While the general machine learning (ML) community has benefited from public datasets, tasks, and models, the progress of ML in healthcare has been hampered by a lack of such shared assets. The success of foundation models creates new challenges for healthcare ML by requiring access to shared pretrained models to validate performance benefits. We help address these challenges through three contributions. First, we publish a new dataset, EHRSHOT, containing de-identified structured data from the electronic health records (EHRs) of 6,712 patients from Stanford Medicine. Unlike MIMIC-III/IV and other popular EHR datasets, EHRSHOT is longitudinal and not restricted to ICU/ED patients. Second, we publish the weights of a 141M parameter clinical foundation model pretrained on the structured EHR data of 2.57M patients. We are one of the first to fully release such a model for coded EHR data; in contrast, most prior models released for clinical data (e.g. GatorTron, ClinicalBERT) only work with unstructured text and cannot process the rich, structured data within an EHR. We provide an end-to-end pipeline for the community to validate and build upon its performance. Third, we define 15 few-shot clinical prediction tasks, enabling evaluation of foundation models on benefits such as sample efficiency and task adaption. The code to reproduce our results, as well as the model and dataset (via a research data use agreement), are available at our Github repo here: //github.com/som-shahlab/ehrshot-benchmark
Considerable research efforts have been devoted to ensuring that large language models (LLMs) align with human values and generate safe text. However, an excessive focus on sensitivity to certain topics can compromise the model's robustness in following instructions, thereby impacting its overall performance in completing tasks. Previous benchmarks for jailbreaking LLMs have primarily focused on evaluating the safety of the models without considering their robustness. In this paper, we propose a benchmark that assesses both the safety and robustness of LLMs, emphasizing the need for a balanced approach. To comprehensively study text safety and output robustness, we introduce a latent jailbreak prompt dataset, each involving malicious instruction embedding. Specifically, we instruct the model to complete a regular task, such as translation, with the text to be translated containing malicious instructions. To further analyze safety and robustness, we design a hierarchical annotation framework. We present a systematic analysis of the safety and robustness of LLMs regarding the position of explicit normal instructions, word replacements (verbs in explicit normal instructions, target groups in malicious instructions, cue words for explicit normal instructions), and instruction replacements (different explicit normal instructions). Our results demonstrate that current LLMs not only prioritize certain instruction verbs but also exhibit varying jailbreak rates for different instruction verbs in explicit normal instructions. Code and data are available at //github.com/qiuhuachuan/latent-jailbreak.
Activation functions are the linchpins of deep learning, profoundly influencing both the representational capacity and training dynamics of neural networks. They shape not only the nature of representations but also optimize convergence rates and enhance generalization potential. Appreciating this critical role, we present the Linear Oscillation (LoC) activation function, defined as $f(x) = x \times \sin(\alpha x + \beta)$. Distinct from conventional activation functions which primarily introduce non-linearity, LoC seamlessly blends linear trajectories with oscillatory deviations. The nomenclature ``Linear Oscillation'' is a nod to its unique attribute of infusing linear activations with harmonious oscillations, capturing the essence of the 'Importance of Confusion'. This concept of ``controlled confusion'' within network activations is posited to foster more robust learning, particularly in contexts that necessitate discerning subtle patterns. Our empirical studies reveal that, when integrated into diverse neural architectures, the LoC activation function consistently outperforms established counterparts like ReLU and Sigmoid. The stellar performance exhibited by the avant-garde Vision Transformer model using LoC further validates its efficacy. This study illuminates the remarkable benefits of the LoC over other prominent activation functions. It champions the notion that intermittently introducing deliberate complexity or ``confusion'' during training can spur more profound and nuanced learning. This accentuates the pivotal role of judiciously selected activation functions in shaping the future of neural network training.
