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Researcher profile

Marinka Zitnik

Marinka Zitnik contributes to research discovery and scholarly infrastructure.

ResearcherAffiliation not importedOpen to collaborate
Machine LearningArtificial IntelligenceSocial and Information NetworksBiomoleculesComputation and LanguageMolecular Networksquant-phQuantitative Methods

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Published work

15 published item(s)

preprint2026arXiv

OptimusKG: Unifying biomedical knowledge in a modern multimodal graph

Biomedical knowledge graphs (KGs) are widely used in the life sciences, yet many are derived from unstructured documents and therefore lack schema-level constrains, whereas graphs assembled from structured resources are difficult to harmonize into a unified representation. We present OptimusKG, a multimodal biomedical labeled property graph (LPG) built from structured and semi-structured resources to preserve factual, type-specific metadata across molecular, anatomical, clinical, and environmental domains. OptimusKG contains 190,531 nodes across 10 entity types, 21,813,816 edges across 26 relation types, and 67,249,863 property instances encoding 110,276,843 values across 150 distinct property keys, derived from 18 ontologies and controlled vocabularies. The graph enforces a top-level schema for nodes and edges and retains granular, type-specific properties, cross-references, and provenance across molecular, anatomical, clinical, and environmental domains. We assessed the validity of OptimusKG by evaluating whether graph relationships are supported by evidence from the scientific literature using a multimodal agent, PaperQA3. PaperQA3 identified supporting evidence for 70.0% of sampled edges, whereas 83.4% of sampled false edges received no supporting evidence. Edges without literature support were concentrated in associations derived from experimental and functional genomics resources, suggesting that OptimusKG captures biomedical knowledge that may precede synthesis in the scientific literature. OptimusKG is distributed as Apache Parquet files, providing a standardized resource for graph-based machine learning, knowledge-grounded retrieval with large language models, and biomedical discovery use cases such as hypothesis generation.

0 citations0 reviewsNo code linkedOpen access
preprint2026arXiv

Token Reduction Should Go Beyond Efficiency in Generative Models -- From Vision, Language to Multimodality

In Transformer architectures, tokens\textemdash discrete units derived from raw data\textemdash are formed by segmenting inputs into fixed-length chunks. Each token is then mapped to an embedding, enabling parallel attention computations while preserving the input's essential information. Due to the quadratic computational complexity of transformer self-attention mechanisms, token reduction has primarily been used as an efficiency strategy. This is especially true in single vision and language domains, where it helps balance computational costs, memory usage, and inference latency. Despite these advances, this paper argues that token reduction should transcend its traditional efficiency-oriented role in the era of large generative models. Instead, we position it as a fundamental principle in generative modeling, critically influencing both model architecture and broader applications. Specifically, we contend that across vision, language, and multimodal systems, token reduction can: (i) facilitate deeper multimodal integration and alignment, (ii) mitigate "overthinking" and hallucinations, (iii) maintain coherence over long inputs, and (iv) enhance training stability, etc. We reframe token reduction as more than an efficiency measure. By doing so, we outline promising future directions, including algorithm design, reinforcement learning-guided token reduction, token optimization for in-context learning, agentic framework design, and broader ML and scientific domains.

0 citations0 reviewsNo code linkedOpen access
preprint2025arXiv

Quantum-machine-assisted Drug Discovery

Drug discovery is lengthy and expensive, with traditional computer-aided design facing limits. This paper examines integrating quantum computing across the drug development cycle to accelerate and enhance workflows and rigorous decision-making. It highlights quantum approaches for molecular simulation, drug-target interaction prediction, and optimizing clinical trials. Leveraging quantum capabilities could accelerate timelines and costs for bringing therapies to market, improving efficiency and ultimately benefiting public health.

0 citations0 reviewsNo code linkedOpen access
preprint2023arXiv

Evaluating Explainability for Graph Neural Networks

As post hoc explanations are increasingly used to understand the behavior of graph neural networks (GNNs), it becomes crucial to evaluate the quality and reliability of GNN explanations. However, assessing the quality of GNN explanations is challenging as existing graph datasets have no or unreliable ground-truth explanations for a given task. Here, we introduce a synthetic graph data generator, ShapeGGen, which can generate a variety of benchmark datasets (e.g., varying graph sizes, degree distributions, homophilic vs. heterophilic graphs) accompanied by ground-truth explanations. Further, the flexibility to generate diverse synthetic datasets and corresponding ground-truth explanations allows us to mimic the data generated by various real-world applications. We include ShapeGGen and several real-world graph datasets into an open-source graph explainability library, GraphXAI. In addition to synthetic and real-world graph datasets with ground-truth explanations, GraphXAI provides data loaders, data processing functions, visualizers, GNN model implementations, and evaluation metrics to benchmark the performance of GNN explainability methods.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Graph-Guided Network for Irregularly Sampled Multivariate Time Series

