To apply federated learning to drug discovery we developed a novel platform in the context of European Innovative Medicines Initiative (IMI) project MELLODDY (grant n{\deg}831472), which was comprised of 10 pharmaceutical companies, academic research labs, large industrial companies and startups. The MELLODDY platform was the first industry-scale platform to enable the creation of a global federated model for drug discovery without sharing the confidential data sets of the individual partners. The federated model was trained on the platform by aggregating the gradients of all contributing partners in a cryptographic, secure way following each training iteration. The platform was deployed on an Amazon Web Services (AWS) multi-account architecture running Kubernetes clusters in private subnets. Organisationally, the roles of the different partners were codified as different rights and permissions on the platform and administrated in a decentralized way. The MELLODDY platform generated new scientific discoveries which are described in a companion paper.
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Reading comprehension of legal text can be a particularly challenging task due to the length and complexity of legal clauses and a shortage of expert-annotated datasets. To address this challenge, we introduce the Merger Agreement Understanding Dataset (MAUD), an expert-annotated reading comprehension dataset based on the American Bar Association's 2021 Public Target Deal Points Study, with over 39,000 examples and over 47,000 total annotations. Our fine-tuned Transformer baselines show promising results, with models performing well above random on most questions. However, on a large subset of questions, there is still room for significant improvement. As the only expert-annotated merger agreement dataset, MAUD is valuable as a benchmark for both the legal profession and the NLP community.
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We demonstrate how efficient autonomous drone swarms can be in detecting and tracking occluded targets in densely forested areas, such as lost people during search and rescue missions. Exploration and optimization of local viewing conditions, such as occlusion density and target view obliqueness, provide much faster and much more reliable results than previous, blind sampling strategies that are based on pre-defined waypoints. An adapted real-time particle swarm optimization and a new objective function are presented that are able to deal with dynamic and highly random through-foliage conditions. Synthetic aperture sensing is our fundamental sampling principle, and drone swarms are employed to approximate the optical signals of extremely wide and adaptable airborne lenses.
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Many problems involve the use of models which learn probability distributions or incorporate randomness in some way. In such problems, because computing the true expected gradient may be intractable, a gradient estimator is used to update the model parameters. When the model parameters directly affect a probability distribution, the gradient estimator will involve score function terms. This paper studies baselines, a variance reduction technique for score functions. Motivated primarily by reinforcement learning, we derive for the first time an expression for the optimal state-dependent baseline, the baseline which results in a gradient estimator with minimum variance. Although we show that there exist examples where the optimal baseline may be arbitrarily better than a value function baseline, we find that the value function baseline usually performs similarly to an optimal baseline in terms of variance reduction. Moreover, the value function can also be used for bootstrapping estimators of the return, leading to additional variance reduction. Our results give new insight and justification for why value function baselines and the generalized advantage estimator (GAE) work well in practice.
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We propose a fairness-aware learning framework that mitigates intersectional subgroup bias associated with protected attributes. Prior research has primarily focused on mitigating one kind of bias by incorporating complex fairness-driven constraints into optimization objectives or designing additional layers that focus on specific protected attributes. We introduce a simple and generic bias mitigation approach that prevents models from learning relationships between protected attributes and output variable by reducing mutual information between them. We demonstrate that our approach is effective in reducing bias with little or no drop in accuracy. We also show that the models trained with our learning framework become causally fair and insensitive to the values of protected attributes. Finally, we validate our approach by studying feature interactions between protected and non-protected attributes. We demonstrate that these interactions are significantly reduced when applying our bias mitigation.
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Automatic segmentation is essential for the brain tumor diagnosis, disease prognosis, and follow-up therapy of patients with gliomas. Still, accurate detection of gliomas and their sub-regions in multimodal MRI is very challenging due to the variety of scanners and imaging protocols. Over the last years, the BraTS Challenge has provided a large number of multi-institutional MRI scans as a benchmark for glioma segmentation algorithms. This paper describes our contribution to the BraTS 2022 Continuous Evaluation challenge. We propose a new ensemble of multiple deep learning frameworks namely, DeepSeg, nnU-Net, and DeepSCAN for automatic glioma boundaries detection in pre-operative MRI. It is worth noting that our ensemble models took first place in the final evaluation on the BraTS testing dataset with Dice scores of 0.9294, 0.8788, and 0.8803, and Hausdorf distance of 5.23, 13.54, and 12.05, for the whole tumor, tumor core, and enhancing tumor, respectively. Furthermore, the proposed ensemble method ranked first in the final ranking on another unseen test dataset, namely Sub-Saharan Africa dataset, achieving mean Dice scores of 0.9737, 0.9593, and 0.9022, and HD95 of 2.66, 1.72, 3.32 for the whole tumor, tumor core, and enhancing tumor, respectively. The docker image for the winning submission is publicly available at (https://hub.docker.com/r/razeineldin/camed22).
