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Publications
Posterior inference of Hi-C contact frequency through sampling
Hi-C is one of the most widely used approaches to study three-dimensional genome conformations. Contacts captured by a Hi-C experiment are r… (voir plus)epresented in a contact frequency matrix. Due to the limited sequencing depth and other factors, Hi-C contact frequency matrices are only approximations of the true interaction frequencies and are further reported without any quantification of uncertainty. Hence, downstream analyses based on Hi-C contact maps (e.g., TAD and loop annotation) are themselves point estimations. Here, we present the Hi-C interaction frequency sampler (HiCSampler) that reliably infers the posterior distribution of the interaction frequency for a given Hi-C contact map by exploiting dependencies between neighboring loci. Posterior predictive checks demonstrate that HiCSampler can infer highly predictive chromosomal interaction frequency. Summary statistics calculated by HiCSampler provide a measurement of the uncertainty for Hi-C experiments, and samples inferred by HiCSampler are ready for use by most downstream analysis tools off the shelf and permit uncertainty measurements in these analyses without modifications.
While Transformers have enabled tremendous progress in various application settings, such architectures still trail behind traditional symbo… (voir plus)lic planners for solving complex decision making tasks. In this work, we demonstrate how to train Transformers to solve complex planning tasks. This is accomplished by training an encoder-decoder Transformer model to predict the search dynamics of the
While Transformers have enabled tremendous progress in various application settings, such architectures still lag behind traditional symboli… (voir plus)c planners for solving complex decision making tasks. In this work, we demonstrate how to train Transformers to solve complex planning tasks and present Searchformer, a Transformer model that optimally solves previously unseen Sokoban puzzles 93.7% of the time, while using up to 26.8% fewer search steps than standard
While Transformers have enabled tremendous progress in various application settings, such architectures still trail behind traditional symbo… (voir plus)lic planners for solving complex decision making tasks. In this work, we demonstrate how to train Transformers to solve complex planning tasks. This is accomplished by training an encoder-decoder Transformer model to predict the search dynamics of the
Human activity recognition (HAR) is a popular research field in computer vision that has already been widely studied. However, it is still a… (voir plus)n active research field since it plays an important role in many current and emerging real-world intelligent systems, like visual surveillance and human-computer interaction. Deep reinforcement learning (DRL) has recently been used to address the activity recognition problem with various purposes, such as finding attention in video data or obtaining the best network structure. DRL-based HAR has only been around for a short time, and it is a challenging, novel field of study. Therefore, to facilitate further research in this area, we have constructed a comprehensive survey on activity recognition methods that incorporate DRL. Throughout the article, we classify these methods according to their shared objectives and delve into how they are ingeniously framed within the DRL framework. As we navigate through the survey, we conclude by shedding light on the prominent challenges and lingering questions that await the attention of future researchers, paving the way for further advancements and breakthroughs in this exciting domain.
2024-02-19
IEEE Transactions on Neural Networks and Learning Systems (publié)
Human activity recognition (HAR) is a popular research field in computer vision that has already been widely studied. However, it is still a… (voir plus)n active research field since it plays an important role in many current and emerging real-world intelligent systems, like visual surveillance and human-computer interaction. Deep reinforcement learning (DRL) has recently been used to address the activity recognition problem with various purposes, such as finding attention in video data or obtaining the best network structure. DRL-based HAR has only been around for a short time, and it is a challenging, novel field of study. Therefore, to facilitate further research in this area, we have constructed a comprehensive survey on activity recognition methods that incorporate DRL. Throughout the article, we classify these methods according to their shared objectives and delve into how they are ingeniously framed within the DRL framework. As we navigate through the survey, we conclude by shedding light on the prominent challenges and lingering questions that await the attention of future researchers, paving the way for further advancements and breakthroughs in this exciting domain.
2024-02-19
IEEE Transactions on Neural Networks and Learning Systems (publié)
In this blogpost we discuss the idea of teaching neural networks to reach fixed points when reasoning. Specifically, on the algorithmic reas… (voir plus)oning benchmark CLRS the current neural networks are told the number of reasoning steps they need. While a quick fix is to add a termination network that predicts when to stop, a much more salient inductive bias is that the neural network shouldn't change it's answer any further once the answer is correct, i.e. it should reach a fixed point. This is supported by denotational semantics, which tells us that while loops that terminate are the minimum fixed points of a function. We implement this idea with the help of deep equilibrium models and discuss several hurdles one encounters along the way. We show on several algorithms from the CLRS benchmark the partial success of this approach and the difficulty in making it work robustly across all algorithms.
