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Deep Learning with Proteins

Hugging Face Blog · huggingface.co · December 2, 2022
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MIT News · Artificial Intelligence Aug 27, 2026

Looking beyond natural sequences

A new machine-learning framework aims to improve the success rate of computational protein design while moving away from results that reproduce sequences found in nature.

Related papers

#machine learning Open access May 2017

What Influences the Speed of Prototyping? An Empirical Investigation of Twenty Software Startups

It is essential for startups to quickly experiment business ideas by building tangible prototypes and collecting user feedback on them. As prototyping is an inevitable part of learning for early stage software startups, how fast startups can learn depends on how fast they can prototype. Despite of the importance, there is a lack of research about prototyping in software startups. In this study, we aimed at understanding what are factors influencing different types of prototyping activities. We conducted a multiple case study on twenty European software startups. The results are two folds; firstly we propose a prototype-centric learning model in early stage software startups. Secondly, we identify factors occur as barriers but also facilitators for prototyping in early stage software startups. The factors are grouped into (1) artifacts, (2) team competence, (3) collaboration, (4) customer and (5) process dimensions. To speed up a startup’s progress at the early stage, it is important to incorporate the learning objective into a well-defined collaborative approach of prototyping.

Anh Nguyen-Duc, Xiaofeng Wang, P. Abrahamsson · 44 citations · ⚡5

Context Before Code: An Experience Report on Vibe Coding in Practice

Code-generating tools are increasingly used in software development, yet experience reports on conversational"vibe coding"under production constraints remain limited. This paper presents an experience report from a small full-stack team that applied contextual prompting and explicit architectural constraints to build (i) a multi-project agent learning platform designed for sustained, production-oriented use and (ii) an academic retrieval-augmented generation system. The agent platform supports multiple isolated projects, each with structured memory and background processing, thereby enforcing project-level isolation. The RAG system provides citation-grounded answers, role-based access control, and evaluation tracking. Across both systems, vibe coding accelerated scaffolding and integration. However, the generated code often under-specified isolation rules and infrastructure constraints when these were not explicitly defined. Consequently, aspects such as multi-tenancy, access control, memory policies, and asynchronous processing required deliberate architectural design and verification. We observe a shift in engineering effort from boilerplate implementation toward constraint specification and enforcement auditing. We also identify recurring architectural"non-delegation zones"where conversational code generation remains insufficient for production reliability.

Md Nasir Uddin Shuvo, M. Islam, Mahade Hasan et al. · 0 citations
#machine learning Review Open access Oct 2014

Software development in startup companies: A systematic mapping study

Context: Software startups are newly created companies with no operating history and fast in producing cutting-edge technologies. These companies develop software under highly uncertain conditions, tackling fast-growing markets under severe lack of resources. Therefore, software startups present a unique combination of characteristics which pose several challenges to software development activities. Objective: This study aims to structure and analyze the literature on software development in startup companies, determining thereby the potential for technology transfer and identifying software development work practices reported by practitioners and researchers. Method: We conducted a systematic mapping study, developing a classification schema, ranking the selected primary studies according their rigor and relevance, and analyzing reported software development work practices in startups. Results: A total of 43 primary studies were identified and mapped, synthesizing the available evidence on software development in startups. Only 16 studies are entirely dedicated to software development in startups, of which 10 result in a weak contribution (advice and implications (6); lesson learned (3); tool (1)). Nineteen studies focus on managerial and organizational factors. Moreover, only 9 studies exhibit high scientific rigor and relevance. From the reviewed primary studies, 213 software engineering work practices were extracted, categorized and analyzed. Conclusion: This mapping study provides the first systematic exploration of the state-of-art on software startup research. The existing body of knowledge is limited to a few high quality studies. Furthermore, the results indicate that software engineering work practices are chosen opportunistically, adapted and configured to provide value under the constrains imposed by the startup context.

Nicolò Paternoster, Carmine Giardino, M. Unterkalmsteiner et al. · 394 citations · ⚡54
#machine learning Review Open access Jun 2014

Why Early-Stage Software Startups Fail: A Behavioral Framework

Software startups are newly created companies with little operating history and oriented towards producing cutting-edge products. As their time and resources are extremely scarce, and one failed project can put them out of business, startups need effective practices to face with those unique challenges. However, only few scientific studies attempt to address characteristics of failure, especially during the early-stage. With this study we aim to raise our understanding of the failure of early-stage software startup companies. This state-of-practice investigation was performed using a literature review followed by a multiple-case study approach. The results present how inconsistency between managerial strategies and execution can lead to failure by means of a behavioral framework. Despite strategies reveal the first need to understand the problem/solution fit, actual executions prioritize the development of the product to launch on the market as quickly as possible to verify product/market fit, neglecting the necessary learning process.

Carmine Giardino, Xiaofeng Wang, P. Abrahamsson · 174 citations · ⚡19