AnalogVNN, a simulation framework built on PyTorch which can simulate the effects of optoelectronic noise, limited precision, and signal normalization present in photonic neural network accelerators. We use this framework to train and optimize linear and convolutional neural networks with up to 9 layers and ~1.7 million parameters, while gaining insights into how normalization, activation function, reduced precision, and noise influence accuracy in analog photonic neural networks. By following the same layer structure design present in PyTorch, the AnalogVNN framework allows users to convert most digital neural network models to their analog counterparts with just a few lines of code, taking full advantage of the open-source optimization, deep learning, and GPU acceleration libraries available through PyTorch. Code is available at https://analogvnn.github.io
Efficient quantum control is necessary for practical quantum computing implementations with current technologies. Conventional algorithms for determining optimal control parameters are computationally expensive, largely excluding them from use outside of the simulation. Existing hardware solutions structured as lookup tables are imprecise and costly. By designing a machine learning model to approximate the results of traditional tools, a more efficient method can be produced. Such a model can then be synthesized into a hardware accelerator for use in quantum systems. In this study, we demonstrate a machine learning algorithm for predicting optimal pulse parameters. This algorithm is lightweight enough to fit on a low-resource FPGA and perform inference with a latency of 175 ns and pipeline interval of 5 ns with $~>~$0.99 gate fidelity. In the long term, such an accelerator could be used near quantum computing hardware where traditional computers cannot operate, enabling quantum control at a reasonable cost at low latencies without incurring large data bandwidths outside of the cryogenic environment.
Ensemble learning has gained success in machine learning with major advantages over other learning methods. Bagging is a prominent ensemble learning method that creates subgroups of data, known as bags, that are trained by individual machine learning methods such as decision trees. Random forest is a prominent example of bagging with additional features in the learning process. Evolutionary algorithms have been prominent for optimisation problems and also been used for machine learning. Evolutionary algorithms are gradient-free methods that work with a population of candidate solutions that maintain diversity for creating new solutions. In conventional bagged ensemble learning, the bags are created once and the content, in terms of the training examples, are fixed over the learning process. In our paper, we propose evolutionary bagged ensemble learning, where we utilise evolutionary algorithms to evolve the content of the bags in order to iteratively enhance the ensemble by providing diversity in the bags. The results show that our evolutionary ensemble bagging method outperforms conventional ensemble methods (bagging and random forests) for several benchmark datasets under certain constraints. We find that evolutionary bagging can inherently sustain a diverse set of bags without reduction in performance accuracy.
The development of autonomous agents which can interact with other agents to accomplish a given task is a core area of research in artificial intelligence and machine learning. Towards this goal, the Autonomous Agents Research Group develops novel machine learning algorithms for autonomous systems control, with a specific focus on deep reinforcement learning and multi-agent reinforcement learning. Research problems include scalable learning of coordinated agent policies and inter-agent communication; reasoning about the behaviours, goals, and composition of other agents from limited observations; and sample-efficient learning based on intrinsic motivation, curriculum learning, causal inference, and representation learning. This article provides a broad overview of the ongoing research portfolio of the group and discusses open problems for future directions.
Due to the high mutation rate of the virus, the COVID-19 pandemic evolved rapidly. Certain variants of the virus, such as Delta and Omicron, emerged with altered viral properties leading to severe transmission and death rates. These variants burdened the medical systems worldwide with a major impact to travel, productivity, and the world economy. Unsupervised machine learning methods have the ability to compress, characterize, and visualize unlabelled data. This paper presents a framework that utilizes unsupervised machine learning methods to discriminate and visualize the associations between major COVID-19 variants based on their genome sequences. These methods comprise a combination of selected dimensionality reduction and clustering techniques. The framework processes the RNA sequences by performing a k-mer analysis on the data and further visualises and compares the results using selected dimensionality reduction methods that include principal component analysis (PCA), t-distributed stochastic neighbour embedding (t-SNE), and uniform manifold approximation projection (UMAP). Our framework also employs agglomerative hierarchical clustering to visualize the mutational differences among major variants of concern and country-wise mutational differences for selected variants (Delta and Omicron) using dendrograms. We also provide country-wise mutational differences for selected variants via dendrograms. We find that the proposed framework can effectively distinguish between the major variants and has the potential to identify emerging variants in the future.
