Ilya Safro

Dorit Ron, Ilya Safro, Achi Brandt

In this paper we generalize and improve the multiscale organization of graphs by introducing a new measure that quantifies the "closeness" between two nodes. The calculation of the measure is linear in the number of edges in the graph and involves just a small number of relaxation sweeps. A similar notion of distance is then calculated and used at each coarser level. We demonstrate the use of this measure in multiscale methods for several important combinatorial optimization problems and discuss the multiscale graph organization.

Bao Bach, Ilya Safro, Ed Younis

With the growth of quantum platforms for gate-based quantum computation, compilation holds a crucial role in deciding the success of the implementation. While there has been rich research in compilation techniques for the superconducting-qubit regime. The trapped-ion architectures, currently leading in robust quantum computations for their reliable operations, still lack competitive compilation strategies. This work introduces a unifying hardware abstraction, the ``position graph'', representing various hardware architectures. With this abstraction, we model trapped-ion Quantum Charge-Coupled Device (QCCD) architectures, enabling high-quality, scalable compilation methods. Specifically, we propose scheduling algorithms called SHuttling-Aware PERmutative (SHAPER) and SHuttling-AWare (SHAW) heuristic searches to tackle the complex constraints and dynamics of trapped-ion machines, with the cooperation of state-of-the-art permutation-aware mapping. These approaches generate executable circuits and native instructions that respect the physical constraints of shuttling-based architectures. We evaluate proposed algorithms across theorized and real architectures using the position graph framework. For completeness, we also introduce a linear program of trapped-ion scheduling that yields the optimal schedules, enabling a direct comparison with our heuristics. Our algorithm can successfully compile programs for extreme architectures where priori algorithms fail. When the baseline does complete, our produced schedules are $1.45$ times faster on average, with best-case speedups up to $4$ times faster.

Ankit Kulshrestha, Xiaoyuan Liu, Hayato Ushijima-Mwesigwa et al.

In the present noisy intermediate scale quantum computing era, there is a critical need to devise methods for the efficient implementation of gate-based variational quantum circuits. This ensures that a range of proposed applications can be deployed on real quantum hardware. The efficiency of quantum circuit is desired both in the number of trainable gates and the depth of the overall circuit. The major concern of barren plateaus has made this need for efficiency even more acute. The problem of efficient quantum circuit realization has been extensively studied in the literature to reduce gate complexity and circuit depth. Another important approach is to design a method to reduce the \emph{parameter complexity} in a variational quantum circuit. Existing methods include hyperparameter-based parameter pruning which introduces an additional challenge of finding the best hyperparameters for different applications. In this paper, we present \emph{QAdaPrune} - an adaptive parameter pruning algorithm that automatically determines the threshold and then intelligently prunes the redundant and non-performing parameters. We show that the resulting sparse parameter sets yield quantum circuits that perform comparably to the unpruned quantum circuits and in some cases may enhance trainability of the circuits even if the original quantum circuit gets stuck in a barren plateau.\\ \noindent{\bf Reproducibility}: The source code and data are available at \url{https://github.com/aicaffeinelife/QAdaPrune.git}

Ankit Kulshrestha, Ilya Safro

Barren plateaus are a notorious problem in the optimization of variational quantum algorithms and pose a critical obstacle in the quest for more efficient quantum machine learning algorithms. Many potential reasons for barren plateaus have been identified but few solutions have been proposed to avoid them in practice. Existing solutions are mainly focused on the initialization of unitary gate parameters without taking into account the changes induced by input data. In this paper, we propose an alternative strategy which initializes the parameters of a unitary gate by drawing from a beta distribution. The hyperparameters of the beta distribution are estimated from the data. To further prevent barren plateau during training we add a novel perturbation at every gradient descent step. Taking these ideas together, we empirically show that our proposed framework significantly reduces the possibility of a complex quantum neural network getting stuck in a barren plateau.

Xiaoyuan Liu, Ilya Tyagin, Hayato Ushijima-Mwesigwa et al.

With the rapid development of machine learning, improving its explainability has become a crucial research goal. We study the problem of making the clusters more explainable by investigating the cluster descriptors. Given a set of objects $S$, a clustering of these objects $π$, and a set of tags $T$ that have not participated in the clustering algorithm. Each object in $S$ is associated with a subset of $T$. The goal is to find a representative set of tags for each cluster, referred to as the cluster descriptors, with the constraint that these descriptors we find are pairwise disjoint, and the total size of all the descriptors is minimized. In general, this problem is NP-hard. We propose a novel explainability model that reinforces the previous models in such a way that tags that do not contribute to explainability and do not sufficiently distinguish between clusters are not added to the optimal descriptors. The proposed model is formulated as a quadratic unconstrained binary optimization problem which makes it suitable for solving on modern optimization hardware accelerators. We experimentally demonstrate how a proposed explainability model can be solved on specialized hardware for accelerating combinatorial optimization, the Fujitsu Digital Annealer, and use real-life Twitter and PubMed datasets for use cases.

