Italy

Predicting protein-protein interactions (PPIs) by learning informative representations from amino acid sequences is a challenging yet important problem in biology. Although various deep learning models in Siamese architecture have been proposed to model PPIs from sequences, these methods are computationally expensive for a large number of PPIs due to the pairwise encoding process. Furthermore, these methods are difficult to interpret because of non-intuitive mappings from protein sequences to their sequence representation. To address these challenges, we present a novel deep framework to model and predict PPIs from sequence alone. Our model incorporates a bidirectional gated recurrent unit to learn sequence representations by leveraging contextualized and sequential information from sequences. We further employ a sparse regularization to model long-range dependencies between amino acids and to select important amino acids (protein motifs), thus enhancing interpretability. Besides, the novel design of the encoding process makes our model computationally efficient and scalable to an increasing number of interactions. Experimental results on up-to-date interaction datasets demonstrate that our model achieves superior performance compared to other state-of-the-art methods. Literature-based case studies illustrate the ability of our model to provide biological insights to interpret the predictions.

ICPR 2020

Interpretable Structured Learning with Sparse Gated Sequence Encoder for Protein-Protein Interaction Prediction

sequence encoder

interpretable deep learning

sparse regularization

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-23 is the Thirty-Seventh AAAI Conference on Artificial Intelligence. The theme of this conference is to create collaborative bridges within and beyond AI. Like previous AAAI conferences, AAAI-23 will feature technical paper presentations, special tracks, invited speakers, workshops, tutorials, poster sessions, senior member presentations, competitions, and exhibit programs, and two new activities: a Bridge Program and a Lab Program. Many of these activities are tailored to the theme of bridges and all are selected according to the highest standards, with additional programs for students and young researchers. 
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AAAI 2023

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.

poster

ICPR 2020 is the premier international conference on Pattern Recognition, gathering leading researchers from around the world to present their latest achievements in Pattern Analysis and Recognition, applied Artificial Intelligence and Machine Learning. The topic of the year is " Putting Artificial intelligence to work on Patterns". 
For the first time, ICPR has employed a two-round review process similar to journal submissions, with new papers allowed to be submitted in either the first or second round and papers submitted in the first round and not accepted allowed to be revised and re-submitted for second round review. 

In this edition of the **ICPR 2020** Conference, there are 1407 Oral/Poster presentations organized in five Tracks: 
- Artificial Intelligence, Machine Learning for Pattern Analysis; 
- Biometrics, Human Analysis and Behavior Understanding; Computer Vision, Robotics and Intelligent Systems; 
- Document and Media Analysis; and 
- Image and Signal Processing. 

The **ICPR 2020** Main Conference program also includes 7 Keynotes from prominent world-renowned scientists, 8 Tutorials, 28 Demos, 8 Challenges, 2 Panels, as well as an Industry/Sponsor Exhibition. In addition, 41 Workshops on a range of important current and emerging research topics complete the ICPR 2020 program. 


A common approach in multi-task learning is to encourage the tasks to share a low dimensional representation. This has led to the popular method of trace norm regularization, which has proved effective in many applications. In this paper, we extend this approach by allowing the tasks to partition into different groups, within which trace norm regularization is separately applied. We propose a continuous bilevel optimization framework to simultaneously identify groups of related tasks and learn a low dimensional representation within each group. Hinging on recent results on the derivative of generalized matrix functions, we devise a smooth approximation of the upper-level objective via a dual forward-backward algorithm with Bregman distances. This allows us to solve the bilevel problem by a gradient-based scheme. Numerical experiments on synthetic and benchmark datasets support the effectiveness of the proposed method.

