United States

Retrosynthesis, which predicts the reactants of a given target molecule, is an essential task for drug discovery. 
In recent years, the machine learing based retrosynthesis methods have achieved promising results.
In this work, we introduce RetroKNN, a local reaction template retrieval method to further boost the performance of template-based systems with non-parametric retrieval. We first build an atom-template store and a bond-template store that contains the local templates in the training data, then retrieve from these templates with a k-nearest-neighbor (KNN) search during inference. The retrieved templates are combined with neural network predictions as the final output.
Furthermore, we propose a lightweight adapter to adjust the weights when combing neural network and KNN predictions conditioned on the hidden representation and the retrieved templates.
We conduct comprehensive experiments on two widely used benchmarks, the USPTO-50K and USPTO-MIT.
Especially for the top-1 accuracy, we improved 7.1\% on the USPTO-50K dataset and 12.0\% on the USPTO-MIT dataset.
These results demonstrate the effectiveness of our method.

AAAI 2023

Retrosynthesis Prediction with Local Template Retrieval

retrosynthesis

bioinformatics

retrieval

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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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

Civic Crowdfunding (CC) uses the ``power of the crowd" to garner contributions towards public projects. As these projects are non-excludable, agents may prefer to ``free-ride,"  resulting in the project not being funded. Researchers introduce refunds for single project CC to incentivize agents to contribute, guaranteeing the project's funding. These funding guarantees are applicable only when agents have an unlimited budget. This paper focuses on a combinatorial setting, where multiple projects are available for CC and agents have a limited budget. We study specific conditions where funding can be guaranteed. Naturally, funding the optimal social welfare subset of projects is desirable when every available project cannot be funded due to budget restrictions. We prove the impossibility of achieving optimal welfare at equilibrium for any monotone refund scheme. Further, given the contributions of other agents, we prove that it is NP-Hard for an agent to determine its optimal strategy. That is, while profitable deviations may exist for agents instead of funding the optimal welfare subset, it is computationally hard for an agent to find its optimal deviation. Consequently, we study different heuristics agents can use to contribute to the projects in practice. We demonstrate the heuristics' performance as the average-case trade-off between the welfare obtained and an agent's utility through simulations.

Combinatorial Civic Crowdfunding with Budgeted Agents: Welfare Optimality at Equilibrium and Optimal Deviation

Regularized discrete optimal transport (OT) is a powerful tool to measure the distance between two discrete distributions that have been constructed from data samples on two different domains. While it has a wide range of applications in machine learning, in some cases the sampled data from only one of the domains will have class labels such as unsupervised domain adaptation. In this kind of problem setting, a group-sparse regularizer is frequently leveraged as a regularization term to handle class labels. In particular, it can preserve the label structure on the data samples by corresponding the data samples with the same class label to one group-sparse regularization term. As a result, we can measure the distance while utilizing label information by solving the regularized optimization problem with gradient-based algorithms. However, the gradient computation is expensive when the number of classes or data samples is large because the number of regularization terms and their respective sizes also turn out to be large. This paper proposes fast discrete OT with group-sparse regularizers. Our method is based on two ideas. The first is to safely skip the computations of the gradients that must be zero. The second is to efficiently extract the gradients that are expected to be nonzero. Our method is guaranteed to return the same value of the objective function as that of the original approach. Experiments demonstrate that our method is up to 8.6 times faster than the original method without degrading accuracy.

Fast Regularized Discrete Optimal Transport with Group-sparse Regularizers

Concept relatedness estimation (CRE) aims to determine whether two given concepts are related. Existing methods only consider the pairwise relationship between concepts, while overlooking the higher-order relationship that could be encoded in a concept-level graph structure. We discover that this underlying graph satisfies a set of intrinsic properties of CRE, including reflexivity, commutativity, and transitivity. In this paper, we formalize the CRE properties and introduce a graph structure named ConcreteGraph. To address the data scarcity issue in CRE, we introduce a novel data augmentation approach to sample new concept pairs from the graph. As it is intractable for data augmentation to fully capture the structural information of the ConcreteGraph due to a large amount of potential concept pairs, we further introduce a novel Graph Component Contrastive Learning framework to implicitly learn the complete structure of the ConcreteGraph. Empirical results on three datasets show significant improvement over the state-of-the-art model. Detailed ablation studies demonstrate that our proposed approach can effectively capture the high-order relationship among concepts.

