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Synergistic drug combinations provide huge potentials to enhance therapeutic efficacy and to reduce adverse reactions. However, effective and synergistic drug combination prediction remains an open question because of the unknown causal disease signaling pathways. Though various deep learning (AI) models have been proposed to quantitatively predict the synergism of drug combinations, the major limitation of existing deep learning methods is that they are inherently not interpretable, which makes the conclusions of AI models untransparent to human experts, henceforth limiting the robustness of the model conclusion and the implementation ability of these models in real-world human--AI healthcare. In this paper, we develop an interpretable graph neural network (GNN) that reveals the underlying essential therapeutic targets and the mechanism of the synergy (MoS) by mining the sub-molecular network of great importance. The key point of the interpretable GNN prediction model is a novel graph pooling layer, a self-attention-based node and edge pool (henceforth SANEpool), that can compute the attention score (importance) of genes and connections based on the genomic features and topology. As such, the proposed GNN model provides a systematic way to predict and interpret the drug combination synergism based on the detected crucial sub-molecular network. Experiments on various well-adopted drug-synergy-prediction datasets demonstrate that (1) the SANEpool model has superior predictive ability to generate accurate synergy score prediction, and (2) the sub-molecular networks detected by the SANEpool are self-explainable and salient for identifying synergistic drug combinations.

Offline imitation learning (IL) is a powerful method to solve decision-making problems from expert demonstrations without reward labels. Existing offline IL methods suffer from severe performance degeneration under limited expert data. Including a learned dynamics model can potentially improve the state-action space coverage of expert data, however, it also faces challenging issues like model approximation/generalization errors and suboptimality of rollout data. In this paper, we propose the Discriminator-guided Model-based offline Imitation Learning (DMIL) framework, which introduces a discriminator to simultaneously distinguish the dynamics correctness and suboptimality of model rollout data against real expert demonstrations. DMIL adopts a novel cooperative-yet-adversarial learning strategy, which uses the discriminator to guide and couple the learning process of the policy and dynamics model, resulting in improved model performance and robustness. Our framework can also be extended to the case when demonstrations contain a large proportion of suboptimal data. Experimental results show that DMIL and its extension achieve superior performance and robustness compared to state-of-the-art offline IL methods under small datasets., Comment: This work has been accepted by CoRL 2022

Extant giant pandas are divided into Sichuan and Qinling subspecies. The giant panda has many species-specific characteristics, including comparatively small organs for body size, small genitalia of male individuals, and low reproduction. Here, we report the most contiguous, high-quality chromosome-level genomes of two extant giant panda subspecies to date, with the first genome assembly of the Qinling subspecies. Compared with the previously assembled giant panda genomes based on short reads, our two assembled genomes increased contiguity over 200-fold at the contig level. Additional sequencing of 25 individuals dated the divergence of the Sichuan and Qinling subspecies into two distinct clusters from 10,000 to 12,000 years ago. Comparative genomic analyses identified the loss of regulatory elements in the dachshund family transcription factor 2 (DACH2) gene and specific changes in the synaptotagmin 6 (SYT6) gene, which may be responsible for the reduced fertility of the giant panda. Positive selection analysis between the two subspecies indicated that the reproduction-associated IQ motif containing D (IQCD) gene may at least partly explain the different reproduction rates of the two subspecies. Furthermore, several genes in the Hippo pathway exhibited signs of rapid evolution with giant panda-specific variants and divergent regulatory elements, which may contribute to the reduced inner organ sizes of the giant panda.