Many engineering organizations are reimplementing and extending deep neural networks from the research community. We describe this process as deep learning model reengineering. Deep learning model reengineering - reusing, reproducing, adapting, and enhancing state-of-the-art deep learning approaches - is challenging for reasons including under-documented reference models, changing requirements, and the cost of implementation and testing. In addition, individual engineers may lack expertise in software engineering, yet teams must apply knowledge of software engineering and deep learning to succeed. Prior work has examined on DL systems from a "product" view, examining defects from projects regardless of the engineers' purpose. Our study is focused on reengineering activities from a "process" view, and focuses on engineers specifically engaged in the reengineering process. Our goal is to understand the characteristics and challenges of deep learning model reengineering. We conducted a case study of this phenomenon, focusing on the context of computer vision. Our results draw from two data sources: defects reported in open-source reeengineering projects, and interviews conducted with open-source project contributors and the leaders of a reengineering team. Our results describe how deep learning-based computer vision techniques are reengineered, analyze the distribution of defects in this process, and discuss challenges and practices. Integrating our quantitative and qualitative data, we proposed a novel reengineering workflow. Our findings inform several future directions, including: measuring additional unknown aspects of model reengineering; standardizing engineering practices to facilitate reengineering; and developing tools to support model reengineering and model reuse.
Computing the Jacobian of the solution of an optimization problem is a central problem in machine learning, with applications in hyperparameter optimization, meta-learning, optimization as a layer, and dataset distillation, to name a few. Unrolled differentiation is a popular heuristic that approximates the solution using an iterative solver and differentiates it through the computational path. This work provides a non-asymptotic convergence-rate analysis of this approach on quadratic objectives for gradient descent and the Chebyshev method. We show that to ensure convergence of the Jacobian, we can either 1) choose a large learning rate leading to a fast asymptotic convergence but accept that the algorithm may have an arbitrarily long burn-in phase or 2) choose a smaller learning rate leading to an immediate but slower convergence. We refer to this phenomenon as the curse of unrolling. Finally, we discuss open problems relative to this approach, such as deriving a practical update rule for the optimal unrolling strategy and making novel connections with the field of Sobolev orthogonal polynomials.
In the field of phase change phenomena, the lack of accessible and diverse datasets suitable for machine learning (ML) training poses a significant challenge. Existing experimental datasets are often restricted, with limited availability and sparse ground truth data, impeding our understanding of this complex multiphysics phenomena. To bridge this gap, we present the BubbleML Dataset \footnote{\label{git_dataset}\url{//github.com/HPCForge/BubbleML}} which leverages physics-driven simulations to provide accurate ground truth information for various boiling scenarios, encompassing nucleate pool boiling, flow boiling, and sub-cooled boiling. This extensive dataset covers a wide range of parameters, including varying gravity conditions, flow rates, sub-cooling levels, and wall superheat, comprising 79 simulations. BubbleML is validated against experimental observations and trends, establishing it as an invaluable resource for ML research. Furthermore, we showcase its potential to facilitate exploration of diverse downstream tasks by introducing two benchmarks: (a) optical flow analysis to capture bubble dynamics, and (b) operator networks for learning temperature dynamics. The BubbleML dataset and its benchmarks serve as a catalyst for advancements in ML-driven research on multiphysics phase change phenomena, enabling the development and comparison of state-of-the-art techniques and models.
Deep reinforcement learning (DRL), leveraging Deep Learning (DL) in reinforcement learning, has shown significant potential in achieving human-level autonomy in a wide range of domains, including robotics, computer vision, and computer games. This potential justifies the enthusiasm and growing interest in DRL in both academia and industry. However, the community currently focuses mostly on the development phase of DRL systems, with little attention devoted to DRL deployment. In this paper, we propose an empirical study on Stack Overflow (SO), the most popular Q&A forum for developers, to uncover and understand the challenges practitioners faced when deploying DRL systems. Specifically, we categorized relevant SO posts by deployment platforms: server/cloud, mobile/embedded system, browser, and game engine. After filtering and manual analysis, we examined 357 SO posts about DRL deployment, investigated the current state, and identified the challenges related to deploying DRL systems. Then, we investigate the prevalence and difficulty of these challenges. Results show that the general interest in DRL deployment is growing, confirming the study's relevance and importance. Results also show that DRL deployment is more difficult than other DRL issues. Additionally, we built a taxonomy of 31 unique challenges in deploying DRL to different platforms. On all platforms, RL environment-related challenges are the most popular, and communication-related challenges are the most difficult among practitioners. We hope our study inspires future research and helps the community overcome the most common and difficult challenges practitioners face when deploying DRL systems.
