Deep Learning and big data have shown tremendous success in bioinformatics and computational biology in recent years; artificial intelligence methods have also significantly contributed in the task of protein function classification. This review paper analyzes the recent developments in approaches for the task of predicting protein function using deep learning. We explain the importance of determining the protein function and why automating the following task is crucial. Then, after reviewing the widely used deep learning techniques for this task, we continue our review and highlight the emergence of the modern State of The Art (SOTA) deep learning models which have achieved groundbreaking results in the field of computer vision, natural language processing and multi-modal learning in the last few years. We hope that this review will provide a broad view of the current role and advances of deep learning in biological sciences, especially in predicting protein function tasks and encourage new researchers to contribute to this area.

The facility location problems (FLPs) are a typical class of NP-hard combinatorial optimization problems, which are widely seen in the supply chain and logistics. Many mathematical and heuristic algorithms have been developed for optimizing the FLP. In addition to the transportation cost, there are usually multiple conflicting objectives in realistic applications. It is therefore desirable to design algorithms that find a set of Pareto solutions efficiently without enormous search cost. In this paper, we consider the multi-objective facility location problem (MO-FLP) that simultaneously minimizes the overall cost and maximizes the system reliability. We develop a learning-based approach to predicting the distribution probability of the entire Pareto set for a given problem. To this end, the MO-FLP is modeled as a bipartite graph optimization problem and two graph neural networks are constructed to learn the implicit graph representation on nodes and edges. The network outputs are then converted into the probability distribution of the Pareto set, from which a set of non-dominated solutions can be sampled non-autoregressively. Experimental results on MO-FLP instances of different scales show that the proposed approach achieves a comparable performance to a widely used multi-objective evolutionary algorithm in terms of the solution quality while significantly reducing the computational cost for search.

The miniaturization of inertial measurement units (IMUs) facilitates their widespread use in a growing number of application domains. Orientation estimation is a prerequisite for most further data processing steps in inertial motion tracking, such as position/velocity estimation, joint angle estimation, and 3D visualization. Errors in the estimated orientations severely affect all further processing steps. Recent systematic comparisons of existing algorithms show that out-of-the-box accuracy is often low and that application-specific tuning is required to obtain high accuracy. In the present work, we propose and extensively evaluate a quaternion-based orientation estimation algorithm that is based on a novel approach of filtering the acceleration measurements in an almost-inertial frame and that includes extensions for gyroscope bias estimation and magnetic disturbance rejection, as well as a variant for offline data processing. In contrast to all existing work, we perform an extensive evaluation, using a large collection of publicly available datasets and eight literature methods for comparison. The proposed method consistently outperforms all literature methods and achieves an average RMSE of 2.9{\deg}, while the errors obtained with literature methods range from 5.3{\deg} to 16.7{\deg}. Since the evaluation was performed with one single fixed parametrization across a very diverse dataset collection, we conclude that the proposed method provides unprecedented out-of-the-box performance for a broad range of motions, sensor hardware, and environmental conditions. This gain in orientation estimation accuracy is expected to advance the field of IMU-based motion analysis and provide performance benefits in numerous applications. The provided open-source implementation makes it easy to employ the proposed method.

While generative models have recently become ubiquitous in many scientific areas, less attention has been paid to their evaluation. For molecular generative models, the state-of-the-art examines their output in isolation or in relation to its input. However, their biological and functional properties, such as ligand-target interaction is not being addressed. In this study, a novel biologically-inspired benchmark for the evaluation of molecular generative models is proposed. Specifically, three diverse reference datasets are designed and a set of metrics are introduced which are directly relevant to the drug discovery process. In particular we propose a recreation metric, apply drug-target affinity prediction and molecular docking as complementary techniques for the evaluation of generative outputs. While all three metrics show consistent results across the tested generative models, a more detailed comparison of drug-target affinity binding and molecular docking scores revealed that unimodal predictiors can lead to erroneous conclusions about target binding on a molecular level and a multi-modal approach is thus preferrable. The key advantage of this framework is that it incorporates prior physico-chemical domain knowledge into the benchmarking process by focusing explicitly on ligand-target interactions and thus creating a highly efficient tool not only for evaluating molecular generative outputs in particular, but also for enriching the drug discovery process in general.

Abstract--Although Deep Neural Networks (DNNs) have shown a strong capacity to solve large-scale problems in many areas, such DNNs with voluminous parameters are hard to be deployed in a real-time system. To tackle this issue, Teacher-Student architectures were first utilized in knowledge distillation, where simple student networks can achieve comparable performance to deep teacher networks. Recently, Teacher-Student architectures have been effectively and widely embraced on various knowledge learning objectives, including knowledge distillation, knowledge expansion, knowledge adaption, and multi-task learning. With the help of Teacher-Student architectures, current studies are able to achieve multiple knowledge-learning objectives through lightweight and effective student networks. In addition, we systematically introduce the knowledge construction and optimization process during the knowledge learning and then analyze various Teacher-Student architectures and effective learning schemes that have been leveraged to learn representative and robust knowledge. This paper also summarizes the latest applications of Teacher-Student architectures based on different purposes (i.e., classification, recognition, and generation). Finally, the potential research directions of knowledge learning are investigated on the Teacher-Student architecture design, the quality of knowledge, and the theoretical studies of regression-based learning, respectively. With this comprehensive survey, both industry practitioners and the academic community can learn insightful guidelines about Teacher-Student architectures on multiple knowledge learning objectives.