As machine learning (ML) models gain traction in clinical applications, understanding the impact of clinician and societal biases on ML models is increasingly important. While biases can arise in the labels used for model training, the many sources from which these biases arise are not yet well-studied. In this paper, we highlight disparate censorship (i.e., differences in testing rates across patient groups) as a source of label bias that clinical ML models may amplify, potentially causing harm. Many patient risk-stratification models are trained using the results of clinician-ordered diagnostic and laboratory tests of labels. Patients without test results are often assigned a negative label, which assumes that untested patients do not experience the outcome. Since orders are affected by clinical and resource considerations, testing may not be uniform in patient populations, giving rise to disparate censorship. Disparate censorship in patients of equivalent risk leads to undertesting in certain groups, and in turn, more biased labels for such groups. Using such biased labels in standard ML pipelines could contribute to gaps in model performance across patient groups. Here, we theoretically and empirically characterize conditions in which disparate censorship or undertesting affect model performance across subgroups. Our findings call attention to disparate censorship as a source of label bias in clinical ML models.
The in situ synchrotron high-energy X-ray powder diffraction (XRD) technique is highly utilized by researchers to analyze the crystallographic structures of materials in functional devices (e.g., battery materials) or in complex sample environments (e.g., diamond anvil cells or syntheses reactors). An atomic structure of a material can be identified by its diffraction pattern, along with detailed analysis such as Rietveld refinement which indicates how the measured structure deviates from the ideal structure (e.g., internal stresses or defects). For in situ experiments, a series of XRD images is usually collected on the same sample at different conditions (e.g., adiabatic conditions), yielding different states of matter, or simply collected continuously as a function of time to track the change of a sample over a chemical or physical process. In situ experiments are usually performed with area detectors, collecting 2D images composed of diffraction rings for ideal powders. Depending on the material's form, one may observe different characteristics other than the typical Debye Scherrer rings for a realistic sample and its environments, such as textures or preferred orientations and single crystal diffraction spots in the 2D XRD image. In this work, we present an investigation of machine learning methods for fast and reliable identification and separation of the single crystal diffraction spots in XRD images. The exclusion of artifacts during an XRD image integration process allows a precise analysis of the powder diffraction rings of interest. We observe that the gradient boosting method can consistently produce high accuracy results when it is trained with small subsets of highly diverse datasets. The method dramatically decreases the amount of time spent on identifying and separating single crystal spots in comparison to the conventional method.
Data-driven machine learning methods have the potential to dramatically accelerate the rate of materials design over conventional human-guided approaches. These methods would help identify or, in the case of generative models, even create novel crystal structures of materials with a set of specified functional properties to then be synthesized or isolated in the laboratory. For crystal structure generation, a key bottleneck lies in developing suitable atomic structure fingerprints or representations for the machine learning model, analogous to the graph-based or SMILES representations used in molecular generation. However, finding data-efficient representations that are invariant to translations, rotations, and permutations, while remaining invertible to the Cartesian atomic coordinates remains an ongoing challenge. Here, we propose an alternative approach to this problem by taking existing non-invertible representations with the desired invariances and developing an algorithm to reconstruct the atomic coordinates through gradient-based optimization using automatic differentiation. This can then be coupled to a generative machine learning model which generates new materials within the representation space, rather than in the data-inefficient Cartesian space. In this work, we implement this end-to-end structure generation approach using atom-centered symmetry functions as the representation and conditional variational autoencoders as the generative model. We are able to successfully generate novel and valid atomic structures of sub-nanometer Pt nanoparticles as a proof of concept. Furthermore, this method can be readily extended to any suitable structural representation, thereby providing a powerful, generalizable framework towards structure-based generation.
Using Machine Learning and Deep Learning to predict cognitive tasks from electroencephalography (EEG) signals is a rapidly advancing field in Brain-Computer Interfaces (BCI). In contrast to the fields of computer vision and natural language processing, the data amount of these trials is still rather tiny. Developing a PC-based machine learning technique to increase the participation of non-expert end-users could help solve this data collection issue. We created a novel algorithm for machine learning called Time Majority Voting (TMV). In our experiment, TMV performed better than cutting-edge algorithms. It can operate efficiently on personal computers for classification tasks involving the BCI. These interpretable data also assisted end-users and researchers in comprehending EEG tests better.
In this paper, we show that the process of continually learning new tasks and memorizing previous tasks introduces unknown privacy risks and challenges to bound the privacy loss. Based upon this, we introduce a formal definition of Lifelong DP, in which the participation of any data tuples in the training set of any tasks is protected, under a consistently bounded DP protection, given a growing stream of tasks. A consistently bounded DP means having only one fixed value of the DP privacy budget, regardless of the number of tasks. To preserve Lifelong DP, we propose a scalable and heterogeneous algorithm, called L2DP-ML with a streaming batch training, to efficiently train and continue releasing new versions of an L2M model, given the heterogeneity in terms of data sizes and the training order of tasks, without affecting DP protection of the private training set. An end-to-end theoretical analysis and thorough evaluations show that our mechanism is significantly better than baseline approaches in preserving Lifelong DP. The implementation of L2DP-ML is available at: https://github.com/haiphanNJIT/PrivateDeepLearning.