Unveiling groups of related tasks in multi-task learning


This paper studies the problem of Person Re-Identification (ReID)
for large-scale applications. Recent research efforts have been devoted
to building complicated part models, which introduce considerably
high computational cost and memory consumption, inhibiting its practicability
in large-scale applications. This paper aims to develop a novel learning
strategy to find efficient feature embeddings while maintaining the
balance of accuracy and model complexity. More specifically, we find
by enhancing the classical triplet loss together with cross-entropy
loss, our method can explore the hard examples and build a discriminant
feature embedding yet compact enough for large-scale applications.
Our method is carried out progressively using Bayesian optimization,
and we call it the Progressive Learning Algorithm (PLA). Extensive
experiments on three large-scale datasets show that our PLA is comparable
or better than the state-of-the-arts. Especially, on the challenging
Market-1501 dataset, we achieve Rank-1=94.7%/mAP=89.4% while saving
at least 30\% parameters than strong part models.

Meta Soft Label Generation for Noisy Labels


We address two long-standing radiogenomic challenges in glioma subtype and survival prediction: (1) how to leverage large amounts of unlabeled magnetic resonance imaging (MRI) data and (2) how to unite MRI data and genomic data. We propose a novel application of multi-task learning (MTL) that leverages unlabeled MRI data by jointly learning an auxiliary tumor segmentation task with glioma subtype prediction and that can learn from patients with and without genomic data. We analyze multi-parametric MRI data from 542 patients in the combined training, validation, and testing sets of the 2018 Multimodal Brain Tumor Segmentation Challenge and somatic copy number alteration (SCNA) data from 1090 patients in The Cancer Genome Atlas' (TCGA) lower-grade glioma and glioblastoma projects. Our MTL model significantly outperforms comparable classification models trained only on labeled MRI data for both IDH1/2 mutation and 1p/19q co-deletion subtype prediction tasks. We also show that embeddings produced by our MTL models improve survival predictions beyond MRI or SCNA on their own.

Leveraging Unlabeled Data for Glioma Molecular Subtype and Survival Prediction

Commercially available light field cameras have difficulty in capturing 5D (4D + time) light field videos. They can only capture still light field images or are excessively expensive for normal users to capture the light field video. To tackle this problem, we propose a deep learning-based method for synthesizing a light field video from a monocular video. We propose a new synthetic light field video dataset that renders
photorealistic scenes using Unreal Engine because no light field video dataset is available. The proposed deep learning framework synthesizes the light field video with a full set (99) of sub-aperture images from a normal monocular video. The proposed network consists of three sub-networks, namely, feature extraction, 5D light field video synthesis, and temporal consistency refinement. Experimental results show that our model can successfully synthesize the light field video for synthetic and real scenes and outperforms the previous frame-by-frame method
quantitatively and qualitatively.

5D Light Field Synthesis from a Monocular Video

Batch Normalization (BN) is a well-known technique used in training deep neural networks. The main idea behind batch normalization is to normalize the features of the layers (i:e:, transforming them to have a mean equal to zero and a variance
equal to one). Such a procedure encourages the optimization landscape of the loss function to be smoother, and improves the learning of the networks for both speed and performance. In this paper, we demonstrate that the performance of the network can be improved, if the distributions of the features of the output in the same layer are similar. As normalizing based on mean and variance does not necessarily make the features to have the same distribution, we propose a new normalization scheme: Batch Normalization with Skewness Reduction (BNSR). Comparing with other normalization approaches, BNSR transforms not just only the mean and variance, but also the skewness of the data. By tackling this property of a distribution, we are able to make the output distributions of the layers to be further similar. The nonlinearity of BNSR may further improve the expressiveness of the underlying network. Comparisons with other normalization schemes are tested on the CIFAR-100 and ImageNet datasets. Experimental results show that the proposed approach can outperform other state-of-the-arts that are not equipped with BNSR.

Improving Batch Normalization with Skewness Reduction for Deep Neural Networks

Object shape is a subtle but important factor for object detection. It has been observed that the object-region-percentage (ORP) can be utilized to improve detection accuracy for elongated objects, which have much lower ORPs than other
types of objects. In this paper, we propose an approach to improve the detection performance for objects with high ORPs. Our method consists of three steps. First, we adjust the ground truth bounding boxes of high-ORP objects to an optimal range. Second, we train an object detector, Faster R-CNN, based on adjusted bounding boxes to achieve high recall. Finally, we train a DCNN to learn the adjustment ratios towards four directions and adjust detected bounding boxes of objects to get better localization for higher precision. We evaluate the effectiveness of our method on
12 high-ORP objects in COCO and 8 objects in a proprietary gearbox dataset. The experimental results show that our method can achieve state-of-the-art Performance on these objects while costing less resources in training and inference stages.

