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Gene regulatory networks (GRNs) consist of gene regulations between transcription factors (TFs) and their target genes. Single-cell RNA sequencing (scRNA-seq) brings both opportunities and challenges to the inference of GRNs. On the one hand, scRNA-seq data reveals statistic information of gene expressions at the single-cell resolution, which is conducive to the construction of GRNs; on the other hand, noises and dropouts pose great difficulties on the analysis of scRNA-seq data, causing low prediction accuracy by traditional methods. In this paper, we propose 3D Co-Expression Matrix Analysis (3DCEMA), which predicts regulatory relationships by classifying 3D co-expression matrices of gene triples using a 3D convolutional neural network. We found that by introducing a third gene as a comparison factor, our method can avoid the disturbance of noises and dropouts, and significantly increase the prediction accuracy of regulations between gene pairs. Compared with other existing GRN inference algorithms on both in-silico datasets and scRNA-Seq datasets, our algorithm based on deep learning shows higher stability and accuracy in the task of GRN inference.

AAAI 2021

Gene Regulatory Network Inference Using 3D Convolutional Neural Network

We are pleased to announce the Thirty-Eighth AAAI Conference on Artificial Intelligence (AAAI-24), which will be held in Vancouver, British Columbia at the Vancouver Convention Centre – West Building from 20-27 February, 2024.

The purpose of the AAAI conference series is to promote research in Artificial Intelligence (AI) and foster scientific exchange between researchers, practitioners, scientists, students, and engineers across the entirety of AI and its affiliated disciplines. AAAI-24 will feature technical paper presentations, special tracks, invited speakers, workshops, tutorials, poster sessions, senior member presentations, competitions, and exhibit programs, and a range of other activities to be announced.

We expect for AAAI-24 to be an in-person conference – one author of all accepted papers will be expected to present work in person unless there are exceptional circumstances that prevent this.<br><br><br><br>

In order to access the AAAI-24 event page you need to register [here](https://aaai.org/aaai-conference/registration/)

AAAI 2024

The purpose of the AAAI conference series is to promote research in Artificial Intelligence (AI) and foster scientific exchange between researchers, practitioners, scientists, students, and engineers across the entirety of AI and its affiliated disciplines. 

technical paper

The purpose of the AAAI conference is to promote research in artificial intelligence (AI) and scientific exchange among AI researchers, practitioners, scientists, and engineers in affiliated disciplines. 

We propose a novel framework that unifies and extends existing methods of transfer learning (TL) for regression. To bridge a pretrained source model to the model on a target task, we introduce a density-ratio reweighting function, which is estimated through the Bayesian framework with a specific prior distribution. By changing two intrinsic hyperparameters and the choice of the density-ratio model, the proposed method can integrate three popular methods of TL: TL based on cross-domain similarity regularization, a probabilistic TL using the density-ratio estimation, and fine-tuning of pretrained neural networks. Moreover, the proposed method can benefit from its simple implementation without any additional cost; the regression model can be fully trained using off-the-shelf libraries for supervised learning in which the original output variable is simply transformed to a new output variable. We demonstrate its simplicity, generality, and applicability using various real data applications.

A General Class of Transfer Learning Regression without Implementation Cost

A steady momentum of innovations and breakthroughs has convincingly pushed the limits of unsupervised image representation learning. Compared to static 2D images, video has one more dimension (time). The inherent supervision existing in such sequential structure offers a fertile ground for building unsupervised learning models. In this paper, we compose a trilogy of exploring the basic and generic supervision in the sequence from spatial, spatiotemporal and sequential perspectives. We materialize the supervisory signals through determining whether a pair of samples is from one frame or from one video, and whether a triplet of samples is in the correct temporal order. We uniquely regard the signals as the foundation in contrastive learning and derive a particular form named Sequence Contrastive Learning (SeCo). SeCo shows superior results under the linear protocol on action recognition (Kinetics), untrimmed activity recognition (ActivityNet) and object tracking (OTB-100). More remarkably, SeCo demonstrates considerable improvements over recent unsupervised pre-training techniques, and leads the accuracy by 2.96% and 6.47% against fully-supervised ImageNet pre-training in action recognition task on UCF101 and HMDB51, respectively. Source code is available at https://github.com/YihengZhang-CV/SeCo-Sequence-Contrastive-Learning.

