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Recently, graph neural networks (GNNs) have been applied with great success to predicting molecular properties, which is one of the most classical cheminformatics tasks with various applications. Despite their effectiveness, we empirically observe that training a single GNN model for diverse molecules with distinct structural patterns limits its prediction performance. In this paper, motivated by this observation, we propose TopExpert to leverage topology-specific prediction models (referred to as experts), each of which is responsible for each molecular group sharing similar topological semantics. That is, each expert learns topology-specific discriminative features while being trained with its corresponding topological group. To tackle the key challenge of grouping molecules by their topological patterns, we introduce a clustering-based gating module that assigns an input molecule into one of the clusters and further optimizes the gating module with two different types of self-supervision: topological semantics induced by GNNs and molecular scaffolds, respectively. Extensive experiments demonstrate that TopExpert successfully boosts the performance for molecular property prediction and also achieves better generalization for new molecules with unseen scaffolds than baselines.

AAAI 2023

Learning Topology-Specific Experts for Molecular Property Prediction

molecular property prediction

mixture of experts

graph neural networks

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

Inspired by the cognitive science theory of the explicit human memory systems, we have modeled an agent with short-term, episodic, and semantic memory systems, each of which is modeled with a knowledge graph. To evaluate this system and analyze the behavior of this agent, we designed and released our own reinforcement learning agent environment, “the Room”, where an agent has to learn how to encode, store, and retrieve memories to maximize its return by answering questions. We show that our deep Q-learning based agent successfully learns whether a short-term memory should be forgotten, or rather be stored in the episodic or semantic memory systems. Our experiments indicate that an agent with human-like memory systems can outperform an agent without this memory structure in the environment.

A Machine with Short-Term, Episodic, and Semantic Memory Systems

With the success of Vision Transformer (ViT) in image classification, its variants have yielded great success in many downstream vision tasks. Among those, the semantic segmentation task has also benefited greatly from the advance of ViT variants. However, most studies of the transformer for semantic segmentation only focus on designing efficient transformer encoders, rarely giving attention to designing the decoder. Several studies make attempts in using the transformer decoder as the segmentation decoder with class-wise learnable query. Instead, we aim to directly use the encoder features as the queries. This paper proposes the Feature Enhancing Decoder transFormer (FeedFormer) that enhances structural information using the transformer decoder. Our goal is to decode the high-level encoder features using the lowest-level encoder feature. We do this by formulating high-level features as queries, and the lowest-level feature as the key and value. This enhances the high-level features by collecting the structural information from the lowest-level feature. Additionally, we use a simple reformation trick of pushing the encoder blocks to take the place of the existing self-attention module of the decoder to improve efficiency. We show the superiority of our decoder with various light-weight transformer-based decoders on popular semantic segmentation datasets. Despite the minute computation, our model has achieved state-of-the-art performance in the performance computation trade-off. Our model FeedFormer-B0 surpasses SegFormer-B0 with 1.8% higher mIoU and 7.1% less computation on ADE20K, and 1.7% higher mIoU and 14.4% less computation on Cityscapes, respectively. Code will be released at: https://github.com/jhshim1995/FeedFormer.

FeedFormer: Revisiting Transformer Decoder for Efficient Semantic Segmentation

Numerical reasoning over hybrid data containing tables and long texts has recently received research attention from the AI community. To generate an executable reasoning program consisting of math and table operations to answer a question, state-of-the-art methods use a retriever-generator pipeline. However, their retrieval results are static, while different generation steps may rely on different sentences. To attend to the retrieved information that is relevant to each generation step, in this paper, we propose DyRRen, an extended retriever-reranker-generator framework where each generation step is enhanced by a dynamic reranking of retrieved sentences. It outperforms existing baselines on the FinQA dataset.

DyRRen: A Dynamic Retriever-Reranker-Generator Model for Numerical Reasoning over Tabular and Textual Data

For many applications of Markov Decision Processes (MDPs), the transition function cannot be specified exactly. Bayes-Adaptive MDPs (BAMDPs) extend Markov Decision Processes (MDPs) to consider transition probabilities governed by latent parameters. To act optimally in BAMDPs, one must maintain a belief distribution over the latent parameters. Typically, this distribution is described by a set of sample MDPs and associated weights which represent the likelihood of a sample MDP being the true underlying MDP. However, this method is sensitive to the size of the set of MDPs. As the latent parameter space’s dimension increases, the number of sample MDPs required to sufficiently cover the space of possible worlds increases exponentially. Thus, we propose an alternative approach for maintaining the belief over the latent parameters. In particular, we consider BAMDPs where the transition probabilities can be expressed in closed form as a polynomial of the latent parameters. We outline a method to maintain a closed-form belief distribution for the latent parameters which results in an accurate belief representation. Furthermore, the closed-form representation does away with the need to tune the number of sample MDPs required to represent the belief. We evaluate two domains and empirically show that the polynomial, closed-form, belief representation results in better plans than a sampling-based belief representation.

Planning with Hidden Parameter Polynomial MDPs

Prompt-based Learning has shown significant success in few-shot classification. The mainstream approach is to concatenate a template for the input text to transform the classification task into a cloze-type task where label mapping plays an important role in finding the ground-truth labels.  While current label mapping methods only use the contexts in one single input, it could be crucial if wrong information is contained in the text. Specifically, it is proved in recent work that even the large language models like BERT/RoBERTa make classification decisions heavily dependent on a specific keyword regardless of the task or the context. Such a word is referred to as a lexical cue and if a misleading lexical cue is included in the instance it will lead the model to make a wrong prediction. We propose a multi-mask prompt-based approach with Multi-Mask Label Mapping (MMLM) to reduce the impact of misleading lexical cues by allowing the model to exploit multiple lexical cues. To satisfy the conditions of few-shot learning, an instance augmentation approach for the cloze-type model is proposed and the misleading cues are gradually excluded through training. We demonstrate the effectiveness of MMLM by both theoretical analysis and empirical studies, and show that MMLM outperforms other existing label mapping approaches.

