Christof Angermueller
Machine learning + Bio
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A Flexible Approach to Autotuning Multi-Pass Machine Learning Compilers
Berkin Ilbeyi
Bjarke Roune
Blake Hechtman
Emma Wang
Karthik Srinivasa Murthy
Mike Burrows
Nikhil Sarda
Rezsa Farahani
Samuel J. Kaufman
Shen Wang
Sudip Roy
Yuanzhong Xu
PACT (2021)
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Search-based techniques have been demonstrated effective in solving complex optimization problems that arise in domain-specific compilers for machine learning (ML). Unfortunately, deploying such techniques in production compilers is impeded by two limitations. First, prior works require factorization of a computation graph into smaller subgraphs over which search is applied. This decomposition is not only non-trivial but also significantly limits the scope of optimization. Second, prior works require search to be applied in a single stage in the compilation flow, which does not fit with the multi-stage layered architecture of most production ML compilers.
This paper presents XTAT, an autotuner for production ML compilers that can tune both graph-level and subgraph-level optimizations across multiple compilation stages. XTAT applies XTAT-M, a flexible search methodology that defines a search formulation for joint optimizations by accurately modeling the interactions between different compiler passes. XTAT tunes tensor layouts, operator fusion decisions, tile sizes, and code generation parameters in XLA, a production ML compiler, using various search strategies. In an evaluation across 150 ML training and inference models on Tensor Processing Units (TPUs) at Google, XTAT offers up to 2.4x and an average 5% execution time speedup over the heavily-optimized XLA compiler.
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Agreement Between Saliency Maps and Human-Labeled Regions of Interest: Applications to Skin Disease Classification
Singh Nalini
Kang Lee
Susan Huang
Aaron Loh
2020 IEEE/CVF Conference on Computer Vision and Pattern Recognition Workshops (CVPRW) (2020)
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We propose to systematically identify potentially problematic patterns in skin disease classification models via quantitative analysis of agreement between saliency maps and human-labeled regions of interest. We further compute summary statistics describing patterns in this agreement for various stratifications of input examples. Through this analysis, we discover candidate spurious associations learned by the classifier and suggest next steps to handle such associations. Our approach can be used as a debugging tool to systematically spot difficult examples and error categories. Insights from this analysis could guide targeted data collection and improve model generalizability.
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Population Based Optimization for Biological Sequence Design
Zelda Mariet
David Martin Dohan
ICML 2020 (2020)
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The use of black-box optimization for the design of new biological sequences is an emerging research area with potentially revolutionary impact. The cost and latency of wet-lab experiments requires methods that find good sequences in few experimental rounds of large batches of sequences --- a setting that off-the-shelf black-box optimization methods are ill-equipped to handle. We find that the performance of existing methods varies drastically across optimization tasks, posing a significant obstacle to real-world applications. To improve robustness, we propose population-based optimization (PBO), which generates batches of sequences by sampling from an ensemble of methods. The number of sequences sampled from any method is proportional to the quality of sequences it previously proposed, allowing PBO to combine the strengths of individual methods while hedging against their innate brittleness. Adapting the population of methods online using evolutionary optimization further improves performance. Through extensive experiments on in-silico optimization tasks, we show that PBO outperforms any single method in its population, proposing both higher quality single sequences as well as more diverse batches. By its robustness and ability to design diverse, high-quality sequences, PBO is shown to be a new state-of-the art approach to the batched black-box optimization of biological sequences.
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Model-Based Reinforcement Learning for Biological Sequence Design
David Dohan
Ramya Deshpande
ICLR 2020 (2020)
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Being able to design biological sequences like DNA or proteins to have desired properties would have considerable impact in medical and industrial applications. However, doing so presents a challenging black-box optimization problem that requires multiple rounds of expensive, time-consuming experiments. In response, we propose using reinforcement learning (RL) for biological sequence design. RL is a flexible framework that allows us to optimize generative sequence policies to achieve a variety of criteria, including diversity among high-quality sequences discovered. We use model-based RL to improve sample efficiency, where at each round the policy is trained offline using a simulator fit on functional measurements from prior rounds. To accommodate the growing number of observations across rounds, the simulator model is automatically selected at each round from a pool of diverse models of varying capacity. On the tasks of designing DNA transcription factor binding sites, designing antimicrobial proteins, and optimizing the energy of Ising models based on protein structures, we find that model-based RL is an attractive alternative to existing methods.
