Assoc Dir , Representation Learning, Data Science

Company: Hispanic Alliance for Career Enhancement
Location: Cambridge
Posted on: June 1, 2025

Job Description:

Job DescriptionTheData Science and Scientific Informatics Teamat Research and Development Sciences IT (RaDS-IT) of our Company is seeking a Lead Data Scientist for Representation Learning.Our team is a diverse collection of scientists and engineers working towards the same goal - enabling and accelerating the next generation of pharmaceutical sciences. We collaborate closely with laboratory and in silico scientists, proposing and implementing innovative solutions that enable new organizational capabilities.An ideal candidate will have a strong background in computational biology, machine learning, and chemistry, with a focus on developing and applying advanced methods for molecular and protein design. This role will involve creating and optimizing foundation models that support the design and evaluation of novel therapeutic candidates, in close collaboration with RaDS-IT product lines supporting the corresponding functionalities under Discovery Chemistry, Discovery Biologics, and IDVAX.Key Responsibilities:Molecular Representation Learning:

• Develop, validate, and implement state-of-the-art machine learning and deep learning algorithms for molecular representation, focusing on capturing complex chemical properties and biological activities.
• Utilize various techniques, including graph neural networks and transformer architectures, to enhance molecular and protein representations.
• Collaborate with cross-functional teams to contribute in the design of novel small molecules and protein constructs tailored to specific therapeutic targets.Protein Design:
  • Apply computational tools and methodologies for de novo protein design and engineering such as RF-Diffusion, ProteinMPNN and AlphaFold, using AI-driven approaches to predict protein stability, function, and interaction.
  • Oversee the integration of structural biology data into machine learning models to improve predictive capabilities.Foundation Models:
    • Lead initiatives to develop foundation models that enable scalable and efficient molecular and protein design workflows.
    • Conduct research on transfer learning and few-shot learning to maximize model performance on diverse datasets.Data Management and Collaboration:
      • Manage and curate large-scale datasets relevant to molecular and protein design, ensuring data integrity and accessibility for team members.
      • Collaborate closely with experimental chemists, biologists, data scientists, and other product teams on RaDS-IT to translate computational insights into practical aMentorship and Leadership:
        • Provide mentorship to junior scientists and researchers on the team, fostering an environment of creativity and scientific rigor.
        • Contribute to strategic planning and project prioritization within the team and at the higher level of the organization.Publications and Presentations:
          • Lead efforts in publishing research findings in peer-reviewed journals and presenting at conferences.
          • Stay abreast of advancements in molecular representation learning and related fields to inform ongoing research and development.Required Skills:
            • Ph.D. in Computational Biology, Bioinformatics, Chemistry, Machine Learning, or a related field, with 3+ years of experience in industry (including full time job and internship/co-op)
            • Proven experience in molecular and/or protein design, with a strong publication record in relevant areas.
            • Proficient in programming languages such as Python and R, and familiarity with ML frameworks (e.g., TensorFlow, PyTorch).
            • Strong understanding of molecular modeling software and tools (e.g., RDKit, OpenMM, AlphaFold, RosettaFold, MPNN, RF-Diffusion).
            • Excellent communication skills and ability to work collaboratively in a multidisciplinary team.
            • Deep knowledge of statistical methods and experimental design as applied to computational biology.
            • Experience with large-scale datasets and big data analytics techniques.Optional Skills:
              • Experience with cloud computing platforms (e.g., AWS, Google Cloud) for computational modeling and data analysis.
              • Familiarity with cheminformatics and bioinformatics databases and tools (e.g., ChEMBL, UniProt).
              • Knowledge of synthetic chemistry or organic chemistry principles.
              • Experience in project management and leading cross-functional research initiatives.
              • Understanding of regulatory requirements in drug development.