Extant giant pandas are divided into Sichuan and Qinling subspecies. The giant panda has many species-specific characteristics, including comparatively small organs for body size, small genitalia of male individuals, and low reproduction. Here, we report the most contiguous, high-quality chromosome-level genomes of two extant giant panda subspecies to date, with the first genome assembly of the Qinling subspecies. Compared with the previously assembled giant panda genomes based on short reads, our two assembled genomes increased contiguity over 200-fold at the contig level. Additional sequencing of 25 individuals dated the divergence of the Sichuan and Qinling subspecies into two distinct clusters from 10,000 to 12,000 years ago. Comparative genomic analyses identified the loss of regulatory elements in the dachshund family transcription factor 2 (DACH2) gene and specific changes in the synaptotagmin 6 (SYT6) gene, which may be responsible for the reduced fertility of the giant panda. Positive selection analysis between the two subspecies indicated that the reproduction-associated IQ motif containing D (IQCD) gene may at least partly explain the different reproduction rates of the two subspecies. Furthermore, several genes in the Hippo pathway exhibited signs of rapid evolution with giant panda-specific variants and divergent regulatory elements, which may contribute to the reduced inner organ sizes of the giant panda.

We investigate molecular mechanisms of resistant or sensitive response of cancer drug combination therapies in an inductive and interpretable manner. Though deep learning algorithms are widely used in the drug synergy prediction problem, it is still an open problem to formulate the prediction model with biological meaning to investigate the mysterious mechanisms of synergy (MoS) for the human-AI collaboration in healthcare systems. To address the challenges, we propose a deep graph neural network, IDSP (Interpretable Deep Signaling Pathways), to incorporate the gene-gene as well as gene-drug regulatory relationships in synergic drug combination predictions. IDSP automatically learns weights of edges based on the gene and drug node relations, i.e., signaling interactions, by a multi-layer perceptron (MLP) and aggregates information in an inductive manner. The proposed architecture generates interpretable drug synergy prediction by detecting important signaling interactions, and can be implemented when the underlying molecular mechanism encounters unseen genes or signaling pathways. We test IDWSP on signaling networks formulated by genes from 46 core cancer signaling pathways and drug combinations from NCI ALMANAC drug combination screening data. The experimental results demonstrated that 1) IDSP can learn from the underlying molecular mechanism to make prediction without additional drug chemical information while achieving highly comparable performance with current state-of-art methods; 2) IDSP show superior generality and flexibility to implement the synergy prediction task on both transductive tasks and inductive tasks. 3) IDSP can generate interpretable results by detecting different salient signaling patterns (i.e. MoS) for different cell lines.

Generating accurate descriptions for online fashion items is important not only for enhancing customers' shopping experiences, but also for the increase of online sales. Besides the need of correctly presenting the attributes of items, the expressions in an enchanting style could better attract customer interests. The goal of this work is to develop a novel learning framework for accurate and expressive fashion captioning. Different from popular work on image captioning, it is hard to identify and describe the rich attributes of fashion items. We seed the description of an item by first identifying its attributes, and introduce attribute-level semantic (ALS) reward and sentence-level semantic (SLS) reward as metrics to improve the quality of text descriptions. We further integrate the training of our model with maximum likelihood estimation (MLE), attribute embedding, and Reinforcement Learning (RL). To facilitate the learning, we build a new FAshion CAptioning Dataset (FACAD), which contains 993K images and 130K corresponding enchanting and diverse descriptions. Experiments on FACAD demonstrate the effectiveness of our model., Comment: In proceedings of ECCV 2020

Color compatibility is important for evaluating the compatibility of a fashion outfit, yet it was neglected in previous studies. We bring this important problem to researchers' attention and present a compatibility learning framework as solution to various fashion tasks. The framework consists of a novel way to model outfit compatibility and an innovative learning scheme. Specifically, we model the outfits as graphs and propose a novel graph construction to better utilize the power of graph neural networks. Then we utilize both ground-truth labels and pseudo labels to train the compatibility model in a weakly-supervised manner.Extensive experimental results verify the importance of color compatibility alone with the effectiveness of our framework. With color information alone, our model's performance is already comparable to previous methods that use deep image features. Our full model combining the aforementioned contributions set the new state-of-the-art in fashion compatibility prediction.

