TorchDrug: A Powerful and Flexible Machine Learning Platform for Drug Discovery

Machine learning has huge potential to revolutionize the field of drug discovery and is attracting increasing attention in recent years. However, lacking domain knowledge (e.g., which tasks to work on), standard benchmarks and data preprocessing pipelines are the main obstacles for machine learning researchers to work in this domain. To facilitate the progress of machine learning for drug discovery, we develop TorchDrug, a powerful and flexible machine learning platform for drug discovery built on top of PyTorch. TorchDrug benchmarks a variety of important tasks in drug discovery, including molecular property prediction, pretrained molecular representations, de novo molecular design and optimization, retrosynthsis prediction, and biomedical knowledge graph reasoning. State-of-the-art techniques based on geometric deep learning (or graph machine learning), deep generative models, reinforcement learning and knowledge graph reasoning are implemented for these tasks. TorchDrug features a hierarchical interface that facilitates customization from both novices and experts in this domain. Tutorials, benchmark results and documentation are available at https://torchdrug.ai. Code is released under Apache License 2.0.

HCSC: Hierarchical Contrastive Selective Coding

Hierarchical semantic structures naturally exist in an image dataset, in which several semantically relevant image clusters can be further integrated into a larger cluster with coarser-grained semantics. Capturing such structures with image representations can greatly benefit the semantic understanding on various downstream tasks. Existing contrastive representation learning methods lack such an important model capability. In addition, the negative pairs used in these methods are not guaranteed to be semantically distinct, which could further hamper the structural correctness of learned image representations. To tackle these limitations, we propose a novel contrastive learning framework called Hierarchical Contrastive Selective Coding (HCSC). In this framework, a set of hierarchical prototypes are constructed and also dynamically updated to represent the hierarchical semantic structures underlying the data in the latent space. To make image representations better fit such semantic structures, we employ and further improve conventional instance-wise and prototypical contrastive learning via an elaborate pair selection scheme. This scheme seeks to select more diverse positive pairs with similar semantics and more precise negative pairs with truly distinct semantics. On extensive downstream tasks, we verify the superior performance of HCSC over state-of-the-art contrastive methods, and the effectiveness of major model components is proved by plentiful analytical studies. Our source code and model weights are available at https://github.com/gyfastas/HCSC

Cross-category Video Highlight Detection via Set-based Learning

Autonomous highlight detection is crucial for enhancing the efficiency of video browsing on social media platforms. To attain this goal in a data-driven way, one may often face the situation where highlight annotations are not available on the target video category used in practice, while the supervision on another video category (named as source video category) is achievable. In such a situation, one can derive an effective highlight detector on target video category by transferring the highlight knowledge acquired from source video category to the target one. We call this problem cross-category video highlight detection, which has been rarely studied in previous works. For tackling such practical problem, we propose a Dual-Learner-based Video Highlight Detection (DL-VHD) framework. Under this framework, we first design a Set-based Learning module (SL-module) to improve the conventional pair-based learning by assessing the highlight extent of a video segment under a broader context. Based on such learning manner, we introduce two different learners to acquire the basic distinction of target category videos and the characteristics of highlight moments on source video category, respectively. These two types of highlight knowledge are further consolidated via knowledge distillation. Extensive experiments on three benchmark datasets demonstrate the superiority of the proposed SL-module, and the DL-VHD method outperforms five typical Unsupervised Domain Adaptation (UDA) algorithms on various cross-category highlight detection tasks. Our code is available at https://github.com/ChrisAllenMing/Cross_Category_Video_Highlight .

PIT: Position-Invariant Transform for Cross-FoV Domain Adaptation

Cross-domain object detection and semantic segmentation have witnessed impressive progress recently. Existing approaches mainly consider the domain shift resulting from external environments including the changes of background, illumination or weather, while distinct camera intrinsic parameters appear commonly in different domains, and their influence for domain adaptation has been very rarely explored. In this paper, we observe that the Field of View (FoV) gap induces noticeable instance appearance differences between the source and target domains. We further discover that the FoV gap between two domains impairs domain adaptation performance under both the FoV-increasing (source FoV < target FoV) and FoV-decreasing cases. Motivated by the observations, we propose the \textbf{Position-Invariant Transform} (PIT) to better align images in different domains. We also introduce a reverse PIT for mapping the transformed/aligned images back to the original image space and design a loss re-weighting strategy to accelerate the training process. Our method can be easily plugged into existing cross-domain detection/segmentation frameworks while bringing about negligible computational overhead. Extensive experiments demonstrate that our method can soundly boost the performance on both cross-domain object detection and segmentation for state-of-the-art techniques. Our code is available at https://github.com/sheepooo/PIT-Position-Invariant-Transform.