SeCo: Exploring Sequence Supervision for Unsupervised Representation Learning

Multi-label text classification (MLTC) aims to annotate documents with the most relevant labels from a number of candidate labels. In real applications, the distribution of label frequency often exhibits a long tail, i.e., a few labels are associated with a large number of  documents (a.k.a. head labels), while a large fraction of labels are associated with a  small number of documents (a.k.a. tail labels). To address the challenge of insufficient training data on tail label classification, we propose a Head-to-Tail Network (HTTN) to transfer the meta-knowledge from the data-rich head labels to data-poor tail labels. The meta-knowledge is the mapping from few-shot network parameters to many-shot network parameters, which aims to promote the generalizability of tail classifiers. Extensive experimental results on three benchmark datasets demonstrate that HTTN consistently outperforms the state-of-the-art methods. The code and hyper-parameter settings are released for reproducibility.

Does Head Label Help for Long-Tailed Multi-Label Text Classification

Human motion prediction from historical pose sequence is at the core of many applications in machine intelligence. However, in current state-of-the-art methods, the predicted future motion is confined within the same activity. One can neither generate predictions that differ from the current activity, nor manipulate the body parts to explore various future possibilities. Undoubtedly, this greatly limits the usefulness and applicability of motion prediction. In this paper, we propose a generalization of the human motion prediction task in which control parameters can be readily incorporated to adjust the forecasted motion. Our method is compelling in that it enables manipulable motion prediction across activity types and allows customization of the human movement in a variety of fine-grained ways. To this aim, a simple yet effective composite GAN structure, consisting of local GANs for different body parts and aggregated via a global GAN is presented. The local GANs game in lower dimensions, while the global GAN adjusts in high dimensional space to avoid mode collapse. Extensive experiments show that our method outperforms state-of-the-art. The codes are available at https://github.com/herolvkd/AM-GAN.

Aggregated Multi-GANs for Controlled 3D Human Motion Prediction

Representing the true label as one-hot vector is the common practice in training text classification models. However, the one-hot representation may not adequately reflect the relation between the instance and labels, as labels are often not completely independent and instances may relate to multiple labels in practice. The inadequate one-hot representations tend to train the model to be over-confident, which may result in arbitrary prediction and model overfitting, especially for confused datasets (datasets with very similar labels) or noisy datasets (datasets with labeling errors). While training models with label smoothing can ease this problem in some degree, it still fails to capture the realistic relation among labels. In this paper, we propose a novel Label Confusion Model (LCM) as an enhancement component to current popular text classification models. LCM can learn label confusion to capture semantic overlap among labels by calculating the similarity between instance and labels during training and generate a better label distribution to replace the original one-hot label vector, thus improving the final classification performance. Extensive experiments on five text classification benchmark datasets reveal the effectiveness of LCM for several widely used deep learning classification models. Further experiments also verify that LCM is especially helpful for confused or noisy datasets and superior to the label smoothing method.

Label Confusion Learning to Enhance Text Classification Models

Generative Adversarial Networks (GAN) are good at generating variant samples of complex data distributions. Generating a sample with certain properties is one of the major tasks in the real-world application of GANs. In this paper, we propose a novel generative adversarial network to generate 3D point clouds from random latent codes, named Controllable Point Cloud Generative Adversarial Network(CPCGAN). A two-stage GAN framework is utilized in CPCGAN and a sparse point cloud containing major structural information is extracted as the middle-level information between the two stages. With their help, CPCGAN has the ability to control the generated structure and generate 3D point clouds with semantic labels for points. Experimental results demonstrate that the proposed CPCGAN outperforms state-of-the-art point cloud GANs.