Ankit Kulshrestha, Xiaoyuan Liu, Hayato Ushijima-Mwesigwa et al.

Quantum Machine Learning is an emerging sub-field in machine learning where one of the goals is to perform pattern recognition tasks by encoding data into quantum states. This extension from classical to quantum domain has been made possible due to the development of hybrid quantum-classical algorithms that allow a parameterized quantum circuit to be optimized using gradient based algorithms that run on a classical computer. The similarities in training of these hybrid algorithms and classical neural networks has further led to the development of Quantum Neural Networks (QNNs). However, in the current training regime for QNNs, the gradients w.r.t objective function have to be computed on the quantum device. This computation is highly non-scalable and is affected by hardware and sampling noise present in the current generation of quantum hardware. In this paper, we propose a training algorithm that does not rely on gradient information. Specifically, we introduce a novel meta-optimization algorithm that trains a \emph{meta-optimizer} network to output parameters for the quantum circuit such that the objective function is minimized. We empirically and theoretically show that we achieve a better quality minima in fewer circuit evaluations than existing gradient based algorithms on different datasets.

Ankit Kulshrestha, Danylo Lykov, Ilya Safro et al.

The current era of quantum computing has yielded several algorithms that promise high computational efficiency. While the algorithms are sound in theory and can provide potentially exponential speedup, there is little guidance on how to design proper quantum circuits to realize the appropriate unitary transformation to be applied to the input quantum state. In this paper, we present \texttt{QArchSearch}, an AI based quantum architecture search package with the \texttt{QTensor} library as a backend that provides a principled and automated approach to finding the best model given a task and input quantum state. We show that the search package is able to efficiently scale the search to large quantum circuits and enables the exploration of more complex models for different quantum applications. \texttt{QArchSearch} runs at scale and high efficiency on high-performance computing systems using a two-level parallelization scheme on both CPUs and GPUs, which has been demonstrated on the Polaris supercomputer.

David Marasco, Ilya Tyagin, Justin Sybrandt et al.

This project demonstrates how medical corpus hypothesis generation, a knowledge discovery field of AI, can be used to derive new research angles for landscape and urban planners. The hypothesis generation approach herein consists of a combination of deep learning with topic modeling, a probabilistic approach to natural language analysis that scans aggregated research databases for words that can be grouped together based on their subject matter commonalities; the word groups accordingly form topics that can provide implicit connections between two general research terms. The hypothesis generation system AGATHA was used to identify likely conceptual relationships between emerging infectious diseases (EIDs) and deforestation, with the objective of providing landscape planners guidelines for productive research directions to help them formulate research hypotheses centered on deforestation and EIDs that will contribute to the broader health field that asserts causal roles of landscape-level issues. This research also serves as a partial proof-of-concept for the application of medical database hypothesis generation to medicine-adjacent hypothesis discovery.

Ilya Tyagin, Ilya Safro

This paper presents a novel benchmarking framework Dyport for evaluating biomedical hypothesis generation systems. Utilizing curated datasets, our approach tests these systems under realistic conditions, enhancing the relevance of our evaluations. We integrate knowledge from the curated databases into a dynamic graph, accompanied by a method to quantify discovery importance. This not only assesses hypothesis accuracy but also their potential impact in biomedical research which significantly extends traditional link prediction benchmarks. Applicability of our benchmarking process is demonstrated on several link prediction systems applied on biomedical semantic knowledge graphs. Being flexible, our benchmarking system is designed for broad application in hypothesis generation quality verification, aiming to expand the scope of scientific discovery within the biomedical research community. Availability and implementation: Dyport framework is fully open-source. All code and datasets are available at: https://github.com/IlyaTyagin/Dyport

Kien X. Nguyen, Ankit Kulshrestha, Ilya Safro et al.

Qubit routing is a fundamental problem in quantum compilation, known to be NP-hard. Its dynamic nature makes local routing decisions propagate and compound over time, making global efficient solutions challenging. Existing heuristic methods rely on local rules with limited lookahead, while recent learning-based approaches often treat routing as a generic sequential decision problem without fully exploiting its underlying structure. In this paper, we introduce QAP-Router, framing qubit routing based on a dynamic Quadratic Assignment Problem (QAP) formulation. By modeling logical interactions, or quantum gates, as flow matrices and hardware topology as a distance matrix, our approach captures the interaction-distance coupling in a unified objective, which defines the reward in the reinforcement learning environment. To further exploit this structure, the policy network employs a solution-aware Transformer backbone that encodes the interaction between the flow matrix and the distance matrix into the attention mechanism. We also integrate a lookahead mechanism that blends naturally into the QAP framework, preventing myopic decisions. Extensive experiments on 1,831 real-world quantum circuits from the MQTBench, AgentQ and QUEKO datasets show that our method substantially reduces the CNOT gate count of routed circuits by 15.7%, 30.4% and 12.1%, respectively, relative to existing industry compilers.

Brent Russon, Bao Bach, Ed Younis et al.

