Molecule representation learning is crucial for various downstream applications, such as understanding and predicting molecular properties and side effects. In this paper, we propose a novel method called GODE, which takes into account the two-level structure of individual molecules. We recognize that molecules have an intrinsic graph structure as well as being a node in a larger molecule knowledge graph. GODE integrates graph representations of individual molecules with multidomain biochemical data from knowledge graphs. By pre-training two graph neural networks (GNNs) on different graph structures, combined with contrastive learning, GODE fuses molecular structures with their corresponding knowledge graph substructures. This fusion results in a more robust and informative representation, which enhances molecular property prediction by harnessing both chemical and biological information. When fine-tuned across 11 chemical property tasks, our model outperforms existing benchmarks, registering an average ROC-AUC uplift of 13.8% for classification tasks and an average RMSE/MAE enhancement of 35.1% for regression tasks. Impressively, it surpasses the current leading model in molecule property predictions with average advancements of 2.1% in classification and 6.4% in regression tasks.
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Deep learning has shown promise in decoding brain signals, such as electroencephalogram (EEG), in the field of brain-computer interfaces (BCIs). However, the non-stationary characteristics of EEG signals pose challenges for training neural networks to acquire appropriate knowledge. Inconsistent EEG signals resulting from these non-stationary characteristics can lead to poor performance. Therefore, it is crucial to investigate and address sample inconsistency to ensure robust performance in spontaneous BCIs. In this study, we introduce the concept of sample dominance as a measure of EEG signal inconsistency and propose a method to modulate its effect on network training. We present a two-stage dominance score estimation technique that compensates for performance degradation caused by sample inconsistencies. Our proposed method utilizes non-parametric estimation to infer sample inconsistency and assigns each sample a dominance score. This score is then aggregated with the loss function during training to modulate the impact of sample inconsistency. Furthermore, we design a curriculum learning approach that gradually increases the influence of inconsistent signals during training to improve overall performance. We evaluate our proposed method using public spontaneous BCI dataset. The experimental results confirm that our findings highlight the importance of addressing sample dominance for achieving robust performance in spontaneous BCIs.
While deep learning gradually penetrates operational planning, its inherent prediction errors may significantly affect electricity prices. This letter examines how prediction errors propagate into electricity prices, revealing notable pricing errors and their spatial disparity in congested power systems. To improve fairness, we propose to embed electricity market-clearing optimization as a deep learning layer. Differentiating through this layer allows for balancing between prediction and pricing errors, as oppose to minimizing prediction errors alone. This layer implicitly optimizes fairness and controls the spatial distribution of price errors across the system. We showcase the price-aware deep learning in the nexus of wind power forecasting and short-term electricity market clearing.
While interests in tabular deep learning has significantly grown, conventional tree-based models still outperform deep learning methods. To narrow this performance gap, we explore the innovative retrieval mechanism, a methodology that allows neural networks to refer to other data points while making predictions. Our experiments reveal that retrieval-based training, especially when fine-tuning the pretrained TabPFN model, notably surpasses existing methods. Moreover, the extensive pretraining plays a crucial role to enhance the performance of the model. These insights imply that blending the retrieval mechanism with pretraining and transfer learning schemes offers considerable potential for advancing the field of tabular deep learning.
Differential privacy (DP) has seen immense applications in learning on tabular, image, and sequential data where instance-level privacy is concerned. In learning on graphs, contrastingly, works on node-level privacy are highly sparse. Challenges arise as existing DP protocols hardly apply to the message-passing mechanism in Graph Neural Networks (GNNs). In this study, we propose a solution that specifically addresses the issue of node-level privacy. Our protocol consists of two main components: 1) a sampling routine called HeterPoisson, which employs a specialized node sampling strategy and a series of tailored operations to generate a batch of sub-graphs with desired properties, and 2) a randomization routine that utilizes symmetric multivariate Laplace (SML) noise instead of the commonly used Gaussian noise. Our privacy accounting shows this particular combination provides a non-trivial privacy guarantee. In addition, our protocol enables GNN learning with good performance, as demonstrated by experiments on five real-world datasets; compared with existing baselines, our method shows significant advantages, especially in the high privacy regime. Experimentally, we also 1) perform membership inference attacks against our protocol and 2) apply privacy audit techniques to confirm our protocol's privacy integrity. In the sequel, we present a study on a seemingly appealing approach \cite{sajadmanesh2023gap} (USENIX'23) that protects node-level privacy via differentially private node/instance embeddings. Unfortunately, such work has fundamental privacy flaws, which are identified through a thorough case study. More importantly, we prove an impossibility result of achieving both (strong) privacy and (acceptable) utility through private instance embedding. The implication is that such an approach has intrinsic utility barriers when enforcing differential privacy.