CPCGAN: A Controllable 3D Point Cloud Generative Adversarial Network with Semantic Label Generating

Trojan (backdoor) attack is a form of adversarial attack on deep neural networks where the attacker provides victims with a model trained/retrained on malicious data. The backdoor can be activated when a normal input is stamped with a certain pattern called trigger, causing misclassification. Many existing trojan attacks have their triggers being input space patches/objects (e.g., a polygon with solid color) or simple input transformations such as Instagram filters. These simple triggers are susceptible to recent backdoor detection algorithms. We propose a novel deep feature space trojan attack with five characteristics: effectiveness, stealthiness, controllability, robustness and reliance on deep features. We conduct extensive experiments on 9 image classifiers on various datasets including ImageNet to demonstrate these properties and show that our attack can evade state-of-the-art defense.

Deep Feature Space Trojan Attack of Neural Networks by Controlled Detoxification

The clear transparency of Deep Neural Networks (DNNs) is hampered by complex internal structures and nonlinear transformations along deep hierarchies. In this paper, we propose a new attribution method, Relative Sectional Propagation (RSP), for fully decomposing the output predictions with the characteristics of class-discriminative attributions and clear objectness. We carefully revisit some shortcomings of backpropagation-based attribution methods, which are trade-off relations in decomposing DNNs. We define hostile factor as an element that interferes with finding the attributions of the target and propagate it in a distinguishable way to overcome the non-suppressed nature of activated neurons. As a result, it is possible to assign the bi-polar relevance scores of the target (positive) and hostile (negative) attributions while maintaining each attribution aligned with the importance. We also present the purging techniques to prevent the decrement of the gap between the relevance scores of the target and hostile attributions during backward propagation by eliminating the conflicting units to channel attribution map. Therefore, our method makes it possible to decompose the predictions of DNNs with clearer class-discriminativeness and detailed elucidations of activation neurons compared to the conventional attribution methods. In a verified experimental environment, we report the results of the assessments: (i) Pointing Game, (ii) mIoU, and (iii) Model Sensitivity with PASCAL VOC 2007, MS COCO 2014, and ImageNet datasets. The results demonstrate that our method outperforms existing backward decomposition methods, including distinctive and intuitive visualizations.

Interpreting Deep Neural Networks with Relative Sectional Propagation by Analyzing Comparative Gradients and Hostile Activations

Recently, 3D medical image reconstruction (MIR) and segmentation (MIS) based on deep neural networks have been developed with promising results, and attention mechanism has been further designed for performance enhancement.
However, the large size of 3D volume images poses a great computational challenge to traditional attention methods. 
In this paper, we propose a folded attention (FA) approach to improve the computational efficiency of traditional attention methods on 3D medical images. 
The main idea is that we apply tensor folding and unfolding operations to construct four small sub-affinity matrices to approximate the original affinity matrix.
Through four consecutive sub-attention modules of FA, each element in the feature tensor can aggregate spatial-channel information from all other elements.
Compared to traditional attention methods, with the moderate improvement of accuracy, FA can substantially reduce the computational complexity and GPU memory consumption.
We demonstrate the superiority of our method on two challenging tasks for 3D MIR and MIS, which are quantitative susceptibility mapping and multiple sclerosis lesion segmentation.

Efficient Folded Attention for Medical Image Reconstruction and Segmentation

Graph Neural Networks (GNNs), a generalization of neural networks to graph-structured data, are often implemented using message passes between entities of a graph. While GNNs are effective for node classification, link prediction and graph classification, they are vulnerable to adversarial attacks, i.e., a small perturbation to the structure can lead to a non-trivial performance degradation. In this work, we propose Uncertainty Matching GNN (UM-GNN), that is aimed at improving the robustness of GNN models, particularly against poisoning attacks to the graph structure, by leveraging epistemic uncertainties from the message passing framework. More specifically, we propose to build a surrogate predictor that does not directly access the graph structure, but systematically extracts reliable knowledge from a standard GNN through a novel uncertainty-matching strategy. Interestingly, this uncoupling makes UM-GNN immune to evasion attacks by design, and achieves significantly improved robustness against poisoning attacks. Using empirical studies with standard benchmarks and a suite of global and target attacks, we demonstrate the effectiveness of UM-GNN, when compared to existing baselines including the state-of-the-art robust GCN.

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