The COVID-19 pandemic has caused devastating economic and social disruption, straining the resources of healthcare institutions worldwide. This has led to a nationwide call for models to predict hospitalization and severe illness in patients with COVID-19 to inform distribution of limited healthcare resources. We respond to one of these calls specific to the pediatric population. To address this challenge, we study two prediction tasks for the pediatric population using electronic health records: 1) predicting which children are more likely to be hospitalized, and 2) among hospitalized children, which individuals are more likely to develop severe symptoms. We respond to the national Pediatric COVID-19 data challenge with a novel machine learning model, MedML. MedML extracts the most predictive features based on medical knowledge and propensity scores from over 6 million medical concepts and incorporates the inter-feature relationships between heterogeneous medical features via graph neural networks (GNN). We evaluate MedML across 143,605 patients for the hospitalization prediction task and 11,465 patients for the severity prediction task using data from the National Cohort Collaborative (N3C) dataset. We also report detailed group-level and individual-level feature importance analyses to evaluate the model interpretability. MedML achieves up to a 7% higher AUROC score and up to a 14% higher AUPRC score compared to the best baseline machine learning models and performs well across all nine national geographic regions and over all three-month spans since the start of the pandemic. Our cross-disciplinary research team has developed a method of incorporating clinical domain knowledge as the framework for a new type of machine learning model that is more predictive and explainable than current state-of-the-art data-driven feature selection methods.
A hallmark of human intelligence is the ability to construct self-contained chunks of knowledge and reuse them in novel combinations for solving different problems. Learning such compositional structures has been a challenge for artificial systems, due to the underlying combinatorial search. To date, research into compositional learning has largely proceeded separately from work on lifelong or continual learning. This dissertation integrated these two lines of work to present a general-purpose framework for lifelong learning of functionally compositional structures. The framework separates the learning into two stages: learning how to combine existing components to assimilate a novel problem, and learning how to adapt the existing components to accommodate the new problem. This separation explicitly handles the trade-off between stability and flexibility. This dissertation instantiated the framework into various supervised and reinforcement learning (RL) algorithms. Supervised learning evaluations found that 1) compositional models improve lifelong learning of diverse tasks, 2) the multi-stage process permits lifelong learning of compositional knowledge, and 3) the components learned by the framework represent self-contained and reusable functions. Similar RL evaluations demonstrated that 1) algorithms under the framework accelerate the discovery of high-performing policies, and 2) these algorithms retain or improve performance on previously learned tasks. The dissertation extended one lifelong compositional RL algorithm to the nonstationary setting, where the task distribution varies over time, and found that modularity permits individually tracking changes to different elements in the environment. The final contribution of this dissertation was a new benchmark for compositional RL, which exposed that existing methods struggle to discover the compositional properties of the environment.
Due to the beyond-classical capability of quantum computing, quantum machine learning is applied independently or embedded in classical models for decision making, especially in the field of finance. Fairness and other ethical issues are often one of the main concerns in decision making. In this work, we define a formal framework for the fairness verification and analysis of quantum machine learning decision models, where we adopt one of the most popular notions of fairness in the literature based on the intuition -- any two similar individuals must be treated similarly and are thus unbiased. We show that quantum noise can improve fairness and develop an algorithm to check whether a (noisy) quantum machine learning model is fair. In particular, this algorithm can find bias kernels of quantum data (encoding individuals) during checking. These bias kernels generate infinitely many bias pairs for investigating the unfairness of the model. Our algorithm is designed based on a highly efficient data structure -- Tensor Networks -- and implemented on Google's TensorFlow Quantum. The utility and effectiveness of our algorithm are confirmed by the experimental results, including income prediction and credit scoring on real-world data, for a class of random (noisy) quantum decision models with 27 qubits ($2^{27}$-dimensional state space) tripling ($2^{18}$ times more than) that of the state-of-the-art algorithms for verifying quantum machine learning models.
Existing adversarial example research focuses on digitally inserted perturbations on top of existing natural image datasets. This construction of adversarial examples is not realistic because it may be difficult, or even impossible, for an attacker to deploy such an attack in the real-world due to sensing and environmental effects. To better understand adversarial examples against cyber-physical systems, we propose approximating the real-world through simulation. In this paper we describe our synthetic dataset generation tool that enables scalable collection of such a synthetic dataset with realistic adversarial examples. We use the CARLA simulator to collect such a dataset and demonstrate simulated attacks that undergo the same environmental transforms and processing as real-world images. Our tools have been used to collect datasets to help evaluate the efficacy of adversarial examples, and can be found at https://github.com/carla-simulator/carla/pull/4992.
