Protein-RNA interaction prediction with deep learning: Structure matters

Protein-RNA interactions are of vital importance to a variety of cellular activities. Both experimental and computational techniques have been developed to study the interactions. Due to the limitation of the previous database, especially the lack of protein structure data, most of the existing computational methods rely heavily on the sequence data, with only a small portion of the methods utilizing the structural information. Recently, AlphaFold has revolutionized the entire protein and biology field. Foreseeably, the protein-RNA interaction prediction will also be promoted significantly in the upcoming years. In this work, we give a thorough review of this field, surveying both the binding site and binding preference prediction problems and covering the commonly used datasets, features, and models. We also point out the potential challenges and opportunities in this field. This survey summarizes the development of the RBP-RNA interaction field in the past and foresees its future development in the post-AlphaFold era.

Double Similarity Distillation for Semantic Image Segmentation

The balance between high accuracy and high speed has always been a challenging task in semantic image segmentation. Compact segmentation networks are more widely used in the case of limited resources, while their performances are constrained. In this paper, motivated by the residual learning and global aggregation, we propose a simple yet general and effective knowledge distillation framework called double similarity distillation (DSD) to improve the classification accuracy of all existing compact networks by capturing the similarity knowledge in pixel and category dimensions, respectively. Specifically, we propose a pixel-wise similarity distillation (PSD) module that utilizes residual attention maps to capture more detailed spatial dependencies across multiple layers. Compared with exiting methods, the PSD module greatly reduces the amount of calculation and is easy to expand. Furthermore, considering the differences in characteristics between semantic segmentation task and other computer vision tasks, we propose a category-wise similarity distillation (CSD) module, which can help the compact segmentation network strengthen the global category correlation by constructing the correlation matrix. Combining these two modules, DSD framework has no extra parameters and only a minimal increase in FLOPs. Extensive experiments on four challenging datasets, including Cityscapes, CamVid, ADE20K, and Pascal VOC 2012, show that DSD outperforms current state-of-the-art methods, proving its effectiveness and generality. The code and models will be publicly available.

2nd Place Solution for Waymo Open Dataset Challenge -- Real-time 2D Object Detection

In an autonomous driving system, it is essential to recognize vehicles, pedestrians and cyclists from images. Besides the high accuracy of the prediction, the requirement of real-time running brings new challenges for convolutional network models. In this report, we introduce a real-time method to detect the 2D objects from images. We aggregate several popular one-stage object detectors and train the models of variety input strategies independently, to yield better performance for accurate multi-scale detection of each category, especially for small objects. For model acceleration, we leverage TensorRT to optimize the inference time of our detection pipeline. As shown in the leaderboard, our proposed detection framework ranks the 2nd place with 75.00% L1 mAP and 69.72% L2 mAP in the real-time 2D detection track of the Waymo Open Dataset Challenges, while our framework achieves the latency of 45.8ms/frame on an Nvidia Tesla V100 GPU.

Asymmetric Loss Functions for Learning with Noisy Labels

Robust loss functions are essential for training deep neural networks with better generalization power in the presence of noisy labels. Symmetric loss functions are confirmed to be robust to label noise. However, the symmetric condition is overly restrictive. In this work, we propose a new class of loss functions, namely \textit{asymmetric loss functions}, which are robust to learning with noisy labels for various types of noise. We investigate general theoretical properties of asymmetric loss functions, including classification calibration, excess risk bound, and noise tolerance. Meanwhile, we introduce the asymmetry ratio to measure the asymmetry of a loss function. The empirical results show that a higher ratio would provide better noise tolerance. Moreover, we modify several commonly-used loss functions and establish the necessary and sufficient conditions for them to be asymmetric. Experimental results on benchmark datasets demonstrate that asymmetric loss functions can outperform state-of-the-art methods. The code is available at \href{https://github.com/hitcszx/ALFs}{https://github.com/hitcszx/ALFs}

A Data-Centric Framework for Composable NLP Workflows

Empirical natural language processing (NLP) systems in application domains (e.g., healthcare, finance, education) involve interoperation among multiple components, ranging from data ingestion, human annotation, to text retrieval, analysis, generation, and visualization. We establish a unified open-source framework to support fast development of such sophisticated NLP workflows in a composable manner. The framework introduces a uniform data representation to encode heterogeneous results by a wide range of NLP tasks. It offers a large repository of processors for NLP tasks, visualization, and annotation, which can be easily assembled with full interoperability under the unified representation. The highly extensible framework allows plugging in custom processors from external off-the-shelf NLP and deep learning libraries. The whole framework is delivered through two modularized yet integratable open-source projects, namely Forte1 (for workflow infrastructure and NLP function processors) and Stave2 (for user interaction, visualization, and annotation).

Object sieving and morphological closing to reduce false detections in wide-area aerial imagery

For object detection in wide-area aerial imagery, post-processing is usually needed to reduce false detections. We propose a two-stage post-processing scheme which comprises an area-thresholding sieving process and a morphological closing operation. We use two wide-area aerial videos to compare the performance of five object detection algorithms in the absence and in the presence of our post-processing scheme. The automatic detection results are compared with the ground-truth objects. Several metrics are used for performance comparison.

