What is Wrong with End-to-End Learning for Phase Retrieval?

For nonlinear inverse problems that are prevalent in imaging science, symmetries in the forward model are common. When data-driven deep learning approaches are used to solve such problems, these intrinsic symmetries can cause substantial learning difficulties. In this paper, we explain how such difficulties arise and, more importantly, how to overcome them by preprocessing the training set before any learning, i.e., symmetry breaking. We take far-field phase retrieval (FFPR), which is central to many areas of scientific imaging, as an example and show that symmetric breaking can substantially improve data-driven learning. We also formulate the mathematical principle of symmetry breaking.

A proximal augmented Lagrangian based algorithm for federated learning with global and local convex conic constraints

This paper considers federated learning (FL) with constraints, where the central server and all local clients collectively minimize a sum of convex local objective functions subject to global and local convex conic constraints. To train the model without moving local data from clients to the central server, we propose an FL framework in which each local client performs multiple updates using the local objective and local constraint, while the central server handles the global constraint and performs aggregation based on the updated local models. In particular, we develop a proximal augmented Lagrangian (AL) based algorithm for FL with global and local convex conic constraints. The subproblems arising in this algorithm are solved by an inexact alternating direction method of multipliers (ADMM) in a federated fashion. Under a local Lipschitz condition and mild assumptions, we establish the worst-case complexity bounds of the proposed algorithm for finding an approximate KKT solution. To the best of our knowledge, this work proposes the first algorithm for FL with global and local constraints. Our numerical experiments demonstrate the practical advantages of our algorithm in performing Neyman-Pearson classification and enhancing model fairness in the context of FL.

A Systematic Evaluation of Federated Learning on Biomedical Natural Language Processing

Language models (LMs) like BERT and GPT have revolutionized natural language processing (NLP). However, privacy-sensitive domains, particularly the medical field, face challenges to train LMs due to limited data access and privacy constraints imposed by regulations like the Health Insurance Portability and Accountability Act (HIPPA) and the General Data Protection Regulation (GDPR). Federated learning (FL) offers a decentralized solution that enables collaborative learning while ensuring the preservation of data privacy. In this study, we systematically evaluate FL in medicine across $2$ biomedical NLP tasks using $6$ LMs encompassing $8$ corpora. Our results showed that: 1) FL models consistently outperform LMs trained on individual client's data and sometimes match the model trained with polled data; 2) With the fixed number of total data, LMs trained using FL with more clients exhibit inferior performance, but pre-trained transformer-based models exhibited greater resilience. 3) LMs trained using FL perform nearly on par with the model trained with pooled data when clients' data are IID distributed while exhibiting visible gaps with non-IID data. Our code is available at: https://github.com/PL97/FedNLP

Predicting the Future of the CMS Detector: Crystal Radiation Damage and Machine Learning at the LHC

The 75,848 lead tungstate crystals in CMS experiment at the CERN Large Hadron Collider are used to measure the energy of electrons and photons produced in the proton-proton collisions. The optical transparency of the crystals degrades slowly with radiation dose due to the beam-beam collisions. The transparency of each crystal is monitored with a laser monitoring system that tracks changes in the optical properties of the crystals due to radiation from the collision products. Predicting the optical transparency of the crystals, both in the short-term and in the long-term, is a critical task for the CMS experiment. We describe here the public data release, following FAIR principles, of the crystal monitoring data collected by the CMS Collaboration between 2016 and 2018. Besides describing the dataset and its access, the problems that can be addressed with it are described, as well as an example solution based on a Long Short-Term Memory neural network developed to predict future behavior of the crystals.

Optimization and Optimizers for Adversarial Robustness

Empirical robustness evaluation (RE) of deep learning models against adversarial perturbations entails solving nontrivial constrained optimization problems. Existing numerical algorithms that are commonly used to solve them in practice predominantly rely on projected gradient, and mostly handle perturbations modeled by the $\ell_1$, $\ell_2$ and $\ell_\infty$ distances. In this paper, we introduce a novel algorithmic framework that blends a general-purpose constrained-optimization solver PyGRANSO with Constraint Folding (PWCF), which can add more reliability and generality to the state-of-the-art RE packages, e.g., AutoAttack. Regarding reliability, PWCF provides solutions with stationarity measures and feasibility tests to assess the solution quality. For generality, PWCF can handle perturbation models that are typically inaccessible to the existing projected gradient methods; the main requirement is the distance metric to be almost everywhere differentiable. Taking advantage of PWCF and other existing numerical algorithms, we further explore the distinct patterns in the solutions found for solving these optimization problems using various combinations of losses, perturbation models, and optimization algorithms. We then discuss the implications of these patterns on the current robustness evaluation and adversarial training.

