Multi-omics Prediction from High-content Cellular Imaging with Deep Learning

High-content cellular imaging, transcriptomics, and proteomics data provide rich and complementary views on the molecular layers of biology that influence cellular states and function. However, the biological determinants through which changes in multi-omics measurements influence cellular morphology have not yet been systematically explored, and the degree to which cell imaging could potentially enable the prediction of multi-omics directly from cell imaging data is therefore currently unclear. Here, we address the question of whether it is possible to predict bulk multi-omics measurements directly from cell images using Image2Omics -- a deep learning approach that predicts multi-omics in a cell population directly from high-content images stained with multiplexed fluorescent dyes. We perform an experimental evaluation in gene-edited macrophages derived from human induced pluripotent stem cell (hiPSC) under multiple stimulation conditions and demonstrate that Image2Omics achieves significantly better performance in predicting transcriptomics and proteomics measurements directly from cell images than predictors based on the mean observed training set abundance. We observed significant predictability of abundances for 5903 (22.43%; 95% CI: 8.77%, 38.88%) and 5819 (22.11%; 95% CI: 10.40%, 38.08%) transcripts out of 26137 in M1 and M2-stimulated macrophages respectively and for 1933 (38.77%; 95% CI: 36.94%, 39.85%) and 2055 (41.22%; 95% CI: 39.31%, 42.42%) proteins out of 4986 in M1 and M2-stimulated macrophages respectively. Our results show that some transcript and protein abundances are predictable from cell imaging and that cell imaging may potentially, in some settings and depending on the mechanisms of interest and desired performance threshold, even be a scalable and resource-efficient substitute for multi-omics measurements.

HSCNet++: Hierarchical Scene Coordinate Classification and Regression for Visual Localization with Transformer

Visual localization is critical to many applications in computer vision and robotics. To address single-image RGB localization, state-of-the-art feature-based methods match local descriptors between a query image and a pre-built 3D model. Recently, deep neural networks have been exploited to regress the mapping between raw pixels and 3D coordinates in the scene, and thus the matching is implicitly performed by the forward pass through the network. However, in a large and ambiguous environment, learning such a regression task directly can be difficult for a single network. In this work, we present a new hierarchical scene coordinate network to predict pixel scene coordinates in a coarse-to-fine manner from a single RGB image. The proposed method, which is an extension of HSCNet, allows us to train compact models which scale robustly to large environments. It sets a new state-of-the-art for single-image localization on the 7-Scenes, 12 Scenes, Cambridge Landmarks datasets, and the combined indoor scenes.

Sparse Bayesian Learning-Based 3D Spectrum Environment Map Construction-Sampling Optimization, Scenario-Dependent Dictionary Construction and Sparse Recovery

The spectrum environment map (SEM), which can visualize the information of invisible electromagnetic spectrum, is vital for monitoring, management, and security of spectrum resources in cognitive radio (CR) networks. In view of a limited number of spectrum sensors and constrained sampling time, this paper presents a new three-dimensional (3D) SEM construction scheme based on sparse Bayesian learning (SBL). Firstly, we construct a scenario-dependent channel dictionary matrix by considering the propagation characteristic of the interested scenario. To improve sampling efficiency, a maximum mutual information (MMI)-based optimization algorithm is developed for the layout of sampling sensors. Then, a maximum and minimum distance (MMD) clustering-based SBL algorithm is proposed to recover the spectrum data at the unsampled positions and construct the whole 3D SEM. We finally use the simulation data of the campus scenario to construct the 3D SEMs and compare the proposed method with the state-of-the-art. The recovery performance and the impact of different sparsity on the constructed SEMs are also analyzed. Numerical results show that the proposed scheme can reduce the required spectrum sensor number and has higher accuracy under the low sampling rate.