Nonresponse after probability sampling is a universal challenge in survey sampling, often necessitating adjustments to mitigate sampling and selection bias simultaneously. This study explored the removal of bias and effective utilization of available information, not just in nonresponse but also in the scenario of data integration, where summary statistics from other data sources are accessible. We reformulate these settings within a two-step monotone missing data framework, where the first step of missingness arises from sampling and the second originates from nonresponse. Subsequently, we derive the semiparametric efficiency bound for the target parameter. We also propose adaptive estimators utilizing methods of moments and empirical likelihood approaches to attain the lower bound. The proposed estimator exhibits both efficiency and double robustness. However, attaining efficiency with an adaptive estimator requires the correct specification of certain working models. To reinforce robustness against the misspecification of working models, we extend the property of double robustness to multiple robustness by proposing a two-step empirical likelihood method that effectively leverages empirical weights. A numerical study is undertaken to investigate the finite-sample performance of the proposed methods. We further applied our methods to a dataset from the National Health and Nutrition Examination Survey data by efficiently incorporating summary statistics from the National Health Interview Survey data.
To facilitate efficient learning, policy gradient approaches to deep reinforcement learning (RL) are typically paired with variance reduction measures and strategies for making large but safe policy changes based on a batch of experiences. Natural policy gradient methods, including Trust Region Policy Optimization (TRPO), seek to produce monotonic improvement through bounded changes in policy outputs. Proximal Policy Optimization (PPO) is a commonly used, first-order algorithm that instead uses loss clipping to take multiple safe optimization steps per batch of data, replacing the bound on the single step of TRPO with regularization on multiple steps. In this work, we find that the performance of PPO, when applied to continuous action spaces, may be consistently improved through a simple change in objective. Instead of the importance sampling objective of PPO, we instead recommend a basic policy gradient, clipped in an equivalent fashion. While both objectives produce biased gradient estimates with respect to the RL objective, they also both display significantly reduced variance compared to the unbiased off-policy policy gradient. Additionally, we show that (1) the clipped-objective policy gradient (COPG) objective is on average "pessimistic" compared to both the PPO objective and (2) this pessimism promotes enhanced exploration. As a result, we empirically observe that COPG produces improved learning compared to PPO in single-task, constrained, and multi-task learning, without adding significant computational cost or complexity. Compared to TRPO, the COPG approach is seen to offer comparable or superior performance, while retaining the simplicity of a first-order method.
Despite the recent progress in deep learning, most approaches still go for a silo-like solution, focusing on learning each task in isolation: training a separate neural network for each individual task. Many real-world problems, however, call for a multi-modal approach and, therefore, for multi-tasking models. Multi-task learning (MTL) aims to leverage useful information across tasks to improve the generalization capability of a model. This thesis is concerned with multi-task learning in the context of computer vision. First, we review existing approaches for MTL. Next, we propose several methods that tackle important aspects of multi-task learning. The proposed methods are evaluated on various benchmarks. The results show several advances in the state-of-the-art of multi-task learning. Finally, we discuss several possibilities for future work.
Federated learning is a new distributed machine learning framework, where a bunch of heterogeneous clients collaboratively train a model without sharing training data. In this work, we consider a practical and ubiquitous issue in federated learning: intermittent client availability, where the set of eligible clients may change during the training process. Such an intermittent client availability model would significantly deteriorate the performance of the classical Federated Averaging algorithm (FedAvg for short). We propose a simple distributed non-convex optimization algorithm, called Federated Latest Averaging (FedLaAvg for short), which leverages the latest gradients of all clients, even when the clients are not available, to jointly update the global model in each iteration. Our theoretical analysis shows that FedLaAvg attains the convergence rate of $O(1/(N^{1/4} T^{1/2}))$, achieving a sublinear speedup with respect to the total number of clients. We implement and evaluate FedLaAvg with the CIFAR-10 dataset. The evaluation results demonstrate that FedLaAvg indeed reaches a sublinear speedup and achieves 4.23% higher test accuracy than FedAvg.
Deep learning has yielded state-of-the-art performance on many natural language processing tasks including named entity recognition (NER). However, this typically requires large amounts of labeled data. In this work, we demonstrate that the amount of labeled training data can be drastically reduced when deep learning is combined with active learning. While active learning is sample-efficient, it can be computationally expensive since it requires iterative retraining. To speed this up, we introduce a lightweight architecture for NER, viz., the CNN-CNN-LSTM model consisting of convolutional character and word encoders and a long short term memory (LSTM) tag decoder. The model achieves nearly state-of-the-art performance on standard datasets for the task while being computationally much more efficient than best performing models. We carry out incremental active learning, during the training process, and are able to nearly match state-of-the-art performance with just 25\% of the original training data.
While existing machine learning models have achieved great success for sentiment classification, they typically do not explicitly capture sentiment-oriented word interaction, which can lead to poor results for fine-grained analysis at the snippet level (a phrase or sentence). Factorization Machine provides a possible approach to learning element-wise interaction for recommender systems, but they are not directly applicable to our task due to the inability to model contexts and word sequences. In this work, we develop two Position-aware Factorization Machines which consider word interaction, context and position information. Such information is jointly encoded in a set of sentiment-oriented word interaction vectors. Compared to traditional word embeddings, SWI vectors explicitly capture sentiment-oriented word interaction and simplify the parameter learning. Experimental results show that while they have comparable performance with state-of-the-art methods for document-level classification, they benefit the snippet/sentence-level sentiment analysis.
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