Recent progress in self-supervised or unsupervised machine learning has opened the possibility of building a full speech processing system from raw audio without using any textual representations or expert labels such as phonemes, dictionaries or parse trees. The contribution of the Zero Resource Speech Challenge series since 2015 has been to break down this long-term objective into four well-defined tasks -- Acoustic Unit Discovery, Spoken Term Discovery, Discrete Resynthesis, and Spoken Language Modeling -- and introduce associated metrics and benchmarks enabling model comparison and cumulative progress. We present an overview of the six editions of this challenge series since 2015, discuss the lessons learned, and outline the areas which need more work or give puzzling results.

In this post, we will be discussing the teachings of the DeepLerning.AI TensorFlow Developer Certification available on Coursera and how what is said here can help you before, during, and/or even after starting your professional career development. To oversimplify this broad and dense field, one could temptingly state that Deep Learning is a method in Machine Learning and Artificial Intelligence that extrapolates data using one to many neural networks, nodes, and/or stages to pinpoint a final result. Similar to like when trying to spread out a deck of cards and then slowly picking out all the correct cards to get a royal flush, Deep Learning algorithms are fed vast amounts of data to store in memory and then are used to scan through and find similarities in new unseen data. Like a well-oiled cybernetic machine, deep learning algorithms use reduction and deduction to solve complex classification and regression problems. Being that said, do keep in mind that the comprehensive reviews seen here do not come from an expert in this field and thus are heavily subjected to a bias of interpretation of just another person that completed this course.

Mobile Edge Caching (MEC) is a revolutionary technology for the Sixth Generation (6G) of wireless networks with the promise to significantly reduce users' latency via offering storage capacities at the edge of the network. The efficiency of the MEC network, however, critically depends on its ability to dynamically predict/update the storage of caching nodes with the top-K popular contents. Conventional statistical caching schemes are not robust to the time-variant nature of the underlying pattern of content requests, resulting in a surge of interest in using Deep Neural Networks (DNNs) for time-series popularity prediction in MEC networks. However, existing DNN models within the context of MEC fail to simultaneously capture both temporal correlations of historical request patterns and the dependencies between multiple contents. This necessitates an urgent quest to develop and design a new and innovative popularity prediction architecture to tackle this critical challenge. The paper addresses this gap by proposing a novel hybrid caching framework based on the attention mechanism. Referred to as the parallel Vision Transformers with Cross Attention (ViT-CAT) Fusion, the proposed architecture consists of two parallel ViT networks, one for collecting temporal correlation, and the other for capturing dependencies between different contents. Followed by a Cross Attention (CA) module as the Fusion Center (FC), the proposed ViT-CAT is capable of learning the mutual information between temporal and spatial correlations, as well, resulting in improving the classification accuracy, and decreasing the model's complexity about 8 times. Based on the simulation results, the proposed ViT-CAT architecture outperforms its counterparts across the classification accuracy, complexity, and cache-hit ratio.

Federated graph representation learning (FedGRL) brings the benefits of distributed training to graph structured data while simultaneously addressing some privacy and compliance concerns related to data curation. However, several interesting real-world graph data characteristics viz. label deficiency and downstream task heterogeneity are not taken into consideration in current FedGRL setups. In this paper, we consider a realistic and novel problem setting, wherein cross-silo clients have access to vast amounts of unlabeled data with limited or no labeled data and additionally have diverse downstream class label domains. We then propose a novel FedGRL formulation based on model interpolation where we aim to learn a shared global model that is optimized collaboratively using a self-supervised objective and gets downstream task supervision through local client models. We provide a specific instantiation of our general formulation using BGRL a SoTA self-supervised graph representation learning method and we empirically verify its effectiveness through realistic cross-slio datasets: (1) we adapt the Twitch Gamer Network which naturally simulates a cross-geo scenario and show that our formulation can provide consistent and avg. 6.1% gains over traditional supervised federated learning objectives and on avg. 1.7% gains compared to individual client specific self-supervised training and (2) we construct and introduce a new cross-silo dataset called Amazon Co-purchase Networks that have both the characteristics of the motivated problem setting. And, we witness on avg. 11.5% gains over traditional supervised federated learning and on avg. 1.9% gains over individually trained self-supervised models. Both experimental results point to the effectiveness of our proposed formulation. Finally, both our novel problem setting and dataset contributions provide new avenues for the research in FedGRL.

Despite tremendous progress in automatic summarization, state-of-the-art methods are predominantly trained to excel in summarizing short newswire articles, or documents with strong layout biases such as scientific articles or government reports. Efficient techniques to summarize financial documents, including facts and figures, have largely been unexplored, majorly due to the unavailability of suitable datasets. In this work, we present ECTSum, a new dataset with transcripts of earnings calls (ECTs), hosted by publicly traded companies, as documents, and short experts-written telegram-style bullet point summaries derived from corresponding Reuters articles. ECTs are long unstructured documents without any prescribed length limit or format. We benchmark our dataset with state-of-the-art summarizers across various metrics evaluating the content quality and factual consistency of the generated summaries. Finally, we present a simple-yet-effective approach, ECT-BPS, to generate a set of bullet points that precisely capture the important facts discussed in the calls.