This paper considers a novel application of deep AUC maximization (DAM) for multi-instance learning (MIL), in which a single class label is assigned to a bag of instances (e.g., multiple 2D slices of a CT scan for a patient). We address a neglected yet non-negligible computational challenge of MIL in the context of DAM, i.e., bag size is too large to be loaded into {GPU} memory for backpropagation, which is required by the standard pooling methods of MIL. To tackle this challenge, we propose variance-reduced stochastic pooling methods in the spirit of stochastic optimization by formulating the loss function over the pooled prediction as a multi-level compositional function. By synthesizing techniques from stochastic compositional optimization and non-convex min-max optimization, we propose a unified and provable muli-instance DAM (MIDAM) algorithm with stochastic smoothed-max pooling or stochastic attention-based pooling, which only samples a few instances for each bag to compute a stochastic gradient estimator and to update the model parameter. We establish a similar convergence rate of the proposed MIDAM algorithm as the state-of-the-art DAM algorithms. Our extensive experiments on conventional MIL datasets and medical datasets demonstrate the superiority of our MIDAM algorithm.

We offer a study that connects robust discriminative classifiers trained with adversarial training (AT) with generative modeling in the form of Energy-based Models (EBM). We do so by decomposing the loss of a discriminative classifier and showing that the discriminative model is also aware of the input data density. Though a common assumption is that adversarial points leave the manifold of the input data, our study finds out that, surprisingly, untargeted adversarial points in the input space are very likely under the generative model hidden inside the discriminative classifier -- have low energy in the EBM. We present two evidence: untargeted attacks are even more likely than the natural data and their likelihood increases as the attack strength increases. This allows us to easily detect them and craft a novel attack called High-Energy PGD that fools the classifier yet has energy similar to the data set. The code is available at github.com/senad96/Robust-Generative

Despite Federated Learning (FL)'s trend for learning machine learning models in a distributed manner, it is susceptible to performance drops when training on heterogeneous data. In addition, FL inevitability faces the challenges of synchronization, efficiency, and privacy. Recently, dataset distillation has been explored in order to improve the efficiency and scalability of FL by creating a smaller, synthetic dataset that retains the performance of a model trained on the local private datasets. We discover that using distilled local datasets can amplify the heterogeneity issue in FL. To address this, we propose a new method, called Federated Virtual Learning on Heterogeneous Data with Local-Global Distillation (FedLGD), which trains FL using a smaller synthetic dataset (referred as virtual data) created through a combination of local and global dataset distillation. Specifically, to handle synchronization and class imbalance, we propose iterative distribution matching to allow clients to have the same amount of balanced local virtual data; to harmonize the domain shifts, we use federated gradient matching to distill global virtual data that are shared with clients without hindering data privacy to rectify heterogeneous local training via enforcing local-global feature similarity. We experiment on both benchmark and real-world datasets that contain heterogeneous data from different sources, and further scale up to an FL scenario that contains large number of clients with heterogeneous and class imbalance data. Our method outperforms state-of-the-art heterogeneous FL algorithms under various settings with a very limited amount of distilled virtual data.

To mitigate the bias exhibited by machine learning models, fairness criteria can be integrated into the training process to ensure fair treatment across all demographics, but it often comes at the expense of model performance. Understanding such tradeoffs, therefore, underlies the design of fair algorithms. To this end, this paper provides a complete characterization of the inherent tradeoff of demographic parity on classification problems, under the most general multi-group, multi-class, and noisy setting. Specifically, we show that the minimum error rate achievable by randomized and attribute-aware fair classifiers is given by the optimal value of a Wasserstein-barycenter problem. On the practical side, our findings lead to a simple post-processing algorithm that derives fair classifiers from score functions, which yields the optimal fair classifier when the score is Bayes optimal. We provide suboptimality analysis and sample complexity for our algorithm, and demonstrate its effectiveness on benchmark datasets.

Objective: To pre-train fair and unbiased patient representations from Electronic Health Records (EHRs) using a novel weighted loss function that reduces bias and improves fairness in deep representation learning models. Methods: We defined a new loss function, called weighted loss function, in the deep representation learning model to balance the importance of different groups of patients and features. We applied the proposed model, called Fair Patient Model (FPM), to a sample of 34,739 patients from the MIMIC-III dataset and learned patient representations for four clinical outcome prediction tasks. Results: FPM outperformed the baseline models in terms of three fairness metrics: demographic parity, equality of opportunity difference, and equalized odds ratio. FPM also achieved comparable predictive performance with the baselines, with an average accuracy of 0.7912. Feature analysis revealed that FPM captured more information from clinical features than the baselines. Conclusion: FPM is a novel method to pre-train fair and unbiased patient representations from EHR data using a weighted loss function. The learned representations can be used for various downstream tasks in healthcare and can be extended to other domains where bias and fairness are important.