              • Exposure to emerging AI techniques, such as reinforcement learning or generative models.Current Employees apply Current Contingent Workers apply US and Puerto Rico Residents Only:Our company is committed to inclusion, ensuring that candidates can engage in a hiring process that exhibits their true capabilities. Please if you need an accommodation during the application or hiring process.As an Equal Employment Opportunity Employer, we provide equal opportunities to all employees and applicants for employment and prohibit discrimination on the basis of race, color, age, religion, sex, sexual orientation, gender identity, national origin, protected veteran status, disability status, or other applicable legally protected characteristics.As a federal contractor, we comply with all affirmative action requirements for protected veterans and individuals with disabilities. For more information about personal rights under the U.S. Equal Opportunity Employment laws, visit:We are proud to be a company that embraces the value of bringing together, talented, and committed people with diverse experiences, perspectives, skills and backgrounds. The fastest way to breakthrough innovation is when people with diverse ideas, broad experiences, backgrounds, and skills come together in an inclusive environment. We encourage our colleagues to respectfully challenge one another's thinking and approach problems collectively.U.S. Hybrid Work ModelEffective September 5, 2023, employees in office-based positions in the U.S. will be working a Hybrid work consisting of three total days on-site per week, Monday - Thursday, although the specific days may vary by site or organization, with Friday designated as a remote-working day, unless business critical tasks require an on-site presence.This Hybrid work model does not apply to, and daily in-person attendance is required for, field-based positions; facility-based, manufacturing-based, or research-based positions where the work to be performed is located at a Company site; positions covered by a collective-bargaining agreement (unless the agreement provides for hybrid work); or any other position for which the Company has determined the job requirements cannot be reasonably met working remotely. Please note, this Hybrid work model guidance also does not apply to roles that have been designated as "remote".The Company is required to provide a reasonable estimate of the salary range for this job in certain states and cities within the United States. Final determinations with respect to salary will take into account a number of factors, which may include, but not be limited to the primary work location and the chosen candidate's relevant skills, experience, and education.Expected US salary range:$153,800.00 - $242,200.00Available benefits include bonus eligibility, long term incentive if applicable, health care and other insurance benefits (for employee and family), retirement benefits, paid holidays, vacation, and sick days. A summary of benefits is listed .San Francisco Residents Only:We will consider qualified applicants with arrest and conviction records for employment in compliance with the San Francisco Fair Chance OrdinanceLos Angeles Residents Only:We will consider for employment all qualified applicants, including those with criminal histories, in a manner consistent with the requirements of applicable state and local laws, including the City of Los Angeles' Fair Chance Initiative for Hiring OrdinanceSearch Firm Representatives Please Read Carefully
                Merck & Co., Inc., Rahway, NJ, USA, also known as Merck Sharp & Dohme LLC, Rahway, NJ, USA, does not accept unsolicited assistance from search firms for employment opportunities. All CVs / resumes submitted by search firms to any employee at our company without a valid written search agreement in place for this position will be deemed the sole property of our company. No fee will be paid in the event a candidate is hired by our company as a result of an agency referral where no pre-existing agreement is in place. Where agency agreements are in place, introductions are position specific. Please, no phone calls or emails.Employee Status:RegularRelocation:DomesticVISA Sponsorship:NoTravel Requirements:25%Flexible Work Arrangements:HybridShift:Not IndicatedValid Driving License:NoHazardous Material(s):n/a
                Required Skills:Business, Business Intelligence (BI), Computational Biology, Computer Programming, Data Analysis, Database Design, Data Engineering, Data Modeling, Data Science, Data Visualization, Drug Development, Machine Learning, Organic Chemistry, Pharmaceutical Sciences, Project Management, Project Prioritization, Protein Modeling, R&D Management, Social Collaboration, Software Development, Stakeholder Relationship Management, Strategic Management, Strategic Planning, Structural Biology, Waterfall Model
                Preferred Skills:Job Posting End Date:06/19/2025*A job posting is effective until 11:59:59PM on the day BEFOREthe listed job posting end date. Please ensure you apply to a job posting no later than the day BEFORE the job posting end date.
                Requisition ID:R350476
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Keywords: Hispanic Alliance for Career Enhancement, Malden , Assoc Dir , Representation Learning, Data Science, Other , Cambridge, Massachusetts