Scalable qubit mapping and routing remain major bottlenecks in quantum compilation, especially for Trapped-Ion Quantum Charge-Coupled device (TI-QCCD) architectures, where qubit interactions require physically shuttling ions under strict movement, congestion, and trap-capacity constraints. We present a compilation framework built around the position graph abstraction, a unified representation of executable locations, movement paths, and routing constraints that enables heuristic mappers to operate directly on shuttling-based hardware. Using this abstraction, we accelerate the SWAP-based BidiREctional heuristic search (SABRE) by implementing relative move scoring, which caches repeated heuristic move evaluations that arise during search, and memoized congestion resolution, which speeds up the resolution of repeated congestion. This optimization removes redundant computation without changing routing/shuttling decisions, improving the scalability of SABRE-based methods on TI-QCCD systems. Our results show that combining an architecture-aware abstraction with memoized heuristic evaluation yields a practical and effective path toward scalable qubit mapping and routing across heterogeneous quantum architectures.

Ilya Tyagin, Saeideh Valipour, Aliaksandra Sikirzhytskaya et al.

We introduce an explainability method for biomedical hypothesis generation systems, built on top of the novel Hypothesis Generation Context Retriever framework. Our approach combines semantic graph-based retrieval and relevant data-restrictive training to simulate real-world discovery constraints. Integrated with large language models (LLMs) via retrieval-augmented generation, the system explains hypotheses with contextual evidence using published scientific literature. We also propose a novel feedback loop approach, which iteratively identifies and corrects flawed parts of LLM-generated explanations, refining both the evidence paths and supporting context. We demonstrate the performance of our method with multiple large language models and evaluate the explanation and context retrieval quality through both expert-curated assessment and large-scale automated analysis. Our code is available at: https://github.com/IlyaTyagin/HGCR.

Ehsan Sadrfaridpour, Korey Palmer, Ilya Safro

The support vector machines (SVM) is one of the most widely used and practical optimization based classification models in machine learning because of its interpretability and flexibility to produce high quality results. However, the big data imposes a certain difficulty to the most sophisticated but relatively slow versions of SVM, namely, the nonlinear SVM. The complexity of nonlinear SVM solvers and the number of elements in the kernel matrix quadratically increases with the number of samples in training data. Therefore, both runtime and memory requirements are negatively affected. Moreover, the parameter fitting has extra kernel parameters to tune, which exacerbate the runtime even further. This paper proposes an adaptive multilevel learning framework for the nonlinear SVM, which addresses these challenges, improves the classification quality across the refinement process, and leverages multi-threaded parallel processing for better performance. The integration of parameter fitting in the hierarchical learning framework and adaptive process to stop unnecessary computation significantly reduce the running time while increase the overall performance. The experimental results demonstrate reduced variance on prediction over validation and test data across levels in the hierarchy, and significant speedup compared to state-of-the-art nonlinear SVM libraries without a decrease in the classification quality. The code is accessible at https://github.com/esadr/amlsvm.

Justin Sybrandt, Angelo Carrabba, Alexander Herzog et al.

The potential for automatic hypothesis generation (HG) systems to improve research productivity keeps pace with the growing set of publicly available scientific information. But as data becomes easier to acquire, we must understand the effect different textual data sources have on our resulting hypotheses. Are abstracts enough for HG, or does it need full-text papers? How many papers does an HG system need to make valuable predictions? How sensitive is a general-purpose HG system to hyperparameter values or input quality? What effect does corpus size and document length have on HG results? To answer these questions we train multiple versions of knowledge network-based HG system, Moliere, on varying corpora in order to compare challenges and trade offs in terms of result quality and computational requirements. Moliere generalizes main principles of similar knowledge network-based HG systems and reinforces them with topic modeling components. The corpora include the abstract and full-text versions of PubMed Central, as well as iterative halves of MEDLINE, which allows us to compare the effect document length and count has on the results. We find that, quantitatively, corpora with a higher median document length result in marginally higher quality results, yet require substantially longer to process. However, qualitatively, full-length papers introduce a significant number of intruder terms to the resulting topics, which decreases human interpretability. Additionally, we find that the effect of document length is greater than that of document count, even if both sets contain only paper abstracts. Reproducibility: Our code and data are available at github.com/jsybran/moliere, and bit.ly/2GxghpM respectively.

Kien X. Nguyen, Ilya Safro

Unsupervised neural combinatorial optimization (NCO) offers an appealing alternative to supervised approaches by training learning-based solvers without ground-truth solutions, directly minimizing instance objectives and constraint violations. Yet for graph node subset-selection problems (e.g., Maximum Clique and Maximum Independent Set), existing unsupervised methods are typically specialized to a single problem class and rely on problem-specific surrogate losses, which hinders learning across classes within a unified framework. In this work, we propose UniHetCO, a unified heterogeneous graph representation for constrained quadratic programming-based combinatorial optimization that encodes problem structure, objective terms, and linear constraints in a single input. This formulation enables training a single model across multiple problem classes with a unified label-free objective. To improve stability under multi-problem learning, we employ a gradient-norm-based dynamic weighting scheme that alleviates gradient imbalance among classes. Experiments on multiple datasets and four constrained problem classes demonstrate competitive performance with state-of-the-art unsupervised NCO baselines, strong cross-problem adaptation potential, and effective warm starts for a commercial classical solver under tight time limits.