Emotion Prediction Oriented method with Multiple Supervisions for Emotion-Cause Pair Extraction

Emotion-cause pair extraction (ECPE) task aims to extract all the pairs of emotions and their causes from an unannotated emotion text. The previous works usually extract the emotion-cause pairs from two perspectives of emotion and cause. However, emotion extraction is more crucial to the ECPE task than cause extraction. Motivated by this analysis, we propose an end-to-end emotion-cause extraction approach oriented toward emotion prediction (EPO-ECPE), aiming to fully exploit the potential of emotion prediction to enhance emotion-cause pair extraction. Considering the strong dependence between emotion prediction and emotion-cause pair extraction, we propose a synchronization mechanism to share their improvement in the training process. That is, the improvement of emotion prediction can facilitate the emotion-cause pair extraction, and then the results of emotion-cause pair extraction can also be used to improve the accuracy of emotion prediction simultaneously. For the emotion-cause pair extraction, we divide it into genuine pair supervision and fake pair supervision, where the genuine pair supervision learns from the pairs with more possibility to be emotion-cause pairs. In contrast, fake pair supervision learns from other pairs. In this way, the emotion-cause pairs can be extracted directly from the genuine pair, thereby reducing the difficulty of extraction. Experimental results show that our approach outperforms the 13 compared systems and achieves new state-of-the-art performance.

UniMSE: Towards Unified Multimodal Sentiment Analysis and Emotion Recognition

Multimodal sentiment analysis (MSA) and emotion recognition in conversation (ERC) are key research topics for computers to understand human behaviors. From a psychological perspective, emotions are the expression of affect or feelings during a short period, while sentiments are formed and held for a longer period. However, most existing works study sentiment and emotion separately and do not fully exploit the complementary knowledge behind the two. In this paper, we propose a multimodal sentiment knowledge-sharing framework (UniMSE) that unifies MSA and ERC tasks from features, labels, and models. We perform modality fusion at the syntactic and semantic levels and introduce contrastive learning between modalities and samples to better capture the difference and consistency between sentiments and emotions. Experiments on four public benchmark datasets, MOSI, MOSEI, MELD, and IEMOCAP, demonstrate the effectiveness of the proposed method and achieve consistent improvements compared with state-of-the-art methods.

Adaptive Behavior Cloning Regularization for Stable Offline-to-Online Reinforcement Learning

Offline reinforcement learning, by learning from a fixed dataset, makes it possible to learn agent behaviors without interacting with the environment. However, depending on the quality of the offline dataset, such pre-trained agents may have limited performance and would further need to be fine-tuned online by interacting with the environment. During online fine-tuning, the performance of the pre-trained agent may collapse quickly due to the sudden distribution shift from offline to online data. While constraints enforced by offline RL methods such as a behaviour cloning loss prevent this to an extent, these constraints also significantly slow down online fine-tuning by forcing the agent to stay close to the behavior policy. We propose to adaptively weigh the behavior cloning loss during online fine-tuning based on the agent's performance and training stability. Moreover, we use a randomized ensemble of Q functions to further increase the sample efficiency of online fine-tuning by performing a large number of learning updates. Experiments show that the proposed method yields state-of-the-art offline-to-online reinforcement learning performance on the popular D4RL benchmark. Code is available: \url{https://github.com/zhaoyi11/adaptive_bc}.

FedDef: Robust Federated Learning-based Network Intrusion Detection Systems Against Gradient Leakage

Deep learning methods have been widely applied to anomaly-based network intrusion detection systems (NIDS) to detect malicious traffic. To expand the usage scenarios of DL-based methods, the federated learning (FL) framework allows intelligent techniques to jointly train a model by multiple individuals on the basis of respecting individual data privacy. However, it has not yet been systematically evaluated how robust FL-based NIDSs are against existing privacy attacks under existing defenses. To address this issue, in this paper we propose two privacy evaluation metrics designed for FL-based NIDSs, including leveraging two reconstruction attacks to recover the training data to obtain the privacy score for traffic features, followed by Generative Adversarial Network (GAN) based attack that generates adversarial examples with the reconstructed benign traffic to evaluate evasion rate against other NIDSs. We conduct experiments to show that existing defenses provide little protection that the corresponding adversarial traffic can even evade the SOTA NIDS Kitsune. To build a more robust FL-based NIDS, we further propose a novel optimization-based input perturbation defense strategy with theoretical guarantee that achieves both high utility by minimizing the gradient distance and strong privacy protection by maximizing the input distance. We experimentally evaluate four existing defenses on four datasets and show that our defense outperforms all the baselines with strong privacy guarantee while maintaining model accuracy loss within 3% under optimal parameter combination.

