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We perform a comprehensive benchmarking of contrastive frameworks for learning multimodal representations in the medical domain. Through this study, we aim to answer the following research questions: (i) How transferable are general-domain representations to the medical domain? (ii) Is multimodal contrastive training sufficient, or does it benefit from unimodal training as well? (iii) What is the impact of feature granularity on the effectiveness of multimodal medical representation learning? To answer these questions, we investigate eight contrastive learning approaches under identical training setups, and train them on 2.8 million image-text pairs from four datasets, and evaluate them on 25 downstream tasks, including classification (zero-shot and linear probing), image-to-text and text-to-image retrieval, and visual question-answering. Our findings suggest a positive answer to the first question, a negative answer to the second question, and the benefit of learning fine-grained features. Finally, we make our code publicly available.

For the first time, we explore few-shot tuning of vision foundation models for class-incremental learning. Unlike existing few-shot class incremental learning (FSCIL) methods, which train an encoder on a base session to ensure forward compatibility for future continual learning, foundation models are generally trained on large unlabelled data without such considerations. This renders prior methods from traditional FSCIL incompatible for FSCIL with the foundation model. To this end, we propose Consistency-guided Asynchronous Contrastive Tuning (CoACT), a new approach to continually tune foundation models for new classes in few-shot settings. CoACT comprises three components: (i) asynchronous contrastive tuning, which learns new classes by including LoRA modules in the pre-trained encoder, while enforcing consistency between two asynchronous encoders; (ii) controlled fine-tuning, which facilitates effective tuning of a subset of the foundation model; and (iii) consistency-guided incremental tuning, which enforces additional regularization during later sessions to reduce forgetting of the learned classes. We perform an extensive study on 16 diverse datasets and demonstrate the effectiveness of CoACT, outperforming the best baseline method by 2.47% on average and with up to 12.52% on individual datasets. Additionally, CoACT shows reduced forgetting and robustness in low-shot experiments. As an added bonus, CoACT shows up to 13.5% improvement in standard FSCIL over the current SOTA on benchmark evaluations. We make our code publicly available at https://github.com/ShuvenduRoy/CoACT-FSCIL.

Transformers have significantly advanced the modeling of Electronic Health Records (EHR), yet their deployment in real-world healthcare is limited by several key challenges. Firstly, the quadratic computational cost and insufficient context length of these models pose significant obstacles for hospitals in processing the extensive medical histories typical in EHR data. Additionally, existing models employ separate finetuning for each clinical task, complicating maintenance in healthcare environments. Moreover, these models focus exclusively on either clinical prediction or EHR forecasting, lacking the flexibility to perform well across both. To overcome these limitations, we introduce EHRMamba, a robust foundation model built on the Mamba architecture. EHRMamba can process sequences up to four times longer than previous models due to its linear computational cost. We also introduce a novel approach to Multitask Prompted Finetuning (MTF) for EHR data, which enables EHRMamba to simultaneously learn multiple clinical tasks in a single finetuning phase, significantly enhancing deployment and cross-task generalization. Furthermore, our model leverages the HL7 FHIR data standard to simplify integration into existing hospital systems. Alongside EHRMamba, we open-source Odyssey, a toolkit designed to support the development and deployment of EHR foundation models, with an emphasis on data standardization and interpretability. Our evaluations on the MIMIC-IV dataset demonstrate that EHRMamba advances state-of-the-art performance across 6 major clinical tasks and excels in EHR forecasting, marking a significant leap forward in the field., Comment: 17 Pages, 4 Figures

The rapid advancement in self-supervised learning (SSL) has highlighted its potential to leverage unlabeled data for learning rich visual representations. However, the existing SSL techniques, particularly those employing different augmentations of the same image, often rely on a limited set of simple transformations that are not representative of real-world data variations. This constrains the diversity and quality of samples, which leads to sub-optimal representations. In this paper, we introduce a novel framework that enriches the SSL paradigm by utilizing generative models to produce semantically consistent image augmentations. By directly conditioning generative models on a source image representation, our method enables the generation of diverse augmentations while maintaining the semantics of the source image, thus offering a richer set of data for self-supervised learning. Our extensive experimental results on various SSL methods demonstrate that our framework significantly enhances the quality of learned visual representations by up to 10\% Top-1 accuracy in downstream tasks. This research demonstrates that incorporating generative models into the SSL workflow opens new avenues for exploring the potential of synthetic data. This development paves the way for more robust and versatile representation learning techniques.

Self-supervised representation learning is heavily dependent on data augmentations to specify the invariances encoded in representations. Previous work has shown that applying diverse data augmentations is crucial to downstream performance, but augmentation techniques remain under-explored. In this work, we propose a new family of local transformations based on Gaussian random fields to generate image augmentations for self-supervised representation learning. These transformations generalize the well-established affine and color transformations (translation, rotation, color jitter, etc.) and greatly increase the space of augmentations by allowing transformation parameter values to vary from pixel to pixel. The parameters are treated as continuous functions of spatial coordinates, and modeled as independent Gaussian random fields. Empirical results show the effectiveness of the new transformations for self-supervised representation learning. Specifically, we achieve a 1.7% top-1 accuracy improvement over baseline on ImageNet downstream classification, and a 3.6% improvement on out-of-distribution iNaturalist downstream classification. However, due to the flexibility of the new transformations, learned representations are sensitive to hyperparameters. While mild transformations improve representations, we observe that strong transformations can degrade the structure of an image, indicating that balancing the diversity and strength of augmentations is important for improving generalization of learned representations.