Ilya Tyagin, Marwa H. Farag, Kyle Sherbert et al.

Quantum computing has the potential to improve our ability to solve certain optimization problems that are computationally difficult for classical computers, by offering new algorithmic approaches that may provide speedups under specific conditions. In this work, we introduce QAOA-GPT, a generative framework that leverages Generative Pretrained Transformers (GPT) to directly synthesize quantum circuits for solving quadratic unconstrained binary optimization problems, and demonstrate it on the MaxCut problem on graphs. To diversify the training circuits and ensure their quality, we have generated a synthetic dataset using the adaptive QAOA approach, a method that incrementally builds and optimizes problem-specific circuits. The experiments conducted on a curated set of graph instances demonstrate that QAOA-GPT, generates high quality quantum circuits for new problem instances unseen in the training as well as successfully parametrizes QAOA. Our results show that using QAOA-GPT to generate quantum circuits will significantly decrease both the computational overhead of classical QAOA and adaptive approaches that often use gradient evaluation to generate the circuit and the classical optimization of the circuit parameters. Our work shows that generative AI could be a promising avenue to generate compact quantum circuits in a scalable way.

Kien X. Nguyen, Bao Bach, Ilya Safro

Quantum Approximate Optimization Algorithm (QAOA) is one of the most promising candidates to achieve the quantum advantage in solving combinatorial optimization problems. The process of finding a good set of variational parameters in the QAOA circuit has proven to be challenging due to multiple factors, such as barren plateaus. As a result, there is growing interest in exploiting parameter transferability, where parameter sets optimized for one problem instance are transferred to another that could be more complex either to estimate the solution or to serve as a warm start for further optimization. But can we transfer parameters from one class of problems to another? Leveraging parameter sets learned from a well-studied class of problems could help navigate the less studied one, reducing optimization overhead and mitigating performance pitfalls. In this paper, we study whether pretrained QAOA parameters of MaxCut can be used as is or to warm start the Maximum Independent Set (MIS) circuits. Specifically, we design machine learning models to find good donor candidates optimized on MaxCut and apply their parameters to MIS acceptors. Our experimental results show that such parameter transfer can significantly reduce the number of optimization iterations required while achieving comparable approximation ratios.

Hanjing Xu, Xiaoyuan Liu, Alex Pothen et al.

The quantum approximate optimization algorithm (QAOA) is one of the promising variational approaches of quantum computing to solve combinatorial optimization problems. In QAOA, variational parameters need to be optimized by solving a series of nonlinear, nonconvex optimization programs. In this work, we propose a QAOA parameter transfer scheme using Graph Attention Networks (GAT) to solve Maximum Independent Set (MIS) problems. We prepare optimized parameters for graphs of 12 and 14 vertices and use GATs to transfer their parameters to larger graphs. Additionally, we design a hybrid distributed resource-aware algorithm for MIS (HyDRA-MIS), which decomposes large problems into smaller ones that can fit onto noisy intermediate-scale quantum (NISQ) computers. We integrate our GAT-based parameter transfer approach to HyDRA-MIS and demonstrate competitive results compared to KaMIS, a state-of-the-art classical MIS solver, on graphs with several thousands vertices.

Hoang-Quan Nguyen, Xuan-Bac Nguyen, Sankalp Pandey et al.

Quantum machine learning (QML) has emerged as a promising direction in the noisy intermediate-scale quantum (NISQ) era, offering computational and memory advantages by harnessing superposition and entanglement. However, QML models often face challenges in scalability and expressiveness due to hardware constraints. In this paper, we propose quantum mixture of experts (QMoE), a novel quantum architecture that integrates the mixture of experts (MoE) paradigm into the QML setting. QMoE comprises multiple parameterized quantum circuits serving as expert models, along with a learnable quantum routing mechanism that selects and aggregates specialized quantum experts per input. The empirical results from the proposed QMoE on quantum classification tasks demonstrate that it consistently outperforms standard quantum neural networks, highlighting its effectiveness in learning complex data patterns. Our work paves the way for scalable and interpretable quantum learning frameworks.

Ankit Kulshrestha, Xiaoyuan Liu, Hayato Ushijima-Mwesigwa et al.

The design of quantum circuits is currently driven by the specific objectives of the quantum algorithm in question. This approach thus relies on a significant manual effort by the quantum algorithm designer to design an appropriate circuit for the task. However this approach cannot scale to more complex quantum algorithms in the future without exponentially increasing the circuit design effort and introducing unwanted inductive biases. Motivated by this observation, we propose to automate the process of cicuit design by drawing inspiration from Neural Architecture Search (NAS). In this work, we propose two Quantum-NAS algorithms that aim to find efficient circuits given a particular quantum task. We choose quantum data compression as our driver quantum task and demonstrate the performance of our algorithms by finding efficient autoencoder designs that outperform baselines on three different tasks - quantum data denoising, classical data compression and pure quantum data compression. Our results indicate that quantum NAS algorithms can significantly alleviate the manual effort while delivering performant quantum circuits for any given task.

