anticipated start date is 1 January 2024, but flexibility in both directions is possible.
Chemical molecules are classically described as undirected graphs of bounded degree, with nodes representing atoms and edges representing bonds. Therefore, chemical reactions can be well described by graph transformation formalisms and methods. A computational framework for executing these methods has been developed, but there is a challenging need to expand it to allow for more detailed chemical information encoded in attributed graphs. This will require the generalization of established algorithmic approaches. One example of this is the canonicalization of molecular graphs that include stereochemical information – highly efficient canonicalization algorithms are key when huge chemical spaces are to be generated by graph transformation-based methods, but current algorithms do not incorporate stereochemical information.
The goal of this PhD project is to combine state-of-the-art approaches from graph theory, algorithms, and algorithm engineering in order to develop the basis of ground-breaking computational methods applicable to the analysis of large networks of chemical reactions.
We are seeking an excellent and highly motivated individual with an MSc degree in computer science or a related subject. The ideal candidate has familiarity with one or more of the following areas: algorithmics, category theory, graph theory, graph transformation, algorithm engineering. Proven competences in programming and ease with formal thinking are a necessity.
This PhD project is a joint degree between University of Southern Denmark (Daniel Merkle, Jakob Lykke Andersen) and Leipzig University (Peter Stadler). Additionally, the student will have a three-months internship at BASF SE (Germany).
The TACsy consortium encompasses 11 partners across six countries in Europe and North America, including both academic institutions and industrial partners. The consortium consists of world-class scientists with competences spanning chemistry, biochemistry, computer science, and machine learning. All fifteen doctoral candidates will work with two research groups, and will obtain a degree from both host institutions, and complete research stays either at world-leading industry partners or at prestigious non-European academic partners:
The candidates will all be part of a strong joint PhD training programme, with a focus on career development, application writing, communication skills, and community building through scientific summer schools.
All candidates will be expected to:
See details about the network as a whole, its scientific content, and the application and selection process here.
Salary, working conditions, application process, etc.
All positions are fully funded, with very competitive salaries. More information on funding from the MSCA programme can be found here (beginning on page 78). Please note that a country correction coefficient (page 109) applies to the living allowance in order to ensure equal treatment and purchasing power parity for all researchers. Salary rules apply to the doctoral candidates hosted in the European Union and will change depending on the host institution.
The TACsy project wishes our staff to reflect the diversity of society and thus welcomes applications from all qualified candidates regardless of personal background. We are searching for a diverse group of candidates with very different backgrounds and qualities, who inspire and motivate each other. We want every talent to feel at home in our organisations and to have the same career opportunities. The position of working hours is flexible in order to accommodate individual needs and allow for the best possible work-life balance for each candidate.
The guaranteed Doctoral Candidate PhD funding from the European Commission is for 36 months. Therefore, appointment as a PhD Research Fellow is for three years. Employment stops automatically at the end of the period. The holder of the scholarship is not allowed to have other paid employment during the three-year period. Additional funding may be possible, depending on the local supervisor and in accordance with the regular PhD time in the country of origin.
Applications must be in English and must include the following:
Applications must be submitted electronically using the link “Apply online”. Attached files must be in Adobe PDF or Word format. Each box can only contain a single file of max. 10 Mb. We strongly recommend that you read “How to apply” before you apply.
Incomplete applications and applications received after the deadline will neither be considered nor evaluated. This also applies to reference letters.
Details on the selection process can be found here. Please note that the recruitment team reserves the right to conduct a second interview. Shortlisting may be used in the assessment process.
Please note that there are two limitations to apply for this programme, as specified in the MSCA regulations. Applicants must:
Contact Information
For further information please contact Daniel Merkle, tel.: +45 6550 2322, e-mail: [email protected].
The successful applicant will, if employed at SDU, be employed in accordance with the agreement on salaried PhD scholars between the Ministry of Finance and AC (the Danish Confederation of Professional Associations).
The successful candidate will, if employed at SDU, be enrolled at this university in accordance with faculty regulations and the Danish Ministerial Order on the PhD Programme at the Universities (PhD order).
These positions are subject to the entry into force of grant agreement no 101072930 by and between the European Research Executive Agency and University of Southern Denmark and thereby funded by the European Union’s Horizon Europe Research and Innovation Programme.
Further information about the PhD-study can be found at the homepage of the University.
Further information for international applicants considering applying for a job at the University of Southern Denmark. Please take a look at the webpage from our International Staff Office (ISO) at The University of Southern Denmark.
Chemical molecules are classically described as undirected graphs of bounded degree, with nodes representing atoms and edges representing bonds. Therefore, chemical reactions can be well described by graph transformation formalisms and methods. A computational framework for executing these methods has been developed, but there is a challenging need to expand it to allow for more detailed chemical information encoded in attributed graphs. This will require the generalization of established algorithmic approaches. One example of this is the canonicalization of molecular graphs that include stereochemical information – highly efficient canonicalization algorithms are key when huge chemical spaces are to be generated by graph transformation-based methods, but current algorithms do not incorporate stereochemical information.
The goal of this PhD project is to combine state-of-the-art approaches from graph theory, algorithms, and algorithm engineering in order to develop the basis of ground-breaking computational methods applicable to the analysis of large networks of chemical reactions.
We are seeking an excellent and highly motivated individual with an MSc degree in computer science or a related subject. The ideal candidate has familiarity with one or more of the following areas: algorithmics, category theory, graph theory, graph transformation, algorithm engineering. Proven competences in programming and ease with formal thinking are a necessity.
This PhD project is a joint degree between University of Southern Denmark (Daniel Merkle, Jakob Lykke Andersen) and Leipzig University (Peter Stadler). Additionally, the student will have a three-months internship at BASF SE (Germany).