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Apollo: Transferable Architecture Exploration
Albin Jones
Ravi Narayanaswami
Sat Chatterjee
ML for Systems Workshop at NeurIPS 2020
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The looming end of Moore's Law and ascending use of deep learning drives the design of custom accelerators that are optimized for specific neural architectures.
Accelerator design forms a challenging constrained optimization problem over a complex, high-dimensional and structured input space with a costly to evaluate objective function. Existing approaches for accelerator design are sample-inefficient do not transfer knowledge between related optimizations tasks with different design constraints (e.g. area budget) or neural architecture configurations. In this work, we propose a transferable architecture exploration framework, dubbed Apollo, that leverages recent advances in black-box function optimization for sample-efficient accelerator design. We use Apollo to optimize accelerator configurations of a diverse set of neural architectures with alternative design constraints. We show that Apollo finds optimal design configurations more sample-efficiently than baseline approaches. We further show that transferring knowledge between target architectures with different design constraints helps to find optimal configurations faster. This encouraging outcome portrays a promising path forward in shortening the timeline for accelerator design.
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A Comparison of Generative Models for Sequence Design
David Dohan
Ramya Deshpande
Olivier Chapelle
Babak Alipanahi
Machine Learning in Computational Biology Workshop (2019)
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In this paper, we compare generative models of different complexity for designing DNA and protein sequences using the Cross Entropy Method.
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Biological Sequences Design using Batched Bayesian Optimization
Zelda Mariet
Ramya Deshpande
David Dohan
Olivier Chapelle
NeurIPS workshop on Bayesian Deep Learning (2019)
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Being able to effectively design biological sequences like DNA and proteins would have transformative impact on medicine. Currently, the most popular method in the life sciences for performing design is directed evolution,which explores sequence space by making small mutations to existing sequences.Alternatively, Bayesian optimization (BO) provides an attractive framework for model-based black-box optimization, and has achieved many recent successes in life sciences applications. However, within the ML community, most large-scale BO efforts have focused on hyper-parameter tuning. These methods often do not translate to biological sequence design, where the search space is over a discrete alphabet, wet-lab experiments are run with considerable parallelism (1K-100K sequences per batch), and experiments are sufficiently slow and expensive that only few rounds of experiments are feasible. This paper discusses the particularities of batched BO on a large discrete space, and investigates the design choices that must be made in order to obtain robust, scalable, and experimentally successful models within this unique context.
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Deep learning for predicting refractive error from retinal fundus images
Avinash Vaidyanathan Varadarajan
Katy Blumer
Reena Chopra
Pearse Keane
Lily Peng
IOVS (2018)
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Objective: Refractive error, one of the leading cause of visual impairment, can be corrected by simple interventions like prescribing eyeglasses, which often starts with autorefraction to estimate the refractive error. In this study, using deep learning, we trained a network to estimate refractive error from fundus photos only.
Design: Retrospective analysis.
Subjects, Participants, and/or Controls: Retinal fundus images from participants in the UK Biobank cohort, which were 45 degree field of view images and the AREDS clinical trial, which contained 30 degree field of view images.
Methods, Intervention, or Testing: Refractive error was measured by autorefraction in the UK Biobank dataset and subjective refraction in the AREDS dataset. We trained a deep learning algorithm to predict refractive error from the fundus photographs and tested the prediction of the algorithm to the documented refractive error measurement. Our model used attention for identifying features that are predictive for refractive error.
Main Outcome Measures: Mean average error (MAE) of the algorithm’s prediction compared to the refractive error obtained in the AREDS and UK Biobank.
Results: The resulting algorithm had a mean average error (MAE) of 0.56 diopters (95% CI: 0.55-0.56) for estimating spherical equivalent on the UK Biobank dataset and 0.91 diopters (95% CI: 0.89-0.92) for the AREDS dataset. The baseline expected MAE (obtained by simply predicting the mean of this population) is 1.81 diopters (95% CI: 1.79-1.84) for UK Biobank and 1.63 (95% CI: 1.60-1.67) for AREDS. Attention maps suggest that the foveal region is one of the most important areas that is used by the algorithm to make this prediction, though other regions also contribute to the prediction.
Conclusions: The ability to estimate refractive error with high accuracy from retinal fundus photos has not been previously known and demonstrates that deep learning can be applied to make novel predictions from medical images. In addition, given that several groups have recently shown that it is feasible to obtain retinal fundus photos using mobile phones and inexpensive attachments, this work may be particularly relevant in regions of the world where autorefractors may not be readily available.
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