Kinship verification aims to identify the kin relation between two given face images. It is a very challenging problem due to the lack of training data and facial similarity variations between kinship pairs. In this work, we build a novel appearance and shape based deep learning pipeline. First we adopt the knowledge learned from general face recognition network to learn general facial features. Afterwards, we learn kinship oriented appearance and shape features from kinship pairs and combine them for the final prediction. We have evaluated the model performance on a widely used popular benchmark and demonstrated the superiority over the state-of-the-art., Comment: ICIP 2019

Face detection is a widely studied problem over the past few decades. Recently, significant improvements have been achieved via the deep neural network, however, it is still challenging to directly apply these techniques to mobile devices for its limited computational power and memory. In this work, we present a proposal generation acceleration framework for real-time face detection. More specifically, we adopt a popular cascaded convolutional neural network (CNN) as the basis, then apply our acceleration approach on the basic framework to speed up the model inference time. We are motivated by the observation that the computation bottleneck of this framework arises from the proposal generation stage, where each level of the dense image pyramid has to go through the network. In this work, we reduce the number of image pyramid levels by utilizing both global and local facial characteristics (i.e., global face and facial parts). Experimental results on public benchmarks WIDER-face and FDDB demonstrate the satisfactory performance and faster speed compared to the state-of-the-arts. %the comparable accuracy to state-of-the-arts with faster speed., Comment: ICIP

Lifelong learning, the problem of continual learning where tasks arrive in sequence, has been lately attracting more attention in the computer vision community. The aim of lifelong learning is to develop a system that can learn new tasks while maintaining the performance on the previously learned tasks. However, there are two obstacles for lifelong learning of deep neural networks: catastrophic forgetting and capacity limitation. To solve the above issues, inspired by the recent breakthroughs in automatically learning good neural network architectures, we develop a Multi-task based lifelong learning via nonexpansive AutoML framework termed Regularize, Expand and Compress (REC). REC is composed of three stages: 1) continually learns the sequential tasks without the learned tasks' data via a newly proposed multi-task weight consolidation (MWC) algorithm; 2) expands the network to help the lifelong learning with potentially improved model capability and performance by network-transformation based AutoML; 3) compresses the expanded model after learning every new task to maintain model efficiency and performance. The proposed MWC and REC algorithms achieve superior performance over other lifelong learning algorithms on four different datasets., Comment: 9 pages, 6 figures

Deep neural networks (DNNs) often suffer from "catastrophic forgetting" during incremental learning (IL) --- an abrupt degradation of performance on the original set of classes when the training objective is adapted to a newly added set of classes. Existing IL approaches tend to produce a model that is biased towards either the old classes or new classes, unless with the help of exemplars of the old data. To address this issue, we propose a class-incremental learning paradigm called Deep Model Consolidation (DMC), which works well even when the original training data is not available. The idea is to first train a separate model only for the new classes, and then combine the two individual models trained on data of two distinct set of classes (old classes and new classes) via a novel double distillation training objective. The two existing models are consolidated by exploiting publicly available unlabeled auxiliary data. This overcomes the potential difficulties due to the unavailability of original training data. Compared to the state-of-the-art techniques, DMC demonstrates significantly better performance in image classification (CIFAR-100 and CUB-200) and object detection (PASCAL VOC 2007) in the single-headed IL setting., Comment: WACV 2020 camera-ready

The key challenge of generative Visual Dialogue (VD) systems is to respond to human queries with informative answers in natural and contiguous conversation flow. Traditional Maximum Likelihood Estimation (MLE)-based methods only learn from positive responses but ignore the negative responses, and consequently tend to yield safe or generic responses. To address this issue, we propose a novel training scheme in conjunction with weighted likelihood estimation (WLE) method. Furthermore, an adaptive multi-modal reasoning module is designed, to accommodate various dialogue scenarios automatically and select relevant information accordingly. The experimental results on the VisDial benchmark demonstrate the superiority of our proposed algorithm over other state-of-the-art approaches, with an improvement of 5.81% on recall@10., Comment: IJCAI 2019