Multi-Mask Label Mapping for Prompt-based Learning

The most recent approaches for clustering single-cell RNA-sequencing data rely on deep auto-encoders. However, three major challenges remain unaddressed. First, current models overlook the impact of the cumulative errors induced by the pseudo-supervised embedding clustering task (Feature Randomness). Second, existing methods neglect the effect of the strong competition between embedding clustering and reconstruction (Feature Drift). Third, the previous deep clustering models regularly fail to consider the topological information of the latent data, even though the local and global latent configurations can bring complementary views to the clustering task. To address these challenges, we propose a novel approach that explores the interaction between local and global latent configurations to progressively adjust the reconstruction and embedding clustering tasks. We elaborate a topological and probabilistic filter to mitigate Feature Randomness and a cell-cell graph structure and content correction mechanism to counteract Feature Drift. The Zero-Inflated Negative Binomial model is also integrated to capture the characteristics of gene expression profiles. We conduct detailed experiments on real-world datasets from multiple representative genome sequencing platforms. Our approach outperforms the state-of-the-art clustering methods in various evaluation metrics. 

Exploring the Interaction between Local and Global Latent Configurations for Clustering Single-cell RNA-seq: A Unified Perspective

Various contrastive learning approaches have been proposed in recent years and achieve significant empirical success. While effective and prevalent, contrastive learning has been less explored for time series data. A key component of contrastive learning is to select appropriate augmentations imposing some priors to construct feasible positive samples, such that an encoder can be trained to learn robust and discriminative representations. Unlike image and language domains where ``desired'' augmented samples can be generated with the rule of thumb guided by prefabricated human priors, the ad-hoc manual selection of time series augmentations is hindered by their diverse and human-unrecognizable temporal structures. How to find the desired augmentations of time series data that are meaningful for given contrastive learning tasks and datasets remains an open question. In this work, we address the problem by encouraging both high \textit{fidelity} and \textit{variety} based upon information theory. A theoretical analysis leads to the criteria for selecting feasible data augmentations. On top of that, we propose a new contrastive learning approach with information-aware augmentations, InfoTS, that adaptively selects optimal augmentations for time series representation learning. Experiments on various datasets show highly competitive performance with up to 12.0\% reduction in MSE on forecasting tasks and up to 3.7\% relative improvement in accuracy on classification tasks over the leading baselines.

Time Series Contrastive Learning with Information-Aware Augmentations

Learning from raw high dimensional data via interaction with a given environment has been effectively achieved through the utilization of deep neural networks. Yet the observed degradation in policy performance caused by imperceptible worst-case policy dependent translations along high sensitivity directions (i.e. adversarial perturbations) raises concerns on the robustness of deep reinforcement learning policies. In our paper, we show that these high sensitivity directions do not lie only along particular worst-case directions, but rather are more abundant in the deep neural policy landscape and can be found via more natural means in a black-box setting. Furthermore, we show that vanilla training techniques intriguingly result in learning more robust policies compared to the policies learnt via the state-of-the-art adversarial training techniques. We believe our work lays out intriguing properties of the deep reinforcement learning policy manifold and our results can help to build robust and generalizable deep reinforcement learning policies.

Adversarial Robust Deep Reinforcement Learning Requires Redefining Robustness

Cross entropy loss has served as the main objective function for classification-based tasks. Widely deployed for learning neural network classifiers, it shows both effectiveness and a probabilistic interpretation.  Recently, after the success of self supervised contrastive representation learning methods, supervised contrastive methods have been proposed to learn representations and have shown superior and more robust performance, compared to solely training with cross entropy loss. However, cross entropy loss is still needed to train the final classification layer. In this work, we investigate the possibility of learning both the representation and the classifier using one objective function that combines the robustness of contrastive learning and the probabilistic interpretation of  cross entropy loss. First,  we revisit a previously proposed contrastive-based objective function that approximates cross entropy loss and present a simple extension to learn  the classifier jointly. Second, we propose a new version of the supervised contrastive training that learns jointly the parameters of the classifier and the backbone of the network. We empirically show that these proposed objective functions demonstrate state-of-the-art performance and show a significant improvement over the standard cross entropy loss with more training stability and robustness in various challenging settings.

Contrastive Classification and Representation Learning with Probabilistic Interpretation

We present Progressively Deblurring Radiance Field (PDRF), a novel approach to efficiently reconstruct high quality radiance fields from blurry images. While current State-of-The-Art (SoTA) scene reconstruction methods achieve photo-realistic renderings from clean source views, their performances suffer when the source views are affected by blur, which is commonly observed in the wild. Previous deblurring methods either do not account for 3D geometry, or are computationally intense. To addresses these issues, PDRF uses a progressively deblurring scheme for radiance field modeling, which can accurately model blur with 3D scene context. PDRF further uses an efficient importance sampling scheme and results in fast scene optimization. We perform extensive experiments and show that PDRF is 15X faster than previous SoTA while achieving better performance on both synthetic and real scenes.

Learning Topology-Specific Experts for Molecular Property Prediction

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