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  1. Contrastive learning is a self-supervised representation learning method that achieves milestone performance in various classification tasks. However, due to its unsupervised fashion, it suffers from the false negative sample problem: randomly drawn negative samples that are assumed to have a different label but actually have the same label as the anchor. This deteriorates the performance of contrastive learning as it contradicts the motivation of contrasting semantically similar and dissimilar pairs. This raised the attention and the importance of finding legitimate negative samples, which should be addressed by distinguishing between 1) true vs. false negatives; 2) easy vs. hard negatives. However, previous works were limited to the statistical approach to handle false negative and hard negative samples with hyperparameters tuning. In this paper, we go beyond the statistical approach and explore the connection between hard negative samples and data bias. We introduce a novel debiased contrastive learning method to explore hard negatives by relative difficulty referencing the bias-amplifying counterpart. We propose triplet loss for training a biased encoder that focuses more on easy negative samples. We theoretically show that the triplet loss amplifies the bias in self-supervised representation learning. Finally, we empirically show the proposed method improves downstream classification performance. 
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    Free, publicly-accessible full text available June 1, 2024
  2. Recent years have witnessed increasing concerns towards unfair decisions made by machine learning algorithms. To improve fairness in model decisions, various fairness notions have been proposed and many fairness-aware methods are developed. However, most of existing definitions and methods focus only on single-label classification. Fairness for multi-label classification, where each instance is associated with more than one labels, is still yet to establish. To fill this gap, we study fairness-aware multi-label classification in this paper. We start by extending Demographic Parity (DP) and Equalized Opportunity (EOp), two popular fairness notions, to multi-label classification scenarios. Through a systematic study, we show that on multi-label data, because of unevenly distributed labels, EOp usually fails to construct a reliable estimate on labels with few instances. We then propose a new framework named Similarity s-induced Fairness (sγ -SimFair). This new framework utilizes data that have similar labels when estimating fairness on a particular label group for better stability, and can unify DP and EOp. Theoretical analysis and experimental results on real-world datasets together demonstrate the advantage of sγ -SimFair over existing methods on multi-label classification tasks.

     
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    Free, publicly-accessible full text available June 27, 2024
  3. Abstract

    Stereoselective ring-opening polymerization catalysts are used to produce degradable stereoregular poly(lactic acids) with thermal and mechanical properties that are superior to those of atactic polymers. However, the process of discovering highly stereoselective catalysts is still largely empirical. We aim to develop an integrated computational and experimental framework for efficient, predictive catalyst selection and optimization. As a proof of principle, we have developed a Bayesian optimization workflow on a subset of literature results for stereoselective lactide ring-opening polymerization, and using the algorithm, we identify multiple new Al complexes that catalyze either isoselective or heteroselective polymerization. In addition, feature attribution analysis uncovers mechanistically meaningful ligand descriptors, such as percent buried volume (%Vbur) and the highest occupied molecular orbital energy (EHOMO), that can access quantitative and predictive models for catalyst development.

     
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  4. Numerous methods have been developed to explain the inner mechanism of deep neural network (DNN) based classifiers. Existing explanation methods are often limited to explaining predictions of a pre-specified class, which answers the question “why is the input classified into this class?” However, such explanations with respect to a single class are inherently insufficient because they do not capture features with class-discriminative power. That is, features that are important for predicting one class may also be important for other classes. To capture features with true class-discriminative power, we should instead ask “why is the input classified into this class, but not others?” To answer this question, we propose a weighted contrastive framework for explaining DNNs. Our framework can easily convert any existing back-propagation explanation methods to build class-contrastive explanations. We theoretically validate our weighted contrast explanation in general back-propagation explanations, and show that our framework enables class-contrastive explanations with significant improvements in both qualitative and quantitative experiments. Based on the results, we point out an important blind spot in the current explainable artificial intelligence (XAI) study, where explanations towards the predicted logits and the probabilities are obfuscated. We suggest that these two aspects should be distinguished explicitly any time explanation methods are applied. 
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  5. Fairness has become an important topic in machine learning. Generally, most literature on fairness assumes that the sensitive information, such as gender or race, is present in the training set, and uses this information to mitigate bias. However, due to practical concerns like privacy and regulation, applications of these methods are restricted. Also, although much of the literature studies supervised learning, in many real-world scenarios, we want to utilize the large unlabelled dataset to improve the model's accuracy. Can we improve fair classification without sensitive information and without labels? To tackle the problem, in this paper, we propose a novel reweighing-based contrastive learning method. The goal of our method is to learn a generally fair representation without observing sensitive attributes.Our method assigns weights to training samples per iteration based on their gradient directions relative to the validation samples such that the average top-k validation loss is minimized. Compared with past fairness methods without demographics, our method is built on fully unsupervised training data and requires only a small labelled validation set. We provide rigorous theoretical proof of the convergence of our model. Experimental results show that our proposed method achieves better or comparable performance than state-of-the-art methods on three datasets in terms of accuracy and several fairness metrics. 
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  6. Most of existing work on fairness assumes available demographic information in the training set. In practice, due to legal or privacy concerns, when demographic information is not available in the training set, it is crucial to find alternative objectives to ensure fairness. Existing work on fairness without demographics follows Rawlsian Max-Min fairness objectives. However, such constraints could be too strict to improve group fairness, and could lead to a great decrease in accuracy. In light of these limitations, in this paper, we propose to solve the problem from a new perspective, i.e., through knowledge distillation. Our method uses soft label from an overfitted teacher model as an alternative, and we show from preliminary experiments that soft labelling is beneficial for improving fairness. We analyze theoretically the fairness of our method, and we show that our method can be treated as an error-based reweighing. Experimental results on three datasets show that our method outperforms state-of-the-art alternatives, with notable improvements in group fairness and with relatively small decrease in accuracy. 
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  7. Embryonic development is a complex phenomenon that integrates genetic regulation and biomechanical cellular behaviors. However, the relative influence of these factors on spatiotemporal morphogen distributions is not well understood. Bone Morphogenetic Proteins (BMPs) are the primary morphogens guiding the dorsal-ventral (DV) patterning of the early zebrafish embryo, and BMP signaling is regulated by a network of extracellular and intracellular factors that impact the range and signaling of BMP ligands. Recent advances in understanding the mechanism of pattern formation support a source-sink mechanism, however, it is not clear how the source-sink mechanism shapes the morphogen patterns in three-dimensional (3D) space, nor how sensitive the pattern is to biophysical rates and boundary conditions along both the anteroposterior (AP) and DV axes of the embryo, nor how the patterns are controlled over time. Throughout blastulation and gastrulation, major cell movement, known as epiboly, happens along with the BMP-mediated DV patterning. The layer of epithelial cells begins to thin as they spread toward the vegetal pole of the embryo until it has completely engulfed the yolk cell. This dynamic domain may influence the distributions of BMP network members through advection. We developed a Finite Element Model (FEM) that incorporates all stages of zebrafish embryonic development data and solves the advection-diffusion-reaction Partial Differential Equations (PDE) in a growing domain. We use the model to investigate mechanisms in underlying BMP-driven DV patterning during epiboly. Solving the PDE is computationally expensive for parameter exploration. To overcome this obstacle, we developed a Neural Network (NN) metamodel of the 3D embryo that is accurate and fast and provided a nonlinear map between high-dimensional input and output that replaces the direct numerical simulation of the PDEs. From the modeling and acceleration by the NN metamodels, we identified the impact of advection on patterning and the influence of the dynamic expression level of regulators on the BMP signaling network. 
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