Farah Alshanik, Amy Apon, Yuheng Du et al.

Query expansion is the process of reformulating the original query by adding relevant words. Choosing which terms to add in order to improve the performance of the query expansion methods or to enhance the quality of the retrieved results is an important aspect of any information retrieval system. Adding words that can positively impact the quality of the search query or are informative enough play an important role in returning or gathering relevant documents that cover a certain topic can result in improving the efficiency of the information retrieval system. Typically, query expansion techniques are used to add or substitute words to a given search query to collect relevant data. In this paper, we design and implement a pipeline of automated query expansion. We outline several tools using different methods to expand the query. Our methods depend on targeting emergent events in streaming data over time and finding the hidden topics from targeted documents using probabilistic topic models. We employ Dynamic Eigenvector Centrality to trigger the emergent events, and the Latent Dirichlet Allocation to discover the topics. Also, we use an external data source as a secondary stream to supplement the primary stream with relevant words and expand the query using the words from both primary and secondary streams. An experimental study is performed on Twitter data (primary stream) related to the events that happened during protests in Baltimore in 2015. The quality of the retrieved results was measured using a quality indicator of the streaming data: tweets count, hashtag count, and hashtag clustering.

Ankit Kulshrestha, Ilya Safro

The rapid growth of data in the recent years has led to the development of complex learning algorithms that are often used to make decisions in real world. While the positive impact of the algorithms has been tremendous, there is a need to mitigate any bias arising from either training samples or implicit assumptions made about the data samples. This need becomes critical when algorithms are used in automated decision making systems that can hugely impact people's lives. Many approaches have been proposed to make learning algorithms fair by detecting and mitigating bias in different stages of optimization. However, due to a lack of a universal definition of fairness, these algorithms optimize for a particular interpretation of fairness which makes them limited for real world use. Moreover, an underlying assumption that is common to all algorithms is the apparent equivalence of achieving fairness and removing bias. In other words, there is no user defined criteria that can be incorporated into the optimization procedure for producing a fair algorithm. Motivated by these shortcomings of existing methods, we propose the CONFAIR procedure that produces a fair algorithm by incorporating user constraints into the optimization procedure. Furthermore, we make the process interpretable by estimating the most predictive features from data. We demonstrate the efficacy of our approach on several real world datasets using different fairness criteria.

Ankit Kulshrestha, Ilya Safro

Machine learning actively impacts our everyday life in almost all endeavors and domains such as healthcare, finance, and energy. As our dependence on the machine learning increases, it is inevitable that these algorithms will be used to make decisions that will have a direct impact on the society spanning all resolutions from personal choices to world-wide policies. Hence, it is crucial to ensure that (un)intentional bias does not affect the machine learning algorithms especially when they are required to take decisions that may have unintended consequences. Algorithmic fairness techniques have found traction in the machine learning community and many methods and metrics have been proposed to ensure and evaluate fairness in algorithms and data collection. In this paper, we study the algorithmic fairness in a supervised learning setting and examine the effect of optimizing a classifier for the Equal Opportunity metric. We demonstrate that such a classifier has an increased false positive rate across sensitive groups and propose a conceptually simple method to mitigate this bias. We rigorously analyze the proposed method and evaluate it on several real world datasets demonstrating its efficacy.

Ilya Tyagin, Ankit Kulshrestha, Justin Sybrandt et al.

In 2020, the White House released the, "Call to Action to the Tech Community on New Machine Readable COVID-19 Dataset," wherein artificial intelligence experts are asked to collect data and develop text mining techniques that can help the science community answer high-priority scientific questions related to COVID-19. The Allen Institute for AI and collaborators announced the availability of a rapidly growing open dataset of publications, the COVID-19 Open Research Dataset (CORD-19). As the pace of research accelerates, biomedical scientists struggle to stay current. To expedite their investigations, scientists leverage hypothesis generation systems, which can automatically inspect published papers to discover novel implicit connections. We present an automated general purpose hypothesis generation systems AGATHA-C and AGATHA-GP for COVID-19 research. The systems are based on graph-mining and the transformer model. The systems are massively validated using retrospective information rediscovery and proactive analysis involving human-in-the-loop expert analysis. Both systems achieve high-quality predictions across domains (in some domains up to 0.97% ROC AUC) in fast computational time and are released to the broad scientific community to accelerate biomedical research. In addition, by performing the domain expert curated study, we show that the systems are able to discover on-going research findings such as the relationship between COVID-19 and oxytocin hormone.

Ruslan Shaydulin, Stuart Hadfield, Tad Hogg et al.