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As language models (LMs) scale, they develop many novel behaviors, good and bad, exacerbating the need to evaluate how they behave. Prior work creates evaluations with crowdwork (which is time-consuming and expensive) or existing data sources (which are not always available). Here, we automatically generate evaluations with LMs. We explore approaches with varying amounts of human effort, from instructing LMs to write yes/no questions to making complex Winogender schemas with multiple stages of LM-based generation and filtering. Crowdworkers rate the examples as highly relevant and agree with 90-100% of labels, sometimes more so than corresponding human-written datasets. We generate 154 datasets and discover new cases of inverse scaling where LMs get worse with size. Larger LMs repeat back a dialog user's preferred answer ("sycophancy") and express greater desire to pursue concerning goals like resource acquisition and goal preservation. We also find some of the first examples of inverse scaling in RL from Human Feedback (RLHF), where more RLHF makes LMs worse. For example, RLHF makes LMs express stronger political views (on gun rights and immigration) and a greater desire to avoid shut down. Overall, LM-written evaluations are high-quality and let us quickly discover many novel LM behaviors.
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Often clickbait articles have a title that is phrased as a question or vague teaser that entices the user to click on the link and read the article to find the explanation. We developed a system that will automatically find the answer or explanation of the clickbait hook from the website text so that the user does not need to read through the text themselves. We fine-tune an extractive question and answering model (RoBERTa) and an abstractive one (T5), using data scraped from the 'StopClickbait' Facebook pages and Reddit's 'SavedYouAClick' subforum. We find that both extractive and abstractive models improve significantly after finetuning. We find that the extractive model performs slightly better according to ROUGE scores, while the abstractive one has a slight edge in terms of BERTscores.
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Structural Health Monitoring (SHM) describes a process for inferring quantifiable metrics of structural condition, which can serve as input to support decisions on the operation and maintenance of infrastructure assets. Given the long lifespan of critical structures, this problem can be cast as a sequential decision making problem over prescribed horizons. Partially Observable Markov Decision Processes (POMDPs) offer a formal framework to solve the underlying optimal planning task. However, two issues can undermine the POMDP solutions. Firstly, the need for a model that can adequately describe the evolution of the structural condition under deterioration or corrective actions and, secondly, the non-trivial task of recovery of the observation process parameters from available monitoring data. Despite these potential challenges, the adopted POMDP models do not typically account for uncertainty on model parameters, leading to solutions which can be unrealistically confident. In this work, we address both key issues. We present a framework to estimate POMDP transition and observation model parameters directly from available data, via Markov Chain Monte Carlo (MCMC) sampling of a Hidden Markov Model (HMM) conditioned on actions. The MCMC inference estimates distributions of the involved model parameters. We then form and solve the POMDP problem by exploiting the inferred distributions, to derive solutions that are robust to model uncertainty. We successfully apply our approach on maintenance planning for railway track assets on the basis of a "fractal value" indicator, which is computed from actual railway monitoring data.
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Scale-invariance is an open problem in many computer vision subfields. For example, object labels should remain constant across scales, yet model predictions diverge in many cases. This problem gets harder for tasks where the ground-truth labels change with the presentation scale. In image quality assessment (IQA), downsampling attenuates impairments, e.g., blurs or compression artifacts, which can positively affect the impression evoked in subjective studies. To accurately predict perceptual image quality, cross-resolution IQA methods must therefore account for resolution-dependent errors induced by model inadequacies as well as for the perceptual label shifts in the ground truth. We present the first study of its kind that disentangles and examines the two issues separately via KonX, a novel, carefully crafted cross-resolution IQA database. This paper contributes the following: 1. Through KonX, we provide empirical evidence of label shifts caused by changes in the presentation resolution. 2. We show that objective IQA methods have a scale bias, which reduces their predictive performance. 3. We propose a multi-scale and multi-column DNN architecture that improves performance over previous state-of-the-art IQA models for this task, including recent transformers. We thus both raise and address a novel research problem in image quality assessment.
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