Detecting objects with high object region percentage

Learning interpretable and interpolatable latent representations has been an emerging research direction, allowing researchers to understand and utilize the derived latent space for further applications such as visual synthesis or recognition.
While most existing approaches derive an interpolatable latent space and induces smooth transition in image appearance, it is still not clear how to observe desirable representations which would contain semantic information of interest. In this paper,
we aim to learn meaningful representations and simultaneously perform semantic-oriented and visually-smooth interpolation. To this end, we propose an angular triplet-neighbor loss (ATNL) that enables learning a latent representation whose distribution matches the semantic information of interest. With the latent space guided by ATNL, we further utilize spherical semantic interpolation for generating semantic warping of images, allowing synthesis of desirable visual data. Experiments on MNIST and CMU Multi-PIE datasets qualitatively and quantitatively verify the effectiveness of our method.

Semantics-Guided Representation Learning with Applications to Visual Synthesis

Explaining decisions of black-box classifiers is paramount in sensitive domains such as medical imaging since clinicians confidence is necessary for adoption. 
Various explanation approaches have been proposed, among which perturbation based approaches are very promising. Within this class of methods, we leverage a learning framework to produce our visual explanations method. From a given classifier, we train two generators to produce from an input image the so called similar and adversarial images. The similar image shall be classified as the input image whereas the adversarial shall not. Visual explanation is built as the difference between these two generated images. Using metrics from the literature, our method outperforms state-of-the-art approaches. The proposed approach is model-agnostic and has a low computation burden at prediction time. Thus, it is adapted for real-time systems. Finally, we show that random geometric augmentations applied to the original image play a regularization role that improves several previously proposed explanation methods. We validate our approach on a large chest X-ray database.

Combining Similarity and Adversarial Learning to Generate Visual Explanation: Application to Medical Image Classification


This paper proposes a new lightweight network, LiNet, that enhancing technical efficiency in lightweight super resolution and operating approximately like very large and costly networks in terms of number of network parameters and operations. The proposed architecture allows the network to learn more abstract properties by avoiding low-level information via multiple links. LiNet introduces a Compact Dense Module, which contains set of inner and outer blocks, to efficiently extract meaningful information, to better leverage multi-level representations before upsampling stage, and to allow an efficient information and gradient flow within the network. Experiments on benchmark datasets show that the proposed LiNet achieves favorable performance against lightweight state-of-the-art methods.

LiNet: A Lightweight Network for Image Super Resolution

Variational autoencoder (VAE) is a widely used generative model for learning latent representations. Burda et al. in their seminal paper showed that learning capacity of VAE is limited by over-pruning. It is a phenomenon where a significant number of latent variables fail to capture any information about the input data and the corresponding hidden units become inactive. This adversely affects learning diverse and interpretable latent representations. As variational graph autoencoder (VGAE) extends VAE for graph-structured data, it inherits the over-pruning problem. In this paper, we adopt a model based approach and propose epitomic VGAE (EVGAE),a generative variational framework for graph datasets which successfully mitigates the over-pruning problem and also boosts the generative ability of VGAE. We consider EVGAE to consist of multiple sparse VGAE models, called epitomes, that are groups of latent variables sharing the latent space. This approach aids in increasing active units as epitomes compete to learn better representation of the graph data. We verify our claims via experiments on three benchmark datasets. Our experiments show that EVGAE has a better generative ability than VGAE. Moreover, EVGAE outperforms VGAE on link prediction task in citation networks.

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Interpretable Structured Learning with Sparse Gated Sequence Encoder for Protein-Protein Interaction Prediction

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Unveiling groups of related tasks in multi-task learning

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