Self-supervised Graph-level Representation Learning with Local and Global Structure

This paper studies unsupervised/self-supervised whole-graph representation learning, which is critical in many tasks such as molecule properties prediction in drug and material discovery. Existing methods mainly focus on preserving the local similarity structure between different graph instances but fail to discover the global semantic structure of the entire data set. In this paper, we propose a unified framework called Local-instance and Global-semantic Learning (GraphLoG) for self-supervised whole-graph representation learning. Specifically, besides preserving the local similarities, GraphLoG introduces the hierarchical prototypes to capture the global semantic clusters. An efficient online expectation-maximization (EM) algorithm is further developed for learning the model. We evaluate GraphLoG by pre-training it on massive unlabeled graphs followed by fine-tuning on downstream tasks. Extensive experiments on both chemical and biological benchmark data sets demonstrate the effectiveness of the proposed approach.

Graphical Modeling for Multi-Source Domain Adaptation

Multi-Source Domain Adaptation (MSDA) focuses on transferring the knowledge from multiple source domains to the target domain, which is a more practical and challenging problem compared to the conventional single-source domain adaptation. In this problem, it is essential to utilize the labeled source data and the unlabeled target data to approach the conditional distribution of semantic label on target domain, which requires the joint modeling across different domains and also an effective domain combination scheme. The graphical structure among different domains is useful to tackle these challenges, in which the interdependency among various instances/categories can be effectively modeled. In this work, we propose two types of graphical models,i.e. Conditional Random Field for MSDA (CRF-MSDA) and Markov Random Field for MSDA (MRF-MSDA), for cross-domain joint modeling and learnable domain combination. In a nutshell, given an observation set composed of a query sample and the semantic prototypes i.e. representative category embeddings) on various domains, the CRF-MSDA model seeks to learn the joint distribution of labels conditioned on the observations. We attain this goal by constructing a relational graph over all observations and conducting local message passing on it. By comparison, MRF-MSDA aims to model the joint distribution of observations over different Markov networks via an energy-based formulation, and it can naturally perform label prediction by summing the joint likelihoods over several specific networks. Compared to the CRF-MSDA counterpart, the MRF-MSDA model is more expressive and possesses lower computational cost. We evaluate these two models on four standard benchmark data sets of MSDA with distinct domain shift and data complexity, and both models achieve superior performance over existing methods on all benchmarks.

Learning to Combine: Knowledge Aggregation for Multi-Source Domain Adaptation

Transferring knowledges learned from multiple source domains to target domain is a more practical and challenging task than conventional single-source domain adaptation. Furthermore, the increase of modalities brings more difficulty in aligning feature distributions among multiple domains. To mitigate these problems, we propose a Learning to Combine for Multi-Source Domain Adaptation (LtC-MSDA) framework via exploring interactions among domains. In the nutshell, a knowledge graph is constructed on the prototypes of various domains to realize the information propagation among semantically adjacent representations. On such basis, a graph model is learned to predict query samples under the guidance of correlated prototypes. In addition, we design a Relation Alignment Loss (RAL) to facilitate the consistency of categories' relational interdependency and the compactness of features, which boosts features' intra-class invariance and inter-class separability. Comprehensive results on public benchmark datasets demonstrate that our approach outperforms existing methods with a remarkable margin. Our code is available at \url{https://github.com/ChrisAllenMing/LtC-MSDA}

Cross-domain Detection via Graph-induced Prototype Alignment

Applying the knowledge of an object detector trained on a specific domain directly onto a new domain is risky, as the gap between two domains can severely degrade model's performance. Furthermore, since different instances commonly embody distinct modal information in object detection scenario, the feature alignment of source and target domain is hard to be realized. To mitigate these problems, we propose a Graph-induced Prototype Alignment (GPA) framework to seek for category-level domain alignment via elaborate prototype representations. In the nutshell, more precise instance-level features are obtained through graph-based information propagation among region proposals, and, on such basis, the prototype representation of each class is derived for category-level domain alignment. In addition, in order to alleviate the negative effect of class-imbalance on domain adaptation, we design a Class-reweighted Contrastive Loss to harmonize the adaptation training process. Combining with Faster R-CNN, the proposed framework conducts feature alignment in a two-stage manner. Comprehensive results on various cross-domain detection tasks demonstrate that our approach outperforms existing methods with a remarkable margin. Our code is available at https://github.com/ChrisAllenMing/GPA-detection.