Graph Component Contrastive Learning for Concept Relatedness Estimation

Due to the powerful capability to gather the information of neighborhood nodes, Graph Convolutional Network (GCN) has become a widely explored hotspot in recent years. As a well-established extension, Graph AutoEncoder (GAE) succeeds in mining underlying node representations via evaluating the quality of adjacency matrix reconstruction from learned features. However, limited works on GAE were devoted to leveraging both semantic and topological graphs, and they only indirectly extracted the relationships between graphs via weights shared by features. To better capture the connections between nodes from these two types of graphs, this paper proposes a graph neural network dubbed Dual Low-Rank Graph AutoEncoder (DLR-GAE), which takes both semantic and topological homophily into consideration. Differing from prior works that share common weights between GCNs, the presented DLR-GAE conducts sustained exploration of low-rank information between two distinct graphs, and reconstructs adjacency matrices from learned latent factors and embeddings. In order to obtain valid adjacency matrices that meet certain conditions, we design some surrogates and projections to restrict the learned factor matrix. We compare the proposed model with state-of-the-art methods on several datasets, which demonstrates the superior accuracy of DLR-GAE in semi-supervised classification.

Dual Low-Rank Graph Autoencoder for Semantic and Topological Networks

The sketch-based image retrieval (SBIR) task has long been researched at the instance level, where both query sketches and candidate images are assumed to contain only one dominant object. This strong assumption constrains its application, especially with the increasingly popular intelligent terminals and human-computer interaction technology. In this work, a more general scene-level SBIR task is explored, where sketches and images can both contain multiple object instances. The new general task is extremely challenging due to several factors: (i) scene-level SBIR inherently shares sketch-specific difficulties with instance-level SBIR (e.g., sparsity, abstractness, and diversity), (ii) the cross-modal similarity is measured between two partially aligned domains (i.e., not all objects in images are drawn in scene sketches), and (iii) besides instance-level visual similarity, a more complex multi-dimensional scene-level feature matching problem is imposed (including appearance, semantics, layout, etc.). Addressing these challenges, a novel Conditional Graph Autoencoder model is proposed to deal with scene-level sketch-images retrieval. More importantly, the model can be trained with only pairwise supervision, which distinguishes our study from others in that elaborate instance-level annotations (for example, bounding boxes) are no longer required. Extensive experiments confirm the ability of our model to robustly retrieve multiple related objects at the scene level and exhibit superior performance beyond strong competitors.

Scene-Level Sketch-Based Image Retrieval with Minimal Pairwise Supervision

Sketch-based image retrieval (SBIR) is an attractive research area where freehand sketches are used as queries to retrieve relevant images. Existing solutions have advanced the task to the challenging zero-shot setting (ZS-SBIR), where the trained models are tested on new classes without seen data. However, they are prone to overfitting under a realistic scenario when the test data includes both seen and unseen classes. In this paper, we study generalized ZS-SBIR (GZS-SBIR) and propose a novel semi-transductive learning paradigm. Transductive learning is performed on the image modality to explore the potential data distribution within unseen classes, and zero-shot learning is performed on the sketch modality sharing the learned knowledge through a semi-heterogeneous architecture. A hybrid metric learning strategy is proposed to establish semantics-aware ranking property and calibrate the joint embedding space. Extensive experiments are conducted on two large-scale benchmarks and four evaluation metrics. The results show that our method is superior over the state-of-the-art competitors in the challenging GZS-SBIR task.