Service Chain Composition with Failures in NFV Systems: A Game-Theoretic Perspective

For state-of-the-art network function virtualization (NFV) systems, it remains a key challenge to conduct effective service chain composition for different network services (NSs) with ultra-low request latencies and minimum network congestion. To this end, existing solutions often require full knowledge of the network state, while ignoring the privacy issues and overlooking the non-cooperative behaviors of users. What is more, they may fall short in the face of unexpected failures such as user unavailability and virtual machine breakdown. In this paper, we formulate the problem of service chain composition in NFV systems with failures as a non-cooperative game. By showing that such a game is a weighted potential game and exploiting the unique problem structure, we propose two effective distributed schemes that guide the service chain compositions of different NSs towards the Nash equilibrium (NE) state with both near-optimal latencies and minimum congestion. Besides, we develop two novel learning-aided schemes as comparisons, which are based on deep reinforcement learning (DRL) and Monte Carlo tree search (MCTS) techniques, respectively. Our theoretical analysis and simulation results demonstrate the effectiveness of our proposed schemes, as well as the adaptivity when faced with failures.

Green Offloading in Fog-Assisted IoT Systems: An Online Perspective Integrating Learning and Control

In fog-assisted IoT systems, it is a common practice to offload tasks from IoT devices to their nearby fog nodes to reduce task processing latencies and energy consumptions. However, the design of online energy-efficient scheme is still an open problem because of various uncertainties in system dynamics such as processing capacities and transmission rates. Moreover, the decision-making process is constrained by resource limits on fog nodes and IoT devices, making the design even more complicated. In this paper, we formulate such a task offloading problem with unknown system dynamics as a combinatorial multi-armed bandit (CMAB) problem with long-term constraints on time-averaged energy consumptions. Through an effective integration of online learning and online control, we propose a \textit{Learning-Aided Green Offloading} (LAGO) scheme. In LAGO, we employ bandit learning methods to handle the exploitation-exploration tradeoff and utilize virtual queue techniques to deal with the long-term constraints. Our theoretical analysis shows that LAGO can reduce the average task latency with a tunable sublinear regret bound over a finite time horizon and satisfy the long-term time-averaged energy constraints. We conduct extensive simulations to verify such theoretical results.

Data-Driven Bandit Learning for Proactive Cache Placement in Fog-Assisted IoT Systems

In Fog-assisted IoT systems, it is a common practice to cache popular content at the network edge to achieve high quality of service. Due to uncertainties in practice such as unknown file popularities, cache placement scheme design is still an open problem with unresolved challenges: 1) how to maintain time-averaged storage costs under budgets, 2) how to incorporate online learning to aid cache placement to minimize performance loss (a.k.a. regret), and 3) how to exploit offline history information to further reduce regret. In this paper, we formulate the cache placement problem with unknown file popularities as a constrained combinatorial multi-armed bandit (CMAB) problem. To solve the problem, we employ virtual queue techniques to manage time-averaged constraints, and adopt data-driven bandit learning methods to integrate offline history information into online learning to handle exploration-exploitation tradeoff. With an effective combination of online control and data-driven online learning, we devise a Cache Placement scheme with Data-driven Bandit Learning called CPDBL. Our theoretical analysis and simulations show that CPDBL achieves a sublinear time-averaged regret under long-term storage cost constraints.

SenWave: Monitoring the Global Sentiments under the COVID-19 Pandemic

Since the first alert launched by the World Health Organization (5 January, 2020), COVID-19 has been spreading out to over 180 countries and territories. As of June 18, 2020, in total, there are now over 8,400,000 cases and over 450,000 related deaths. This causes massive losses in the economy and jobs globally and confining about 58% of the global population. In this paper, we introduce SenWave, a novel sentimental analysis work using 105+ million collected tweets and Weibo messages to evaluate the global rise and falls of sentiments during the COVID-19 pandemic. To make a fine-grained analysis on the feeling when we face this global health crisis, we annotate 10K tweets in English and 10K tweets in Arabic in 10 categories, including optimistic, thankful, empathetic, pessimistic, anxious, sad, annoyed, denial, official report, and joking. We then utilize an integrated transformer framework, called simpletransformer, to conduct multi-label sentimental classification by fine-tuning the pre-trained language model on the labeled data. Meanwhile, in order for a more complete analysis, we also translate the annotated English tweets into different languages (Spanish, Italian, and French) to generated training data for building sentiment analysis models for these languages. SenWave thus reveals the sentiment of global conversation in six different languages on COVID-19 (covering English, Spanish, French, Italian, Arabic and Chinese), followed the spread of the epidemic. The conversation showed a remarkably similar pattern of rapid rise and slow decline over time across all nations, as well as on special topics like the herd immunity strategies, to which the global conversation reacts strongly negatively. Overall, SenWave shows that optimistic and positive sentiments increased over time, foretelling a desire to seek, together, a reset for an improved COVID-19 world.