EC-KitY is a comprehensive Python library for doing evolutionary computation (EC), licensed under the BSD 3-Clause License, and compatible with scikit-learn. Designed with modern software engineering and machine learning integration in mind, EC-KitY can support all popular EC paradigms, including genetic algorithms, genetic programming, coevolution, evolutionary multi-objective optimization, and more. This paper provides an overview of the package, including the ease of setting up an EC experiment, the architecture, the main features, and a comparison with other libraries.
We demonstrate two sampling procedures assisted by machine learning models via regression and classification. The main objective is the use of a neural network to suggest points likely inside regions of interest, reducing the number of evaluations of time consuming calculations. We compare results from this approach with results from other sampling methods, namely Markov chain Monte Carlo and MultiNest, obtaining results that range from comparably similar to arguably better. In particular, we augment our classifier method with a boosting technique that rapidly increases the efficiency within a few iterations. We show results from our methods applied to a toy model and the type II 2HDM, using 3 and 7 free parameters, respectively. The code used for this paper and instructions are publicly available on the web.
The rapid spread of the COVID-19 pandemic has resulted in an unprecedented amount of sequence data of the SARS-CoV-2 genome -- millions of sequences and counting. This amount of data, while being orders of magnitude beyond the capacity of traditional approaches to understanding the diversity, dynamics, and evolution of viruses is nonetheless a rich resource for machine learning (ML) approaches as alternatives for extracting such important information from these data. It is of hence utmost importance to design a framework for testing and benchmarking the robustness of these ML models. This paper makes the first effort (to our knowledge) to benchmark the robustness of ML models by simulating biological sequences with errors. In this paper, we introduce several ways to perturb SARS-CoV-2 genome sequences to mimic the error profiles of common sequencing platforms such as Illumina and PacBio. We show from experiments on a wide array of ML models that some simulation-based approaches are more robust (and accurate) than others for specific embedding methods to certain adversarial attacks to the input sequences. Our benchmarking framework may assist researchers in properly assessing different ML models and help them understand the behavior of the SARS-CoV-2 virus or avoid possible future pandemics.
Internet of Things (IoT) is transforming the industry by bridging the gap between Information Technology (IT) and Operational Technology (OT). Machines are being integrated with connected sensors and managed by intelligent analytics applications, accelerating digital transformation and business operations. Bringing Machine Learning (ML) to industrial devices is an advancement aiming to promote the convergence of IT and OT. However, developing an ML application in industrial IoT (IIoT) presents various challenges, including hardware heterogeneity, non-standardized representations of ML models, device and ML model compatibility issues, and slow application development. Successful deployment in this area requires a deep understanding of hardware, algorithms, software tools, and applications. Therefore, this paper presents a framework called Semantic Low-Code Engineering for ML Applications (SeLoC-ML), built on a low-code platform to support the rapid development of ML applications in IIoT by leveraging Semantic Web technologies. SeLoC-ML enables non-experts to easily model, discover, reuse, and matchmake ML models and devices at scale. The project code can be automatically generated for deployment on hardware based on the matching results. Developers can benefit from semantic application templates, called recipes, to fast prototype end-user applications. The evaluations confirm an engineering effort reduction by a factor of at least three compared to traditional approaches on an industrial ML classification case study, showing the efficiency and usefulness of SeLoC-ML. We share the code and welcome any contributions.
We introduce the initial release of our software Robustar, which aims to improve the robustness of vision classification machine learning models through a data-driven perspective. Building upon the recent understanding that the lack of machine learning model's robustness is the tendency of the model's learning of spurious features, we aim to solve this problem from its root at the data perspective by removing the spurious features from the data before training. In particular, we introduce a software that helps the users to better prepare the data for training image classification models by allowing the users to annotate the spurious features at the pixel level of images. To facilitate this process, our software also leverages recent advances to help identify potential images and pixels worthy of attention and to continue the training with newly annotated data. Our software is hosted at the GitHub Repository https://github.com/HaohanWang/Robustar.
We introduce a novel machine learning strategy, kernel addition Gaussian process regression (KA-GPR), in molecular-orbital-based machine learning (MOB-ML) to learn the total correlation energies of general electronic structure theories for closed- and open-shell systems by introducing a machine learning strategy. The learning efficiency of MOB-ML (KA-GPR) is the same as the original MOB-ML method for the smallest criegee molecule, which is a closed-shell molecule with multi-reference characters. In addition, the prediction accuracies of different small free radicals could reach the chemical accuracy of 1 kcal/mol by training on one example structure. Accurate potential energy surfaces for the H10 chain (closed-shell) and water OH bond dissociation (open-shell) could also be generated by MOB-ML (KA-GPR). To explore the breadth of chemical systems that KA-GPR can describe, we further apply MOB-ML to accurately predict the large benchmark datasets for closed- (QM9, QM7b-T, GDB-13-T) and open-shell (QMSpin) molecules.