Yale University, founded in 1701 in New Haven, Connecticut, is a private Ivy League research university and one of the oldest institutions of higher education in the United States. It is renowned for its commitment to educating leaders and contributors across all sectors of society, with a rich history of academic excellence and public service. NEC Labs America collaborates with Yale University to study fairness in machine learning, robust language generation, and the development of ethical AI systems. Please read about our latest news and collaborative publications with Yale University.

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Pathologist-Read vs AI-Driven Assessment of Tumor-Infiltrating Lymphocytes in Melanoma

Tumor-infiltrating lymphocytes (TILs) are a provocative biomarker in melanoma, influencing diagnosis, prognosis, and immunotherapy outcomes; however, traditional pathologistreadTIL assessment on hematoxylin and eosin–stained slides is prone to interobserver variability, leading to inconsistent clinical decisions. Therefore, development of newer TIL scoring approachesthat produce more reliable and consistent readouts is important.

A Quantum Variational Autoencoder Utilizing Regularized Mixed-state Latent Representations

A major challenge in near-term quantum computing is its application to large real-world datasets due to scarce quantum hardware resources. One approach to enabling tractable quantum models for such datasets involves finding low-dimensional representations that preserve essential information for downstream analysis. Inclassical machine learning, variational autoencoders (VAEs) facilitate efficient data compression, representationlearning for subsequent tasks, and novel data generation. However, no quantum model has been proposed thatexactly captures all of these features for direct application to quantum data on quantum computers. Some existingquantum models for data compression lack regularization of latent representations, thus preventing direct use forgeneration and control of generalization. Others are hybrid models with only some internal quantum components,impeding direct training on quantum data. To address this, we present a fully quantum framework, ?-QVAE,which encompasses all the capabilities of classical VAEs and can be directly applied to map both classicaland quantum data to a lower-dimensional space, while effectively reconstructing much of the original statefrom it. Our model utilizes regularized mixed states to attain optimal latent representations. It accommodatesvarious divergences for reconstruction and regularization. Furthermore, by accommodating mixed states at everystage, it can utilize the full data density matrix and allow for a training objective defined on probabilisticmixtures of input data. Doing so, in turn, makes efficient optimization possible and has potential implications forprivate and federated learning. In addition to exploring the theoretical properties of ?-QVAE, we demonstrateits performance on representative genomics and synthetic data. Our results indicate that ?-QVAE consistentlylearns representations that better utilize the capacity of the latent space and exhibits similar or better performancecompared with matched classical models.

Top 10 Most Legendary College Pranks of All-Time for April Fools’ Day

At NEC Labs America, we celebrate innovation in all forms—even the brilliantly engineered college prank. From MIT’s police car on the Great Dome to Caltech hacking the Rose Bowl, these legendary stunts showcase next-level planning, stealth, and technical genius. Our Top 10 list honors the creativity behind pranks that made history (and headlines). This April Fools’ Day, we salute the hackers, makers, and mischief-makers who prove that brilliance can be hilarious.

Spatial Signatures for Predicting Immunotherapy Outcomes Using Multi-Omics in Non-Small Cell Lung Cancer

Non-small cell lung cancer (NSCLC) shows variable responses to immunotherapy, highlighting the need for biomarkers to guide patient selection. We applied a spatial multi-omics approach to 234 advanced NSCLC patients treated with programmed death 1-based immunotherapy across three cohorts to identify biomarkers associated with outcome. Spatial proteomics (n?=?67) and spatial compartment-based transcriptomics (n?=?131) enabled profiling of the tumor immune microenvironment (TIME). Using spatial proteomics, we identified a resistance cell-type signature including proliferating tumor cells, granulocytes, vessels (hazard ratio (HR)?=?3.8, P?=?0.004), and a response signature, including M1/M2 macrophages and CD4 T cells (HR?=?0.4, P?=?0.019). We then generated a cell-to-gene resistance signature using spatial transcriptomics, which was predictive of poor outcomes (HR?=?5.3, 2.2, 1.7 across Yale, University of Queensland and University of Athens cohorts), while a cell-to-gene response signature predicted favorable outcomes (HR?=?0.22, 0.38 and 0.56, respectively). This framework enables robust TIME modeling and identifies biomarkers to support precision immunotherapy in NSCLC.