In many domains, including healthcare, biology, and climate science, time series are irregularly sampled with varying time intervals between successive readouts and different subsets of variables (sensors) observed at different time points. Here, we introduce RAINDROP, a graph neural network that embeds irregularly sampled and multivariate time series while also learning the dynamics of sensors purely from observational data. RAINDROP represents every sample as a separate sensor graph and models time-varying dependencies between sensors with a novel message passing operator. It estimates the latent sensor graph structure and leverages the structure together with nearby observations to predict misaligned readouts. This model can be interpreted as a graph neural network that sends messages over graphs that are optimized for capturing time-varying dependencies among sensors. We use RAINDROP to classify time series and interpret temporal dynamics on three healthcare and human activity datasets. RAINDROP outperforms state-of-the-art methods by up to 11.4% (absolute F1-score points), including techniques that deal with irregular sampling using fixed discretization and set functions. RAINDROP shows superiority in diverse setups, including challenging leave-sensor-out settings.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Multimodal Learning on Graphs for Disease Relation Extraction

Objective: Disease knowledge graphs are a way to connect, organize, and access disparate information about diseases with numerous benefits for artificial intelligence (AI). To create knowledge graphs, it is necessary to extract knowledge from multimodal datasets in the form of relationships between disease concepts and normalize both concepts and relationship types. Methods: We introduce REMAP, a multimodal approach for disease relation extraction and classification. The REMAP machine learning approach jointly embeds a partial, incomplete knowledge graph and a medical language dataset into a compact latent vector space, followed by aligning the multimodal embeddings for optimal disease relation extraction. Results: We apply REMAP approach to a disease knowledge graph with 96,913 relations and a text dataset of 1.24 million sentences. On a dataset annotated by human experts, REMAP improves text-based disease relation extraction by 10.0% (accuracy) and 17.2% (F1-score) by fusing disease knowledge graphs with text information. Further, REMAP leverages text information to recommend new relationships in the knowledge graph, outperforming graph-based methods by 8.4% (accuracy) and 10.4% (F1-score). Conclusion: REMAP is a multimodal approach for extracting and classifying disease relationships by fusing structured knowledge and text information. REMAP provides a flexible neural architecture to easily find, access, and validate AI-driven relationships between disease concepts.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Rethinking Stability for Attribution-based Explanations

As attribution-based explanation methods are increasingly used to establish model trustworthiness in high-stakes situations, it is critical to ensure that these explanations are stable, e.g., robust to infinitesimal perturbations to an input. However, previous works have shown that state-of-the-art explanation methods generate unstable explanations. Here, we introduce metrics to quantify the stability of an explanation and show that several popular explanation methods are unstable. In particular, we propose new Relative Stability metrics that measure the change in output explanation with respect to change in input, model representation, or output of the underlying predictor. Finally, our experimental evaluation with three real-world datasets demonstrates interesting insights for seven explanation methods and different stability metrics.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Structure Inducing Pre-Training

Language model pre-training and derived methods are incredibly impactful in machine learning. However, there remains considerable uncertainty on exactly why pre-training helps improve performance for fine-tuning tasks. This is especially true when attempting to adapt language-model pre-training to domains outside of natural language. Here, we analyze this problem by exploring how existing pre-training methods impose relational structure in their induced per-sample latent spaces -- i.e., what constraints do pre-training methods impose on the distance or geometry between the pre-trained embeddings of two samples $\vec x_i$ and $\vec x_j$. Through a comprehensive review of existing pre-training methods, we find that this question remains open. This is true despite theoretical analyses demonstrating the importance of understanding this form of induced structure. Based on this review, we introduce a descriptive framework for pre-training that allows for a granular, comprehensive understanding of how relational structure can be induced. We present a theoretical analysis of this framework from first principles and establish a connection between the relational inductive bias of pre-training and fine-tuning performance. We also show how to use the framework to define new pre-training methods. We build upon these findings with empirical studies on benchmarks spanning 3 data modalities and ten fine-tuning tasks. These experiments validate our theoretical analyses, inform the design of novel pre-training methods, and establish consistent improvements over a compelling suite of baseline methods.

