Decision support in portfolio/planning

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Big picture and reviews (no specific models)

• Predictive validity in drug discovery: what it is, why it matters and how to improve it
• How to improve R&D productivity: the pharmaceutical industry’s grand challenge
• Decision-support challenges in the chemical-pharmaceutical industry: Findings and future research directions
• Challenges and opportunities in enterprise-wide optimization in the pharmaceutical industry
• Decision-support challenges in the chemical-pharmaceutical industry: Findings and future research directions
• Process industry supply chains: Advances and challenges
• Decision-making in product portfolios of pharmaceutical research and development – managing streams of innovation in highly regulated markets

Pharma R&D pipeline mgmt

• Pharmaceutical R & D pipeline management under trial duration uncertainty
• New Product Development with Discrete Event Simulation: Application to Portfolio Management for the Pharmaceutical Industry
• Managing a Portfolio of Interdependent New Product Candidates in the Pharmaceutical Industry
• Heuristic solution approaches to the pharmaceutical R&D pipeline management problem
• A stochastic programming approach for clinical trial planning in new drug development
• Portfolio-wide Optimization of Pharmaceutical R&D Activities Using Mathematical Programming, probably worth checking the refs and citing literature for good stuff
• Integrated production planning and inventory management in a multinational pharmaceutical supply chain and its precursor model Integrated supply chain planning for multinational pharmaceutical enterprises would be good places to start
• A mathematical model for maximizing the value of phase 3 drug development portfolios incorporating budget constraints and risk

Industrial scheduling

• Resource-Constrained Scheduling of Tests in New Product Development
• Variants to a knapsack decomposition heuristic for solving R&D pipeline management problems
• Optimal planning in large multi-site production networks
• Supply chain design and multilevel planning—An industrial case
• General framework and modeling approach classification for chemical production scheduling
• Multiproject Scheduling with Limited Resources: A Zero-One Programming Approach (1969)
• Integrating information, financial, and material flows in a chemical supply chain

Scheduling specific to Petri Nets

• van der Aalst, Wil MP. "Petri net based scheduling." Operations-Research-Spektrum 18 (1996): 219-229.
• Tuncel, Gonca, and G. Mirac Bayhan. "Applications of Petri nets in production scheduling: a review." The International Journal of Advanced Manufacturing Technology 34 (2007): 762-773.
• Huang, Bo, et al. "Scheduling of resource allocation systems with timed Petri nets: A survey." ACM Computing Surveys 55.11 (2023): 1-27.
• Rosell, Jan. "Assembly and task planning using Petri nets: a survey." Proceedings of the institution of mechanical engineers, part B: journal of engineering manufacture 218.8 (2004): 987-994.
• Tuncel, Gonca, and G. Mirac Bayhan. "Applications of Petri nets in production scheduling: a review." The International Journal of Advanced Manufacturing Technology 34 (2007): 762-773.

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One thing we want to consider is how can formal tools help move "seamlessly" between time-ignorant or discrete time representations such as MILP models and more "dynamic" models like PNs.

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Scheduling stuff:

• https://www.sciencedirect.com/science/article/pii/S2405896315001044?ref=pdf_download&fr=RR-2&rr=872ee255fdef7d76
• http://egon.cheme.cmu.edu/ewo/docs/CMU_EWO_Sep_08.pdf
• https://www.hrpub.org/download/20141101/UJME1-15102566.pdf
• https://hal.science/hal-00361395/document

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Implement state task networks and resource-task networks

• RTN refs 2022, Applications of the RTN scheduling model in the chemical industry and 1994, Unified frameworks for optimal process planning and scheduling
• STN refs (simpler, start here) 1993, A general algorithm for short-term scheduling of batch operations—I. MILP formulation and 1993, A general algorithm for short-term scheduling of batch operations—II. Computational issues
• Lots of MIPs done very clearly for STN: https://www.sciencedirect.com/science/article/abs/pii/S0098135405000463 "Review, extensions and computational comparison of MILP formulations for scheduling of batch processes"