We study the relationship between the Quantum Approximate Optimization Algorithm (QAOA) and the underlying symmetries of the objective function to be optimized. Our approach formalizes the connection between quantum symmetry properties of the QAOA dynamics and the group of classical symmetries of the objective function. The connection is general and includes but is not limited to problems defined on graphs. We show a series of results exploring the connection and highlight examples of hard problem classes where a nontrivial symmetry subgroup can be obtained efficiently. In particular we show how classical objective function symmetries lead to invariant measurement outcome probabilities across states connected by such symmetries, independent of the choice of algorithm parameters or number of layers. To illustrate the power of the developed connection, we apply machine learning techniques towards predicting QAOA performance based on symmetry considerations. We provide numerical evidence that a small set of graph symmetry properties suffices to predict the minimum QAOA depth required to achieve a target approximation ratio on the MaxCut problem, in a practically important setting where QAOA parameter schedules are constrained to be linear and hence easier to optimize.

Farah Alshanik, Amy Apon, Alexander Herzog et al.

Text preprocessing is an essential step in text mining. Removing words that can negatively impact the quality of prediction algorithms or are not informative enough is a crucial storage-saving technique in text indexing and results in improved computational efficiency. Typically, a generic stop word list is applied to a dataset regardless of the domain. However, many common words are different from one domain to another but have no significance within a particular domain. Eliminating domain-specific common words in a corpus reduces the dimensionality of the feature space, and improves the performance of text mining tasks. In this paper, we present a novel mathematical approach for the automatic extraction of domain-specific words called the hyperplane-based approach. This new approach depends on the notion of low dimensional representation of the word in vector space and its distance from hyperplane. The hyperplane-based approach can significantly reduce text dimensionality by eliminating irrelevant features. We compare the hyperplane-based approach with other feature selection methods, namely \c{hi}2 and mutual information. An experimental study is performed on three different datasets and five classification algorithms, and measure the dimensionality reduction and the increase in the classification performance. Results indicate that the hyperplane-based approach can reduce the dimensionality of the corpus by 90% and outperforms mutual information. The computational time to identify the domain-specific words is significantly lower than mutual information.

Fei Ding, Xiaohong Zhang, Justin Sybrandt et al.

Graph representation learning based on graph neural networks (GNNs) can greatly improve the performance of downstream tasks, such as node and graph classification. However, the general GNN models do not aggregate node information in a hierarchical manner, and can miss key higher-order structural features of many graphs. The hierarchical aggregation also enables the graph representations to be explainable. In addition, supervised graph representation learning requires labeled data, which is expensive and error-prone. To address these issues, we present an unsupervised graph representation learning method, Unsupervised Hierarchical Graph Representation (UHGR), which can generate hierarchical representations of graphs. Our method focuses on maximizing mutual information between "local" and high-level "global" representations, which enables us to learn the node embeddings and graph embeddings without any labeled data. To demonstrate the effectiveness of the proposed method, we perform the node and graph classification using the learned node and graph embeddings. The results show that the proposed method achieves comparable results to state-of-the-art supervised methods on several benchmarks. In addition, our visualization of hierarchical representations indicates that our method can capture meaningful and interpretable clusters.

Justin Sybrandt, Ilya Safro

Biomedical research papers use significantly different language and jargon when compared to typical English text, which reduces the utility of pre-trained NLP models in this domain. Meanwhile Medline, a database of biomedical abstracts, introduces nearly a million new documents per-year. Applications that could benefit from understanding this wealth of publicly available information, such as scientific writing assistants, chat-bots, or descriptive hypothesis generation systems, require new domain-centered approaches. A conditional language model, one that learns the probability of words given some a priori criteria, is a fundamental building block in many such applications. We propose a transformer-based conditional language model with a shallow encoder "condition" stack, and a deep "language model" stack of multi-headed attention blocks. The condition stack encodes metadata used to alter the output probability distribution of the language model stack. We sample this distribution in order to generate biomedical abstracts given only a proposed title, an intended publication year, and a set of keywords. Using typical natural language generation metrics, we demonstrate that this proposed approach is more capable of producing non-trivial relevant entities within the abstract body than the 1.5B parameter GPT-2 language model.

Justin Sybrandt, Ilya Tyagin, Michael Shtutman et al.

Medical research is risky and expensive. Drug discovery, as an example, requires that researchers efficiently winnow thousands of potential targets to a small candidate set for more thorough evaluation. However, research groups spend significant time and money to perform the experiments necessary to determine this candidate set long before seeing intermediate results. Hypothesis generation systems address this challenge by mining the wealth of publicly available scientific information to predict plausible research directions. We present AGATHA, a deep-learning hypothesis generation system that can introduce data-driven insights earlier in the discovery process. Through a learned ranking criteria, this system quickly prioritizes plausible term-pairs among entity sets, allowing us to recommend new research directions. We massively validate our system with a temporal holdout wherein we predict connections first introduced after 2015 using data published beforehand. We additionally explore biomedical sub-domains, and demonstrate AGATHA's predictive capacity across the twenty most popular relationship types. This system achieves best-in-class performance on an established benchmark, and demonstrates high recommendation scores across subdomains. Reproducibility: All code, experimental data, and pre-trained models are available online: sybrandt.com/2020/agatha