0 citations0 reviewsNo code linkedOpen access
preprint2021arXiv

Contrastive Learning Improves Critical Event Prediction in COVID-19 Patients

Machine Learning (ML) models typically require large-scale, balanced training data to be robust, generalizable, and effective in the context of healthcare. This has been a major issue for developing ML models for the coronavirus-disease 2019 (COVID-19) pandemic where data is highly imbalanced, particularly within electronic health records (EHR) research. Conventional approaches in ML use cross-entropy loss (CEL) that often suffers from poor margin classification. For the first time, we show that contrastive loss (CL) improves the performance of CEL especially for imbalanced EHR data and the related COVID-19 analyses. This study has been approved by the Institutional Review Board at the Icahn School of Medicine at Mount Sinai. We use EHR data from five hospitals within the Mount Sinai Health System (MSHS) to predict mortality, intubation, and intensive care unit (ICU) transfer in hospitalized COVID-19 patients over 24 and 48 hour time windows. We train two sequential architectures (RNN and RETAIN) using two loss functions (CEL and CL). Models are tested on full sample data set which contain all available data and restricted data set to emulate higher class imbalance.CL models consistently outperform CEL models with the restricted data set on these tasks with differences ranging from 0.04 to 0.15 for AUPRC and 0.05 to 0.1 for AUROC. For the restricted sample, only the CL model maintains proper clustering and is able to identify important features, such as pulse oximetry. CL outperforms CEL in instances of severe class imbalance, on three EHR outcomes with respect to three performance metrics: predictive power, clustering, and feature importance. We believe that the developed CL framework can be expanded and used for EHR ML work in general.

0 citations0 reviewsNo code linkedOpen access
preprint2021arXiv

Graph Meta Learning via Local Subgraphs

Prevailing methods for graphs require abundant label and edge information for learning. When data for a new task are scarce, meta-learning can learn from prior experiences and form much-needed inductive biases for fast adaption to new tasks. Here, we introduce G-Meta, a novel meta-learning algorithm for graphs. G-Meta uses local subgraphs to transfer subgraph-specific information and learn transferable knowledge faster via meta gradients. G-Meta learns how to quickly adapt to a new task using only a handful of nodes or edges in the new task and does so by learning from data points in other graphs or related, albeit disjoint label sets. G-Meta is theoretically justified as we show that the evidence for a prediction can be found in the local subgraph surrounding the target node or edge. Experiments on seven datasets and nine baseline methods show that G-Meta outperforms existing methods by up to 16.3%. Unlike previous methods, G-Meta successfully learns in challenging, few-shot learning settings that require generalization to completely new graphs and never-before-seen labels. Finally, G-Meta scales to large graphs, which we demonstrate on a new Tree-of-Life dataset comprising of 1,840 graphs, a two-orders of magnitude increase in the number of graphs used in prior work.

0 citations0 reviewsNo code linkedOpen access
preprint2021arXiv

Open Graph Benchmark: Datasets for Machine Learning on Graphs

We present the Open Graph Benchmark (OGB), a diverse set of challenging and realistic benchmark datasets to facilitate scalable, robust, and reproducible graph machine learning (ML) research. OGB datasets are large-scale, encompass multiple important graph ML tasks, and cover a diverse range of domains, ranging from social and information networks to biological networks, molecular graphs, source code ASTs, and knowledge graphs. For each dataset, we provide a unified evaluation protocol using meaningful application-specific data splits and evaluation metrics. In addition to building the datasets, we also perform extensive benchmark experiments for each dataset. Our experiments suggest that OGB datasets present significant challenges of scalability to large-scale graphs and out-of-distribution generalization under realistic data splits, indicating fruitful opportunities for future research. Finally, OGB provides an automated end-to-end graph ML pipeline that simplifies and standardizes the process of graph data loading, experimental setup, and model evaluation. OGB will be regularly updated and welcomes inputs from the community. OGB datasets as well as data loaders, evaluation scripts, baseline code, and leaderboards are publicly available at https://ogb.stanford.edu .