A Variational Graph Partitioning Approach to Modeling Protein Liquid-liquid Phase Separation

Graph neural networks (GNNs) have emerged as powerful tools for representation learning. Their efficacy depends on their having an optimal underlying graph. In many cases, the most relevant information comes from specific subgraphs. In this work, we introduce a GNN-based framework (graph-partitioned GNN [GP-GNN]) to partition the GNN graph to focus on the most relevant subgraphs. Our approach jointly learns task-dependent graph partitions and node representations, making it particularly effective when critical features reside within initially unidentified subgraphs. Protein liquid-liquid phase separation (LLPS) is a problem especially well-suited to GP-GNNs because intrinsically disordered regions (IDRs) are known to function as protein subdomains in it, playing a key role in the phase separation process. In this study, we demonstrate how GP-GNN accurately predicts LLPS by partitioning protein graphs into task-relevant subgraphs consistent with known IDRs. Our model achieves state-of-the-art accuracy in predicting LLPS and offers biological insights valuable for downstream investigation.

Variational methods for Learning Multilevel Genetic Algorithms using the Kantorovich Monad

Levels of selection and multilevel evolutionary processes are essential concepts in evolutionary theory, and yet there is a lack of common mathematical models for these core ideas. Here, we propose a unified mathematical framework for formulating and optimizing multilevel evolutionary processes and genetic algorithms over arbitrarily many levels based on concepts from category theory and population genetics. We formulate a multilevel version of the Wright-Fisher process using this approach, and we show that this model can be analyzed to clarify key features of multilevel selection. Particularly, we derive an extended multilevel probabilistic version of Price’s Equation via the Kantorovich Monad, and we use this to characterize regimes of parameter space within which selection acts antagonistically or cooperatively across levels. Finally, we show how our framework can provide a unified setting for learning genetic algorithms (GAs), and we show how we can use a Variational Optimization and a multi-level analogue of coalescent analysis to fit multilevel GAs to simulated data.

Predicting Spatially Resolved Gene Expression via Tissue Morphology using Adaptive Spatial GNNs (ECCB)

Spatial transcriptomics technologies, which generate a spatial map of gene activity, can deepen the understanding of tissue architecture and its molecular underpinnings in health and disease. However, the high cost makes these technologies difficult to use in practice. Histological images co-registered with targeted tissues are more affordable and routinely generated in many research and clinical studies. Hence, predicting spatial gene expression from the morphological clues embedded in tissue histological images provides a scalable alternative approach to decoding tissue complexity.

Spatially Informed Gene Signatures for Response to Immunotherapy in Melanoma

We aim to improve the prediction of response or resistance to immunotherapies in patients with melanoma. This goal is based on the hypothesis that current gene signatures predicting immunotherapy outcomes show only modest accuracy due to the lack of spatial information about cellular functions and molecular processes within tumors and their microenvironment.

zeta-QVAE: A Quantum Variational Autoencoder utilizing Regularized Mixed-state Latent Representations

A major challenge in near-term quantum computing is its application to large real-world datasets due to scarce quantum hardware resources. One approach to enabling tractable quantum models for such datasets involves compressing the original data to manageable dimensions while still representing essential information for downstream analysis. In classical machine learning, variational autoencoders (VAEs) facilitate efficient data compression, representation learning for subsequent tasks, and novel data generation. However, no model has been proposed that exactly captures all of these features for direct application to quantum data on quantum computers. Some existing quantum models for data compression lack regularization of latent representations, thus preventing direct use for generation and control of generalization. Others are hybrid models with only some internal quantum components, impeding direct training on quantum data. To bridge this gap, we present a fully quantum framework, ?-QVAE, which encompasses all the capabilities of classical VAEs and can be directly applied for both classical and quantum data compression. Our model utilizes regularized mixed states to attain optimal latent representations. It accommodates various divergences for reconstruction and regularization. Furthermore, by accommodating mixed states at every stage, it can utilize the full-data density matrix and allow for a “global” training objective. Doing so, in turn, makes efficient optimization possible and has potential implications for private and federated learning. In addition to exploring the theoretical properties of ?-QVAE, we demonstrate its performance on representative genomics and synthetic data. Our results consistently indicate that ?-QVAE exhibits similar or better performance compared to matched classical models.

Predicting Spatially Resolved Gene Expression via Tissue Morphology using Adaptive Spatial GNNs

Motivation Spatial transcriptomics technologies, which generate a spatial map of gene activity, can deepen the understanding of tissue architecture and its molecular underpinnings in health and disease. However, the high cost makes these technologies difficult to use in practice. Histological images co-registered with targeted tissues are more affordable and routinely generated in many research and clinical studies. Hence, predicting spatial gene expression from the morphological clues embedded in tissue histological images, provides a scalable alternative approach to decoding tissue complexity