Richard Chen

Guillaume Jaume, Anurag Vaidya, Richard Chen et al.

Integrating whole-slide images (WSIs) and bulk transcriptomics for predicting patient survival can improve our understanding of patient prognosis. However, this multimodal task is particularly challenging due to the different nature of these data: WSIs represent a very high-dimensional spatial description of a tumor, while bulk transcriptomics represent a global description of gene expression levels within that tumor. In this context, our work aims to address two key challenges: (1) how can we tokenize transcriptomics in a semantically meaningful and interpretable way?, and (2) how can we capture dense multimodal interactions between these two modalities? Specifically, we propose to learn biological pathway tokens from transcriptomics that can encode specific cellular functions. Together with histology patch tokens that encode the different morphological patterns in the WSI, we argue that they form appropriate reasoning units for downstream interpretability analyses. We propose fusing both modalities using a memory-efficient multimodal Transformer that can model interactions between pathway and histology patch tokens. Our proposed model, SURVPATH, achieves state-of-the-art performance when evaluated against both unimodal and multimodal baselines on five datasets from The Cancer Genome Atlas. Our interpretability framework identifies key multimodal prognostic factors, and, as such, can provide valuable insights into the interaction between genotype and phenotype, enabling a deeper understanding of the underlying biological mechanisms at play. We make our code public at: https://github.com/ajv012/SurvPath.

Anitha Kannan, Richard Chen, Vignesh Venkataraman et al.

The COVID-19 pandemic has magnified an already existing trend of people looking for healthcare solutions online. One class of solutions are symptom checkers, which have become very popular in the context of COVID-19. Traditional symptom checkers, however, are based on manually curated expert systems that are inflexible and hard to modify, especially in a quickly changing situation like the one we are facing today. That is why all COVID-19 existing solutions are manual symptom checkers that can only estimate the probability of this disease and cannot contemplate alternative hypothesis or come up with a differential diagnosis. While machine learning offers an alternative, the lack of reliable data does not make it easy to apply to COVID-19 either. In this paper we present an approach that combines the strengths of traditional AI expert systems and novel deep learning models. In doing so we can leverage prior knowledge as well as any amount of existing data to quickly derive models that best adapt to the current state of the world and latest scientific knowledge. We use the approach to train a COVID-19 aware differential diagnosis model that can be used for medical decision support both for doctors or patients. We show that our approach is able to accurately model new incoming data about COVID-19 while still preserving accuracy on conditions that had been modeled in the past. While our approach shows evident and clear advantages for an extreme situation like the one we are currently facing, we also show that its flexibility generalizes beyond this concrete, but very important, example.

Arthur G. Rattew, Shaohan Hu, Marco Pistoia et al.

Variational quantum algorithms have shown promise in numerous fields due to their versatility in solving problems of scientific and commercial interest. However, leading algorithms for Hamiltonian simulation, such as the Variational Quantum Eigensolver (VQE), use fixed preconstructed ansatzes, limiting their general applicability and accuracy. Thus, variational forms---the quantum circuits that implement ansatzes ---are either crafted heuristically or by encoding domain-specific knowledge. In this paper, we present an Evolutionary Variational Quantum Eigensolver (EVQE), a novel variational algorithm that uses evolutionary programming techniques to minimize the expectation value of a given Hamiltonian by dynamically generating and optimizing an ansatz. The algorithm is equally applicable to optimization problems in all domains, obtaining accurate energy evaluations with hardware-efficient ansatzes. In molecular simulations, the variational forms generated by EVQE are up to $18.6\times$ shallower and use up to $12\times$ fewer CX gates than those obtained by VQE with a unitary coupled cluster ansatz. EVQE demonstrates significant noise-resistance properties, obtaining results in noisy simulation with at least $3.6\times$ less error than VQE using any tested ansatz configuration. We successfully evaluated EVQE on a real 5-qubit IBMQ quantum computer. The experimental results, which we obtained both via simulation and on real quantum hardware, demonstrate the effectiveness of EVQE for general-purpose optimization on the quantum computers of the present and near future.