Justin Sybrandt, Ruslan Shaydulin, Ilya Safro

Problems in scientific computing, such as distributing large sparse matrix operations, have analogous formulations as hypergraph partitioning problems. A hypergraph is a generalization of a traditional graph wherein "hyperedges" may connect any number of nodes. As a result, hypergraph partitioning is an NP-Hard problem to both solve or approximate. State-of-the-art algorithms that solve this problem follow the multilevel paradigm, which begins by iteratively "coarsening" the input hypergraph to smaller problem instances that share key structural features. Once identifying an approximate problem that is small enough to be solved directly, that solution can be interpolated and refined to the original problem. While this strategy represents an excellent trade off between quality and running time, it is sensitive to coarsening strategy. In this work we propose using graph embeddings of the initial hypergraph in order to ensure that coarsened problem instances retrain key structural features. Our approach prioritizes coarsening within self-similar regions within the input graph, and leads to significantly improved solution quality across a range of considered hypergraphs. Reproducibility: All source code, plots and experimental data are available at https://sybrandt.com/2019/partition.

Justin Sybrandt, Ilya Safro

Typical graph embeddings may not capture type-specific bipartite graph features that arise in such areas as recommender systems, data visualization, and drug discovery. Machine learning methods utilized in these applications would be better served with specialized embedding techniques. We propose two embeddings for bipartite graphs that decompose edges into sets of indirect relationships between node neighborhoods. When sampling higher-order relationships, we reinforce similarities through algebraic distance on graphs. We also introduce ensemble embeddings to combine both into a "best of both worlds" embedding. The proposed methods are evaluated on link prediction and recommendation tasks and compared with other state-of-the-art embeddings. While being all highly beneficial in applications, we demonstrate that none of the considered embeddings is clearly superior (in contrast to what is claimed in many papers), and discuss the trade offs present among them. Reproducibility: Our code, data sets, and results are all publicly available online at: http://sybrandt.com/2020/fobe_hobe.

Justin Sybrandt, Michael Shtutman, Ilya Safro

The first step of many research projects is to define and rank a short list of candidates for study. In the modern rapidity of scientific progress, some turn to automated hypothesis generation (HG) systems to aid this process. These systems can identify implicit or overlooked connections within a large scientific corpus, and while their importance grows alongside the pace of science, they lack thorough validation. Without any standard numerical evaluation method, many validate general-purpose HG systems by rediscovering a handful of historical findings, and some wishing to be more thorough may run laboratory experiments based on automatic suggestions. These methods are expensive, time consuming, and cannot scale. Thus, we present a numerical evaluation framework for the purpose of validating HG systems that leverages thousands of validation hypotheses. This method evaluates a HG system by its ability to rank hypotheses by plausibility; a process reminiscent of human candidate selection. Because HG systems do not produce a ranking criteria, specifically those that produce topic models, we additionally present novel metrics to quantify the plausibility of hypotheses given topic model system output. Finally, we demonstrate that our proposed validation method aligns with real-world research goals by deploying our method within Moliere, our recent topic-driven HG system, in order to automatically generate a set of candidate genes related to HIV-associated neurodegenerative disease (HAND). By performing laboratory experiments based on this candidate set, we discover a new connection between HAND and Dead Box RNA Helicase 3 (DDX3). Reproducibility: code, validation data, and results can be found at sybrandt.com/2018/validation.

Justin Sybrandt, Michael Shtutman, Ilya Safro

Hypothesis generation is becoming a crucial time-saving technique which allows biomedical researchers to quickly discover implicit connections between important concepts. Typically, these systems operate on domain-specific fractions of public medical data. MOLIERE, in contrast, utilizes information from over 24.5 million documents. At the heart of our approach lies a multi-modal and multi-relational network of biomedical objects extracted from several heterogeneous datasets from the National Center for Biotechnology Information (NCBI). These objects include but are not limited to scientific papers, keywords, genes, proteins, diseases, and diagnoses. We model hypotheses using Latent Dirichlet Allocation applied on abstracts found near shortest paths discovered within this network, and demonstrate the effectiveness of MOLIERE by performing hypothesis generation on historical data. Our network, implementation, and resulting data are all publicly available for the broad scientific community.

Ehsan Sadrfaridpour, Sandeep Jeereddy, Ken Kennedy et al.

The support vector machine is a flexible optimization-based technique widely used for classification problems. In practice, its training part becomes computationally expensive on large-scale data sets because of such reasons as the complexity and number of iterations in parameter fitting methods, underlying optimization solvers, and nonlinearity of kernels. We introduce a fast multilevel framework for solving support vector machine models that is inspired by the algebraic multigrid. Significant improvement in the running has been achieved without any loss in the quality. The proposed technique is highly beneficial on imbalanced sets. We demonstrate computational results on publicly available and industrial data sets.