With the growing use of machine learning (ML) models in critical domains such as finance and healthcare, the need to offer recourse for those adversely affected by the decisions of ML models has become more important; individuals ought to be provided with recommendations on actions to take for improving their situation and thus receive a favorable decision. Prior work on sequential algorithmic recourse -- which recommends a series of changes -- focuses on action feasibility and uses the proximity of feature changes to determine action costs. However, the uncertainties of feature changes and the risk of higher than average costs in recourse have not been considered. It is undesirable if a recourse could (with some probability) result in a worse situation from which recovery requires an extremely high cost. It is essential to incorporate risks when computing and evaluating recourse. We call the recourse computed with such risk considerations as Safer Algorithmic Recourse (SafeAR). The objective is to empower people to choose a recourse based on their risk tolerance. In this work, we discuss and show how existing recourse desiderata can fail to capture the risk of higher costs. We present a method to compute recourse policies that consider variability in cost and connect algorithmic recourse literature with risk-sensitive reinforcement learning. We also adopt measures ``Value at Risk'' and ``Conditional Value at Risk'' from the financial literature to summarize risk concisely. We apply our method to two real-world datasets and compare policies with different levels of risk-aversion using risk measures and recourse desiderata (sparsity and proximity).
In pace with developments in the research field of artificial intelligence, knowledge graphs (KGs) have attracted a surge of interest from both academia and industry. As a representation of semantic relations between entities, KGs have proven to be particularly relevant for natural language processing (NLP), experiencing a rapid spread and wide adoption within recent years. Given the increasing amount of research work in this area, several KG-related approaches have been surveyed in the NLP research community. However, a comprehensive study that categorizes established topics and reviews the maturity of individual research streams remains absent to this day. Contributing to closing this gap, we systematically analyzed 507 papers from the literature on KGs in NLP. Our survey encompasses a multifaceted review of tasks, research types, and contributions. As a result, we present a structured overview of the research landscape, provide a taxonomy of tasks, summarize our findings, and highlight directions for future work.
The incredible development of federated learning (FL) has benefited various tasks in the domains of computer vision and natural language processing, and the existing frameworks such as TFF and FATE has made the deployment easy in real-world applications. However, federated graph learning (FGL), even though graph data are prevalent, has not been well supported due to its unique characteristics and requirements. The lack of FGL-related framework increases the efforts for accomplishing reproducible research and deploying in real-world applications. Motivated by such strong demand, in this paper, we first discuss the challenges in creating an easy-to-use FGL package and accordingly present our implemented package FederatedScope-GNN (FS-G), which provides (1) a unified view for modularizing and expressing FGL algorithms; (2) comprehensive DataZoo and ModelZoo for out-of-the-box FGL capability; (3) an efficient model auto-tuning component; and (4) off-the-shelf privacy attack and defense abilities. We validate the effectiveness of FS-G by conducting extensive experiments, which simultaneously gains many valuable insights about FGL for the community. Moreover, we employ FS-G to serve the FGL application in real-world E-commerce scenarios, where the attained improvements indicate great potential business benefits. We publicly release FS-G, as submodules of FederatedScope, at //github.com/alibaba/FederatedScope to promote FGL's research and enable broad applications that would otherwise be infeasible due to the lack of a dedicated package.
There recently has been a surge of interest in developing a new class of deep learning (DL) architectures that integrate an explicit time dimension as a fundamental building block of learning and representation mechanisms. In turn, many recent results show that topological descriptors of the observed data, encoding information on the shape of the dataset in a topological space at different scales, that is, persistent homology of the data, may contain important complementary information, improving both performance and robustness of DL. As convergence of these two emerging ideas, we propose to enhance DL architectures with the most salient time-conditioned topological information of the data and introduce the concept of zigzag persistence into time-aware graph convolutional networks (GCNs). Zigzag persistence provides a systematic and mathematically rigorous framework to track the most important topological features of the observed data that tend to manifest themselves over time. To integrate the extracted time-conditioned topological descriptors into DL, we develop a new topological summary, zigzag persistence image, and derive its theoretical stability guarantees. We validate the new GCNs with a time-aware zigzag topological layer (Z-GCNETs), in application to traffic forecasting and Ethereum blockchain price prediction. Our results indicate that Z-GCNET outperforms 13 state-of-the-art methods on 4 time series datasets.