Deep neural networks have enabled researchers to create powerful generalized frameworks, such as transformers, that can be used to solve well-studied problems in various application domains, such as text and image. However, such generalized frameworks are not available for solving graph problems. Graph structures are ubiquitous in many applications around us and many graph problems have been widely studied over years. In recent times, there has been a surge in deep neural network based approaches to solve graph problems, with growing availability of graph structured datasets across diverse domains. Nevertheless, existing methods are mostly tailored to solve a specific task and lack the capability to create a generalized model leading to solutions for different downstream tasks. In this work, we propose a novel, resource-efficient framework named \emph{U}nified \emph{G}raph \emph{N}etwork (UGN) by leveraging the feature extraction capability of graph convolutional neural networks (GCN) and 2-dimensional convolutional neural networks (Conv2D). UGN unifies various graph learning tasks, such as link prediction, node classification, community detection, graph-to-graph translation, knowledge graph completion, and more, within a cohesive framework, while exercising minimal task-specific extensions (e.g., formation of supernodes for coarsening massive networks to increase scalability, use of \textit{mean target connectivity matrix} (MTCM) representation for achieving scalability in graph translation task, etc.) to enhance the generalization capability of graph learning and analysis. We test the novel UGN framework for six uncorrelated graph problems, using twelve different datasets. Experimental results show that UGN outperforms the state-of-the-art baselines by a significant margin on ten datasets, while producing comparable results on the remaining dataset.
Graph diffusion models, dominant in graph generative modeling, remain underexplored for graph-to-graph translation tasks like chemical reaction prediction. We demonstrate that standard permutation equivariant denoisers face fundamental limitations in these tasks due to their inability to break symmetries in noisy inputs. To address this, we propose aligning input and target graphs to break input symmetries while preserving permutation equivariance in non-matching graph portions. Using retrosynthesis (i.e., the task of predicting precursors for synthesis of a given target molecule) as our application domain, we show how alignment dramatically improves discrete diffusion model performance from 5% to a SOTA-matching 54.7% top-1 accuracy. Code is available at https://github.com/Aalto-QuML/DiffAlign.
Graph translation is very promising research direction and has a wide range of potential real-world applications. Graph is a natural structure for representing relationship and interactions, and its translation can encode the intrinsic semantic changes of relationships in different scenarios. However, despite its seemingly wide possibilities, usage of graph translation so far is still quite limited. One important reason is the lack of high-quality paired dataset. For example, we can easily build graphs representing peoples' shared music tastes and those representing co-purchase behavior, but a well paired dataset is much more expensive to obtain. Therefore, in this work, we seek to provide a graph translation model in the semi-supervised scenario. This task is non-trivial, because graph translation involves changing the semantics in the form of link topology and node attributes, which is difficult to capture due to the combinatory nature and inter-dependencies. Furthermore, due to the high order of freedom in graph's composition, it is difficult to assure the generalization ability of trained models. These difficulties impose a tighter requirement for the exploitation of unpaired samples. Addressing them, we propose to construct a dual representation space, where transformation is performed explicitly to model the semantic transitions. Special encoder/decoder structures are designed, and auxiliary mutual information loss is also adopted to enforce the alignment of unpaired/paired examples. We evaluate the proposed method in three different datasets.
The problem of accelerating drug discovery relies heavily on automatic tools to optimize precursor molecules to afford them with better biochemical properties. Our work in this paper substantially extends prior state-of-the-art on graph-to-graph translation methods for molecular optimization. In particular, we realize coherent multi-resolution representations by interweaving the encoding of substructure components with the atom-level encoding of the original molecular graph. Moreover, our graph decoder is fully autoregressive, and interleaves each step of adding a new substructure with the process of resolving its attachment to the emerging molecule. We evaluate our model on multiple molecular optimization tasks and show that our model significantly outperforms previous state-of-the-art baselines.
We view molecular optimization as a graph-to-graph translation problem. The goal is to learn to map from one molecular graph to another with better properties based on an available corpus of paired molecules. Since molecules can be optimized in different ways, there are multiple viable translations for each input graph. A key challenge is therefore to model diverse translation outputs. Our primary contributions include a junction tree encoder-decoder for learning diverse graph translations along with a novel adversarial training method for aligning distributions of molecules. Diverse output distributions in our model are explicitly realized by low-dimensional latent vectors that modulate the translation process. We evaluate our model on multiple molecular optimization tasks and show that our model outperforms previous state-of-the-art baselines.