A Cross-institutional Evaluation on Breast Cancer Phenotyping NLP Algorithms on Electronic Health Records

Objective: The generalizability of clinical large language models is usually ignored during the model development process. This study evaluated the generalizability of BERT-based clinical NLP models across different clinical settings through a breast cancer phenotype extraction task. Materials and Methods: Two clinical corpora of breast cancer patients were collected from the electronic health records from the University of Minnesota and the Mayo Clinic, and annotated following the same guideline. We developed three types of NLP models (i.e., conditional random field, bi-directional long short-term memory and CancerBERT) to extract cancer phenotypes from clinical texts. The models were evaluated for their generalizability on different test sets with different learning strategies (model transfer vs. locally trained). The entity coverage score was assessed with their association with the model performances. Results: We manually annotated 200 and 161 clinical documents at UMN and MC, respectively. The corpora of the two institutes were found to have higher similarity between the target entities than the overall corpora. The CancerBERT models obtained the best performances among the independent test sets from two clinical institutes and the permutation test set. The CancerBERT model developed in one institute and further fine-tuned in another institute achieved reasonable performance compared to the model developed on local data (micro-F1: 0.925 vs 0.932). Conclusions: The results indicate the CancerBERT model has the best learning ability and generalizability among the three types of clinical NLP models. The generalizability of the models was found to be correlated with the similarity of the target entities between the corpora.

Robust Autoencoders for Collective Corruption Removal

Robust PCA is a standard tool for learning a linear subspace in the presence of sparse corruption or rare outliers. What about robustly learning manifolds that are more realistic models for natural data, such as images? There have been several recent attempts to generalize robust PCA to manifold settings. In this paper, we propose $\ell_1$- and scaling-invariant $\ell_1/\ell_2$-robust autoencoders based on a surprisingly compact formulation built on the intuition that deep autoencoders perform manifold learning. We demonstrate on several standard image datasets that the proposed formulation significantly outperforms all previous methods in collectively removing sparse corruption, without clean images for training. Moreover, we also show that the learned manifold structures can be generalized to unseen data samples effectively.

Welfare and Fairness Dynamics in Federated Learning: A Client Selection Perspective

Federated learning (FL) is a privacy-preserving learning technique that enables distributed computing devices to train shared learning models across data silos collaboratively. Existing FL works mostly focus on designing advanced FL algorithms to improve the model performance. However, the economic considerations of the clients, such as fairness and incentive, are yet to be fully explored. Without such considerations, self-motivated clients may lose interest and leave the federation. To address this problem, we designed a novel incentive mechanism that involves a client selection process to remove low-quality clients and a money transfer process to ensure a fair reward distribution. Our experimental results strongly demonstrate that the proposed incentive mechanism can effectively improve the duration and fairness of the federation.

Interpretable Deep Learning Methods for Multiview Learning

Technological advances have enabled the generation of unique and complementary types of data or views (e.g. genomics, proteomics, metabolomics) and opened up a new era in multiview learning research with the potential to lead to new biomedical discoveries. We propose iDeepViewLearn (Interpretable Deep Learning Method for Multiview Learning) for learning nonlinear relationships in data from multiple views while achieving feature selection. iDeepViewLearn combines deep learning flexibility with the statistical benefits of data and knowledge-driven feature selection, giving interpretable results. Deep neural networks are used to learn view-independent low-dimensional embedding through an optimization problem that minimizes the difference between observed and reconstructed data, while imposing a regularization penalty on the reconstructed data. The normalized Laplacian of a graph is used to model bilateral relationships between variables in each view, therefore, encouraging selection of related variables. iDeepViewLearn is tested on simulated and two real-world data, including breast cancer-related gene expression and methylation data. iDeepViewLearn had competitive classification results and identified genes and CpG sites that differentiated between individuals who died from breast cancer and those who did not. The results of our real data application and simulations with small to moderate sample sizes suggest that iDeepViewLearn may be a useful method for small-sample-size problems compared to other deep learning methods for multiview learning.

Practical Phase Retrieval Using Double Deep Image Priors

Phase retrieval (PR) concerns the recovery of complex phases from complex magnitudes. We identify the connection between the difficulty level and the number and variety of symmetries in PR problems. We focus on the most difficult far-field PR (FFPR), and propose a novel method using double deep image priors. In realistic evaluation, our method outperforms all competing methods by large margins. As a single-instance method, our method requires no training data and minimal hyperparameter tuning, and hence enjoys good practicality.