Continuous Monte Carlo Graph Search

In many complex sequential decision making tasks, online planning is crucial for high-performance. For efficient online planning, Monte Carlo Tree Search (MCTS) employs a principled mechanism for trading off between exploration and exploitation. MCTS outperforms comparison methods in various discrete decision making domains such as Go, Chess, and Shogi. Following, extensions of MCTS to continuous domains have been proposed. However, the inherent high branching factor and the resulting explosion of search tree size is limiting existing methods. To solve this problem, this paper proposes Continuous Monte Carlo Graph Search (CMCGS), a novel extension of MCTS to online planning in environments with continuous state and action spaces. CMCGS takes advantage of the insight that, during planning, sharing the same action policy between several states can yield high performance. To implement this idea, at each time step CMCGS clusters similar states into a limited number of stochastic action bandit nodes, which produce a layered graph instead of an MCTS search tree. Experimental evaluation with limited sample budgets shows that CMCGS outperforms comparison methods in several complex continuous DeepMind Control Suite benchmarks and a 2D navigation task.

CM-MLP: Cascade Multi-scale MLP with Axial Context Relation Encoder for Edge Segmentation of Medical Image

The convolutional-based methods provide good segmentation performance in the medical image segmentation task. However, those methods have the following challenges when dealing with the edges of the medical images: (1) Previous convolutional-based methods do not focus on the boundary relationship between foreground and background around the segmentation edge, which leads to the degradation of segmentation performance when the edge changes complexly. (2) The inductive bias of the convolutional layer cannot be adapted to complex edge changes and the aggregation of multiple-segmented areas, resulting in its performance improvement mostly limited to segmenting the body of segmented areas instead of the edge. To address these challenges, we propose the CM-MLP framework on MFI (Multi-scale Feature Interaction) block and ACRE (Axial Context Relation Encoder) block for accurate segmentation of the edge of medical image. In the MFI block, we propose the cascade multi-scale MLP (Cascade MLP) to process all local information from the deeper layers of the network simultaneously and utilize a cascade multi-scale mechanism to fuse discrete local information gradually. Then, the ACRE block is used to make the deep supervision focus on exploring the boundary relationship between foreground and background to modify the edge of the medical image. The segmentation accuracy (Dice) of our proposed CM-MLP framework reaches 96.96%, 96.76%, and 82.54% on three benchmark datasets: CVC-ClinicDB dataset, sub-Kvasir dataset, and our in-house dataset, respectively, which significantly outperform the state-of-the-art method. The source code and trained models will be available at https://github.com/ProgrammerHyy/CM-MLP.

Reinforced MOOCs Concept Recommendation in Heterogeneous Information Networks

Massive open online courses (MOOCs), which provide a large-scale interactive participation and open access via the web, are becoming a modish way for online and distance education. To help users have a better study experience, many MOOC platforms have provided the services of recommending courses to users. However, we argue that directly recommending a course to users will ignore the expertise levels of different users. To fill this gap, this paper studies the problem of concept recommendation in a more fine-grained view. We propose a novel Heterogeneous Information Networks based Concept Recommender with Reinforcement Learning (HinCRec-RL) incorporated for concept recommendation in MOOCs. Specifically, we first formulate the concept recommendation in MOOCs as a reinforcement learning problem to better model the dynamic interaction among users and knowledge concepts. In addition, to mitigate the data sparsity issue which also exists in many other recommendation tasks, we consider a heterogeneous information network (HIN) among users, courses, videos and concepts, to better learn the semantic representation of users. In particular, we use the meta-paths on HIN to guide the propagation of users' preferences and propose a heterogeneous graph attention network to represent the meta-paths. To validate the effectiveness of our proposed approach, we conduct comprehensive experiments on a real-world dataset from XuetangX, a popular MOOC platform from China. The promising results show that our proposed approach can outperform other baselines.