Chris Gropp, Alexander Herzog, Ilya Safro et al.

Topic modeling, a method for extracting the underlying themes from a collection of documents, is an increasingly important component of the design of intelligent systems enabling the sense-making of highly dynamic and diverse streams of text data. Traditional methods such as Dynamic Topic Modeling (DTM) do not lend themselves well to direct parallelization because of dependencies from one time step to another. In this paper, we introduce and empirically analyze Clustered Latent Dirichlet Allocation (CLDA), a method for extracting dynamic latent topics from a collection of documents. Our approach is based on data decomposition in which the data is partitioned into segments, followed by topic modeling on the individual segments. The resulting local models are then combined into a global solution using clustering. The decomposition and resulting parallelization leads to very fast runtime even on very large datasets. Our approach furthermore provides insight into how the composition of topics changes over time and can also be applied using other data partitioning strategies over any discrete features of the data, such as geographic features or classes of users. In this paper CLDA is applied successfully to seventeen years of NIPS conference papers (2,484 documents and 3,280,697 words), seventeen years of computer science journal abstracts (533,560 documents and 32,551,540 words), and to forty years of the PubMed corpus (4,025,978 documents and 273,853,980 words).

Neela Avudaiappan, Alexander Herzog, Sneha Kadam et al.

Methods for detecting and summarizing emergent keywords have been extensively studied since social media and microblogging activities have started to play an important role in data analysis and decision making. We present a system for monitoring emergent keywords and summarizing a document stream based on the dynamic semantic graphs of streaming documents. We introduce the notion of dynamic eigenvector centrality for ranking emergent keywords, and present an algorithm for summarizing emergent events that is based on the minimum weight set cover. We demonstrate our system with an analysis of streaming Twitter data related to public security events.

Talayeh Razzaghi, Oleg Roderick, Ilya Safro et al.

This work is motivated by the needs of predictive analytics on healthcare data as represented by Electronic Medical Records. Such data is invariably problematic: noisy, with missing entries, with imbalance in classes of interests, leading to serious bias in predictive modeling. Since standard data mining methods often produce poor performance measures, we argue for development of specialized techniques of data-preprocessing and classification. In this paper, we propose a new method to simultaneously classify large datasets and reduce the effects of missing values. It is based on a multilevel framework of the cost-sensitive SVM and the expected maximization imputation method for missing values, which relies on iterated regression analyses. We compare classification results of multilevel SVM-based algorithms on public benchmark datasets with imbalanced classes and missing values as well as real data in health applications, and show that our multilevel SVM-based method produces fast, and more accurate and robust classification results.

Talayeh Razzaghi, Oleg Roderick, Ilya Safro et al.

In medical domain, data features often contain missing values. This can create serious bias in the predictive modeling. Typical standard data mining methods often produce poor performance measures. In this paper, we propose a new method to simultaneously classify large datasets and reduce the effects of missing values. The proposed method is based on a multilevel framework of the cost-sensitive SVM and the expected maximization imputation method for missing values, which relies on iterated regression analyses. We compare classification results of multilevel SVM-based algorithms on public benchmark datasets with imbalanced classes and missing values as well as real data in health applications, and show that our multilevel SVM-based method produces fast, and more accurate and robust classification results.

Talayeh Razzaghi, Ilya Safro

Solving different types of optimization models (including parameters fitting) for support vector machines on large-scale training data is often an expensive computational task. This paper proposes a multilevel algorithmic framework that scales efficiently to very large data sets. Instead of solving the whole training set in one optimization process, the support vectors are obtained and gradually refined at multiple levels of coarseness of the data. The proposed framework includes: (a) construction of hierarchy of large-scale data coarse representations, and (b) a local processing of updating the hyperplane throughout this hierarchy. Our multilevel framework substantially improves the computational time without loosing the quality of classifiers. The algorithms are demonstrated for both regular and weighted support vector machines. Experimental results are presented for balanced and imbalanced classification problems. Quality improvement on several imbalanced data sets has been observed.

Sven Leyffer, Ilya Safro

We present a strategy for designing fast methods of response to cyber attacks and infection spread on complex weighted networks. In these networks, nodes can be interpreted as primitive elements of the system, and weighted edges reflect the strength of interaction among these elements. The proposed strategy belongs to the family of multiscale methods whose goal is to approximate the system at multiple scales of coarseness and to obtain a solution of microscopic scale by combining the information from coarse scales. In recent years these methods have demonstrated their potential for solving optimization and analysis problems on large-scale networks. We consider an optimization problem that is based on the SIS epidemiological model. The objective is to detect the network nodes that have to be immunized in order to keep a low level of infection in the system.

Dorit Ron, Ilya Safro, Achi Brandt

The two-dimensional layout optimization problem reinforced by the efficient space utilization demand has a wide spectrum of practical applications. Formulating the problem as a nonlinear minimization problem under planar equality and/or inequality density constraints, we present a linear time multigrid algorithm for solving correction to this problem. The method is demonstrated on various graph drawing (visualization) instances.