The TACsy consortium encompasses 11 partners across six countries in Europe and North America, including both academic institutions and industrial partners. The consortium consists of world-class scientists with competences spanning chemistry, biochemistry, computer science, and machine learning. All fifteen doctoral candidates will work with two research groups, and will obtain a degree from both host institutions, and complete research stays either at world-leading industry partners or at prestigious non-European academic partners:
- University of Southern Denmark (DK)
- University of Vienna (AT)
- Leipzig University (DE)
- Friedrich-Schiller-University Jena (DE)
- TU Vienna (AT)
- The University of Sheffield (UK)
- European Molecular Biology Laboratory (EMBL)
- BASF SE (DE)
- Fluigent SA (FR)
- Thermo Fisher Scientific GMBH (DE)
- Harvard Medical School (US)
The candidates will all be part of a strong joint PhD training programme, with a focus on career development, application writing, communication skills, and community building through scientific summer schools.
All candidates will be expected to:
- Have potential for conducting outstanding research, as demonstrated by scientific accomplishments (in particular quality of thesis, but also publications, code repositories, conference presentations, outreach activities, etc.).
- Be interested in working in a multidisciplinary and international research environment.
- Have excellent communication skills in English, verbally as well as in scientific writing.
- Be willing to undertake international research stays, internships, and travels.
See details about the network as a whole, its scientific content, and the application and selection process here.
Salary, working conditions, application process, etc.
All positions are fully funded, with very competitive salaries. More information on funding from the MSCA programme can be found here (beginning on page 78). Please note that a country correction coefficient (page 109) applies to the living allowance in order to ensure equal treatment and purchasing power parity for all researchers. Salary rules apply to the doctoral candidates hosted in the European Union and will change depending on the host institution.
The TACsy project wishes our staff to reflect the diversity of society and thus welcomes applications from all qualified candidates regardless of personal background. We are searching for a diverse group of candidates with very different backgrounds and qualities, who inspire and motivate each other. We want every talent to feel at home in our organisations and to have the same career opportunities. The position of working hours is flexible in order to accommodate individual needs and allow for the best possible work-life balance for each candidate.
The guaranteed Doctoral Candidate PhD funding from the European Commission is for 36 months. Therefore, appointment as a PhD Research Fellow is for three years. Employment stops automatically at the end of the period. The holder of the scholarship is not allowed to have other paid employment during the three-year period. Additional funding may be possible, depending on the local supervisor and in accordance with the regular PhD time in the country of origin.
Applications must be in English and must include the following:
- A research proposal/description of your approach to the project in question (max one page excluding references). This should be attached under the “Project description” option.
- A letter stating your specific interest, motivation, and qualifications for the project (max. two pages). This letter should be attached under the "Application form" option. (There is no application form.)
- Detailed CV, including personal contact information of two or three references. This should be attached under the “CV” option.
- Copies of diplomas, Bachelor as well as Master’s degree, including transcript of notes/grades. This should be collated into one document and attached under the “Certificates” option.
- At least two signed reference letters. These should be combined into one file and attached under the “References” option. Should your referees wish to send their letters directly to us, please have them send these to [email protected] mentioning your name and the title of the position in the subject line. And please note that these also need to reach us before the deadline.
Applications must be submitted electronically using the link “Apply online”. Attached files must be in Adobe PDF or Word format. Each box can only contain a single file of max. 10 Mb. We strongly recommend that you read “How to apply” before you apply.
Incomplete applications and applications received after the deadline will neither be considered nor evaluated. This also applies to reference letters.
Details on the selection process can be found here. Please note that the recruitment team reserves the right to conduct a second interview. Shortlisting may be used in the assessment process.
Please note that there are two limitations to apply for this programme, as specified in the MSCA regulations. Applicants must:
- Not be in possession of a PhD degree at the date of recruitment.
- Meet the Marie-Curie mobility rule (see pages 81-82 here). In TACsy, this means the applicants are not eligible for a specific position if it is true for both host institutions of the position that the applicant for more than 12 of the last 36 months has resided or performed a main activity (work, studies, etc.) in the country of that host institution. The host institutions relevant to this rule are for the present call located in (DC 1: Denmark and Germany), (DC 3: Austria and Germany), (DC 6: Austria and Germany), (DC 12: Austria and Denmark), (DC 13: Austria and Denmark).
Contact Information
For further information please contact Daniel Merkle, tel.: +45 6550 2322, e-mail: [email protected].
The successful applicant will, if employed at SDU, be employed in accordance with the agreement on salaried PhD scholars between the Ministry of Finance and AC (the Danish Confederation of Professional Associations).
The successful candidate will, if employed at SDU, be enrolled at this university in accordance with faculty regulations and the Danish Ministerial Order on the PhD Programme at the Universities (PhD order).
These positions are subject to the entry into force of grant agreement no 101072930 by and between the European Research Executive Agency and University of Southern Denmark and thereby funded by the European Union’s Horizon Europe Research and Innovation Programme.
Further information about the PhD-study can be found at the homepage of the University.
Further information for international applicants considering applying for a job at the University of Southern Denmark. Please take a look at the webpage from our International Staff Office (ISO) at The University of Southern Denmark.
Information og data
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Arbejdsstedet er beliggende i Hele Danmark
Jobbet er oprettet på vores service den 22.9.2023, men kan have været deaktiveret og genaktiveret igen.
Dagligt opdateret: Dette job opdateres dagligt ud fra jobudbyderens hjemmeside via vores søgemaskineteknologi og er aktivt lige nu.
- Forsker
- Mandag den 23. oktober 2023
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