Modeling protein-protein interactions requires accurate scoring functions that can rank potential poses (conformations) of a protein-protein complex to differentiate near-native poses from incorrect ones. Here, we propose a general framework for improving protein-protein pose ranking and other biomolecular interaction models using the LambdaLoss loss function from the Learning-to-Rank field. We test this framework by fine-tuning the energy prediction head of DFMDock with the LambdaLoss on an augmented dataset of 2.9M decoy poses derived from the DIPS dataset. On targets from the CAPRI score set benchmark, our fine-tuned ranking model LambdaDockScore is better at identifying correct poses in its top-1 and top-5 predictions compared to EuDockScore, a state-of-the-art method. LambdaDockScore also improves upon baseline DFMDock ranking performance for scoring antibody-antigen complexes and protein-protein complexes with very large or small binding interfaces.
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.· Information and Software Tec...· 394 citations· ⚡54
The possibility of inferring high-dimensional data inference in a model that consists of a prior and an auxiliary differentiable constraint given some additional information is considered, thereby allowing a range of potential applications in adapting models to new domains and tasks.
Alexandros Graikos, Esmeralda S. Whitammer, N. Jojic et al.· Neural Information Processin...· 316 citations· ⚡15
It is proved that any global minimizer of the trajectory balance objective can define a policy that samples exactly from the target distribution, and empirically demonstrate the benefits of the trajectories balance objective for GFlowNet convergence, diversity of generated samples, and robustness to long action sequenc...
Esmeralda S. Whitammer, Moksh Jain, Emmanuel Bengio et al.· Neural Information Processin...· 302 citations· ⚡60
An algorithm is proposed which leverages disentangled semantic factors to generate adversarial perturbation by altering controlled semantic attributes to fool the learner towards various "adversarial" targets.
Haonan Qiu, Chaowei Xiao, Lei Yang et al.· arXiv.org· 208 citations· ⚡17
This work proposes a HALO that directly maximizes the utility of generations instead of maximizing the log-likelihood of preferences, and suggests that the best loss depends on the inductive biases most appropriate for a given setting, an oft-overlooked consideration.
This state-of-practice investigation was performed using a literature review followed by a multiple-case study approach and presents how inconsistency between managerial strategies and execution can lead to failure by means of a behavioral framework.
Carmine Giardino, Xiaofeng Wang, P. Abrahamsson· International Conference on...· 175 citations· ⚡19
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