Semi-Transductive Learning for Generalized Zero-Shot Sketch-Based Image Retrieval

Humans naturally use referring expressions with verbal utterances and nonverbal gestures to refer to objects and events. As these referring expressions can be interpreted differently from the speaker's or the observer's perspective, people effectively decide on the perspective in comprehending the expressions. However, existing models do not explicitly learn perspective grounding, which often causes the models to perform poorly in understanding embodied referring expressions. To make it exacerbate, these models are often trained on datasets collected in non-embodied settings without nonverbal gestures and curated from an exocentric perspective. To address these issues, in this paper, we present a perspective-aware multitask learning model, called PATRON, for relation and object grounding tasks in embodied settings by utilizing verbal utterances and nonverbal cues. In PATRON, we have developed a guided fusion approach, where a perspective grounding task guides the relation and object grounding task. Through this approach, PATRON learns disentangled task-specific and task-guidance representations, where task-guidance representations guide the extraction of salient multimodal features to ground the relation and object accurately. Furthermore, we have curated a synthetic dataset of embodied referring expressions with multimodal cues, called CAESAR-PRO. The experimental results suggest that PATRON outperforms the evaluated state-of-the-art visual-language models. Additionally, the results indicate that learning to ground perspective helps machine learning models to improve the performance of the relation and object grounding task. Furthermore, the insights from the extensive experimental results and the proposed dataset will enable researchers to evaluate visual-language models' effectiveness in understanding referring expressions in other embodied settings.

PATRON: Perspective-aware Multitask Model for Referring Expression Grounding using Embodied Multimodal Cues

Exemplar rehearsal-based methods with knowledge distillation (KD) have been widely used in class incremental learning (CIL) scenarios. However, they still suffer from performance degradation because of severely distribution discrepancy between training and test set caused by the limited storage memory on previous classes. In this paper, we mathematically model the data distribution and the discrepancy at the incremental stages with mixture uniform distribution (MUD). Then, we propose the asymmetric mix distillation method to uniformly minimize the error of each class from distribution discrepancy perspective. Specifically, we firstly promote mixup in CIL scenarios with the incremental mix samplers and incremental mix factor to calibrate the raw training data distribution. Next, mix distillation label augmentation is incorporated into the data distribution to inherit the knowledge information from the previous models. Based on the above augmented data distribution, our trained model effectively alleviates the performance degradation and extensive experimental results validate that our method exhibits superior performance on CIL benchmarks. 

Mixture Uniform Distribution Modeling and Asymmetric Mix Distillation for Class Incremental Learning

In robust optimization, finding a solution that solely respects the constraints is not enough.
Usually, the uncertainty and unknown parameters of the model are represented by random variables.
In such conditions, a good solution is a solution robust to most-likely assignments of these random variables.
The Confidence constraint allows us to enforce this type of robustness in constraint programming.
In this paper, we generalize the Confidence constraint and introduce the Multi-valued Decision Diagram (MDD) confidence. 
The MDD Confidence constraint is defined over a set of random variables. 
Then, for a given constraint represented as an MDD, and given a threshold, the generalized Confidence constraint ensures that the probability for the constraint to be respected by a sample of the variables is greater than the threshold.
On the one hand, constraints that random variables should respect often depend on decision variables.
On the other hand, the MDD represents the constraint that random variables should respect.
That is why this paper proposes several ways to constrain the MDD using decision variables during search.
These constraints are a generalization of the Confidence constraint recently introduced by Mercier-Aubin et al.
In fact, the existing constraint is restricted to a conjunction of binary inequalities.
The proposed generalization can be applied to any constraint, and filtering algorithms are provided using their MDD representation.
Moreover, the original work was restricted to independent random variables, while our generalization can be used with Markov chains, 
allowing a better expressiveness.
Finally, the experimental section shows the efficiency of the proposed methodology on a chemical deliveries problem in factories 
where the chemicals uses are uncertain.

Generalized Confidence Constraints

The field of emergent communication aims to understand the characteristics of communication as it emerges from artificial agents solving tasks that require information exchange. Communication with discrete messages is considered a desired characteristic, for scientific and applied reasons. However,  training a multi-agent system with discrete communication is not straightforward, requiring either reinforcement learning algorithms or relaxing the discreteness requirement via a continuous approximation such as the Gumbel-softmax. Both these solutions result in poor performance compared to fully continuous communication. In this work, we propose an alternative approach to achieve discrete communication -- quantization of communicated message. Using message quantization allows us to train the model end-to-end, achieving superior performance in multiple setups. Moreover, quantization is a natural framework that runs the gamut from continuous to discrete communication. Thus,  it sets the ground for a broader view of multi-agent communication in the deep learning era. 

Retrosynthesis Prediction with Local Template Retrieval

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