0 citations0 reviewsNo code linkedOpen access
preprint2021arXiv

Towards a Unified Framework for Fair and Stable Graph Representation Learning

As the representations output by Graph Neural Networks (GNNs) are increasingly employed in real-world applications, it becomes important to ensure that these representations are fair and stable. In this work, we establish a key connection between counterfactual fairness and stability and leverage it to propose a novel framework, NIFTY (uNIfying Fairness and stabiliTY), which can be used with any GNN to learn fair and stable representations. We introduce a novel objective function that simultaneously accounts for fairness and stability and develop a layer-wise weight normalization using the Lipschitz constant to enhance neural message passing in GNNs. In doing so, we enforce fairness and stability both in the objective function as well as in the GNN architecture. Further, we show theoretically that our layer-wise weight normalization promotes counterfactual fairness and stability in the resulting representations. We introduce three new graph datasets comprising of high-stakes decisions in criminal justice and financial lending domains. Extensive experimentation with the above datasets demonstrates the efficacy of our framework.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

Interpretability of machine learning based prediction models in healthcare

There is a need of ensuring machine learning models that are interpretable. Higher interpretability of the model means easier comprehension and explanation of future predictions for end-users. Further, interpretable machine learning models allow healthcare experts to make reasonable and data-driven decisions to provide personalized decisions that can ultimately lead to higher quality of service in healthcare. Generally, we can classify interpretability approaches in two groups where the first focuses on personalized interpretation (local interpretability) while the second summarizes prediction models on a population level (global interpretability). Alternatively, we can group interpretability methods into model-specific techniques, which are designed to interpret predictions generated by a specific model, such as a neural network, and model-agnostic approaches, which provide easy-to-understand explanations of predictions made by any machine learning model. Here, we give an overview of interpretability approaches and provide examples of practical interpretability of machine learning in different areas of healthcare, including prediction of health-related outcomes, optimizing treatments or improving the efficiency of screening for specific conditions. Further, we outline future directions for interpretable machine learning and highlight the importance of developing algorithmic solutions that can enable machine-learning driven decision making in high-stakes healthcare problems.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

Network Medicine Framework for Identifying Drug Repurposing Opportunities for COVID-19

The current pandemic has highlighted the need for methodologies that can quickly and reliably prioritize clinically approved compounds for their potential effectiveness for SARS-CoV-2 infections. In the past decade, network medicine has developed and validated multiple predictive algorithms for drug repurposing, exploiting the sub-cellular network-based relationship between a drug's targets and disease genes. Here, we deployed algorithms relying on artificial intelligence, network diffusion, and network proximity, tasking each of them to rank 6,340 drugs for their expected efficacy against SARS-CoV-2. To test the predictions, we used as ground truth 918 drugs that had been experimentally screened in VeroE6 cells, and the list of drugs under clinical trial, that capture the medical community's assessment of drugs with potential COVID-19 efficacy. We find that while most algorithms offer predictive power for these ground truth data, no single method offers consistently reliable outcomes across all datasets and metrics. This prompted us to develop a multimodal approach that fuses the predictions of all algorithms, showing that a consensus among the different predictive methods consistently exceeds the performance of the best individual pipelines. We find that 76 of the 77 drugs that successfully reduced viral infection do not bind the proteins targeted by SARS-CoV-2, indicating that these drugs rely on network-based actions that cannot be identified using docking-based strategies. These advances offer a methodological pathway to identify repurposable drugs for future pathogens and neglected diseases underserved by the costs and extended timeline of de novo drug development.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

Strategies for Pre-training Graph Neural Networks

Many applications of machine learning require a model to make accurate pre-dictions on test examples that are distributionally different from training ones, while task-specific labels are scarce during training. An effective approach to this challenge is to pre-train a model on related tasks where data is abundant, and then fine-tune it on a downstream task of interest. While pre-training has been effective in many language and vision domains, it remains an open question how to effectively use pre-training on graph datasets. In this paper, we develop a new strategy and self-supervised methods for pre-training Graph Neural Networks (GNNs). The key to the success of our strategy is to pre-train an expressive GNN at the level of individual nodes as well as entire graphs so that the GNN can learn useful local and global representations simultaneously. We systematically study pre-training on multiple graph classification datasets. We find that naive strategies, which pre-train GNNs at the level of either entire graphs or individual nodes, give limited improvement and can even lead to negative transfer on many downstream tasks. In contrast, our strategy avoids negative transfer and improves generalization significantly across downstream tasks, leading up to 9.4% absolute improvements in ROC-AUC over non-pre-trained models and achieving state-of-the-art performance for molecular property prediction and protein function prediction.

0 citations0 reviewsNo code linkedOpen access