Conventional federated learning algorithms train a single global model by leveraging all participating clients' data. However, due to heterogeneity in client generative distributions and predictive models, these approaches may not appropriately approximate the predictive process, converge to an optimal state, or generalize to new clients. We study personalization and generalization in stateless cross-device federated learning setups assuming heterogeneity in client data distributions and predictive models. We first propose a hierarchical generative model and formalize it using Bayesian Inference. We then approximate this process using Variational Inference to train our model efficiently. We call this algorithm Federated Variational Inference (FedVI). We use PAC-Bayes analysis to provide generalization bounds for FedVI. We evaluate our model on FEMNIST and CIFAR-100 image classification and show that FedVI beats the state-of-the-art on both tasks., Comment: 16 pages, 6 figures

Transformer models have achieved great success across many NLP problems. However, previous studies in automated ICD coding concluded that these models fail to outperform some of the earlier solutions such as CNN-based models. In this paper we challenge this conclusion. We present a simple and scalable method to process long text with the existing transformer models such as BERT. We show that this method significantly improves the previous results reported for transformer models in ICD coding, and is able to outperform one of the prominent CNN-based methods.

Dual encoding models that encode a pair of inputs are widely used for representation learning. Many approaches train dual encoding models by maximizing agreement between pairs of encodings on centralized training data. However, in many scenarios, datasets are inherently decentralized across many clients (user devices or organizations) due to privacy concerns, motivating federated learning. In this work, we focus on federated training of dual encoding models on decentralized data composed of many small, non-IID (independent and identically distributed) client datasets. We show that existing approaches that work well in centralized settings perform poorly when naively adapted to this setting using federated averaging. We observe that, we can simulate large-batch loss computation on individual clients for loss functions that are based on encoding statistics. Based on this insight, we propose a novel federated training approach, Distributed Cross Correlation Optimization (DCCO), which trains dual encoding models using encoding statistics aggregated across clients, without sharing individual data samples. Our experimental results on two datasets demonstrate that the proposed DCCO approach outperforms federated variants of existing approaches by a large margin., Comment: ICLR 2023 Workshop on Pitfalls of Limited Data and Computation for Trustworthy ML

Neural bandits have been shown to provide an efficient solution to practical sequential decision tasks that have nonlinear reward functions. The main contributor to that success is approximate Bayesian inference, which enables neural network (NN) training with uncertainty estimates. However, Bayesian NNs often suffer from a prohibitive computational overhead or operate on a subset of parameters. Alternatively, certain classes of infinite neural networks were shown to directly correspond to Gaussian processes (GP) with neural kernels (NK). NK-GPs provide accurate uncertainty estimates and can be trained faster than most Bayesian NNs. We propose to guide common bandit policies with NK distributions and show that NK bandits achieve state-of-the-art performance on nonlinear structured data. Moreover, we propose a framework for measuring independently the ability of a bandit algorithm to learn representations and explore, and use it to analyze the impact of NK distributions w.r.t.~those two aspects. We consider policies based on a GP and a Student's t-process (TP). Furthermore, we study practical considerations, such as training frequency and model partitioning. We believe our work will help better understand the impact of utilizing NKs in applied settings., Comment: Extended version. Added a major experiment comparing NK distribution w.r.t. exploration and exploitation. Submitted to ICLR 2023

Neural combinatorial optimization (NCO) aims at designing problem-independent and efficient neural network-based strategies for solving combinatorial problems. The field recently experienced growth by successfully adapting architectures originally designed for machine translation. Even though the results are promising, a large gap still exists between NCO models and classic deterministic solvers, both in terms of accuracy and efficiency. One of the drawbacks of current approaches is the inefficiency of training on multiple problem sizes. Curriculum learning strategies have been shown helpful in increasing performance in the multi-task setting. In this work, we focus on designing a curriculum learning-based training procedure that can help existing architectures achieve competitive performance on a large range of problem sizes simultaneously. We provide a systematic investigation of several training procedures and use the insights gained to motivate application of a psychologically-inspired approach to improve upon the classic curriculum method., Comment: Presented at Workshop on Learning Meets Combinatorial Algorithms at NeurIPS 2020

We consider the problem of simultaneously learning to linearly combine a very large number of kernels and learn a good predictor based on the learnt kernel. When the number of kernels $d$ to be combined is very large, multiple kernel learning methods whose computational cost scales linearly in $d$ are intractable. We propose a randomized version of the mirror descent algorithm to overcome this issue, under the objective of minimizing the group $p$-norm penalized empirical risk. The key to achieve the required exponential speed-up is the computationally efficient construction of low-variance estimates of the gradient. We propose importance sampling based estimates, and find that the ideal distribution samples a coordinate with a probability proportional to the magnitude of the corresponding gradient. We show the surprising result that in the case of learning the coefficients of a polynomial kernel, the combinatorial structure of the base kernels to be combined allows the implementation of sampling from this distribution to run in $O(\log(d))$ time, making the total computational cost of the method to achieve an $\epsilon$-optimal solution to be $O(\log(d)/\epsilon^2)$, thereby allowing our method to operate for very large values of $d$. Experiments with simulated and real data confirm that the new algorithm is computationally more efficient than its state-of-the-art alternatives.

The success of kernel-based learning methods depend on the choice of kernel. Recently, kernel learning methods have been proposed that use data to select the most appropriate kernel, usually by combining a set of base kernels. We introduce a new algorithm for kernel learning that combines a {\em continuous set of base kernels}, without the common step of discretizing the space of base kernels. We demonstrate that our new method achieves state-of-the-art performance across a variety of real-world datasets. Furthermore, we explicitly demonstrate the importance of combining the right dictionary of kernels, which is problematic for methods based on a finite set of base kernels chosen a priori. Our method is not the first approach to work with continuously parameterized kernels. However, we show that our method requires substantially less computation than previous such approaches, and so is more amenable to multiple dimensional parameterizations of base kernels, which we demonstrate.