Over the past decade, machine learning has revolutionized computers' ability to analyze text through flexible computational models. Due to their structural similarity to written language, transformer-based architectures have also shown promise as tools to make sense of a range of multi-variate sequences from protein-structures, music, electronic health records to weather-forecasts. We can also represent human lives in a way that shares this structural similarity to language. From one perspective, lives are simply sequences of events: People are born, visit the pediatrician, start school, move to a new location, get married, and so on. Here, we exploit this similarity to adapt innovations from natural language processing to examine the evolution and predictability of human lives based on detailed event sequences. We do this by drawing on arguably the most comprehensive registry data in existence, available for an entire nation of more than six million individuals across decades. Our data include information about life-events related to health, education, occupation, income, address, and working hours, recorded with day-to-day resolution. We create embeddings of life-events in a single vector space showing that this embedding space is robust and highly structured. Our models allow us to predict diverse outcomes ranging from early mortality to personality nuances, outperforming state-of-the-art models by a wide margin. Using methods for interpreting deep learning models, we probe the algorithm to understand the factors that enable our predictions. Our framework allows researchers to identify new potential mechanisms that impact life outcomes and associated possibilities for personalized interventions.

As a main field of artificial intelligence, natural language processing (NLP) has achieved remarkable success via deep neural networks. Plenty of NLP tasks have been addressed in a unified manner, with various tasks being associated with each other through sharing the same paradigm. However, neural networks are black boxes and rely on probability computation. Making mistakes is inevitable. Therefore, estimating the reliability and trustworthiness (in other words, uncertainty) of neural networks becomes a key research direction, which plays a crucial role in reducing models' risks and making better decisions. Therefore, in this survey, we provide a comprehensive review of uncertainty-relevant works in the NLP field. Considering the data and paradigms characteristics, we first categorize the sources of uncertainty in natural language into three types, including input, system, and output. Then, we systemically review uncertainty quantification approaches and the main applications. Finally, we discuss the challenges of uncertainty estimation in NLP and discuss potential future directions, taking into account recent trends in the field. Though there have been a few surveys about uncertainty estimation, our work is the first to review uncertainty from the NLP perspective.

Entity standardization maps noisy mentions from free-form text to standard entities in a knowledge base. The unique challenge of this task relative to other entity-related tasks is the lack of surrounding context and numerous variations in the surface form of the mentions, especially when it comes to generalization across domains where labeled data is scarce. Previous research mostly focuses on developing models either heavily relying on context, or dedicated solely to a specific domain. In contrast, we propose CoSiNES, a generic and adaptable framework with Contrastive Siamese Network for Entity Standardization that effectively adapts a pretrained language model to capture the syntax and semantics of the entities in a new domain. We construct a new dataset in the technology domain, which contains 640 technical stack entities and 6,412 mentions collected from industrial content management systems. We demonstrate that CoSiNES yields higher accuracy and faster runtime than baselines derived from leading methods in this domain. CoSiNES also achieves competitive performance in four standard datasets from the chemistry, medicine, and biomedical domains, demonstrating its cross-domain applicability.

GBM (Glioblastoma multiforme) is the most aggressive type of brain tumor in adults that has a short survival rate even after aggressive treatment with surgery and radiation therapy. The changes on magnetic resonance imaging (MRI) for patients with GBM after radiotherapy are indicative of either radiation-induced necrosis (RN) or recurrent brain tumor (rBT). Screening for rBT and RN at an early stage is crucial for facilitating faster treatment and better outcomes for the patients. Differentiating rBT from RN is challenging as both may present with similar radiological and clinical characteristics on MRI. Moreover, learning-based rBT versus RN classification using MRI may suffer from class imbalance due to lack of patient data. While synthetic data generation using generative models has shown promise to address class imbalance, the underlying data representation may be different in synthetic or augmented data. This study proposes computational modeling with statistically rigorous repeated random sub-sampling to balance the subset sample size for rBT and RN classification. The proposed pipeline includes multiresolution radiomic feature (MRF) extraction followed by feature selection with statistical significance testing (p<0.05). The five-fold cross validation results show the proposed model with MRF features classifies rBT from RN with an area under the curve (AUC) of 0.8920+-.055. Moreover, considering the dependence between survival time and censor time (where patients are not followed up until death), we demonstrate the feasibility of using MRF radiomic features as a non-invasive biomarker to identify patients who are at higher risk of recurrence or radiation necrosis. The cross-validated results show that the MRF model provides the best overall performance with an AUC of 0.770+-.032.

Behavioural experiments often happen in specialised arenas, but this may confound the analysis. To address this issue, we provide tools to study mice in the homecage environment, equipping biologists with the possibility to capture the temporal aspect of the individual's behaviour and model the interaction and interdependence between cage-mates with minimal human intervention. We develop the Activity Labelling Module (ALM) to automatically classify mouse behaviour from video, and a novel Group Behaviour Model (GBM) for summarising their joint behaviour across cages, using a permutation matrix to match the mouse identities in each cage to the model. We also release two datasets, ABODe for training behaviour classifiers and IMADGE for modelling behaviour.