Abstract Epigenomics is the study of molecular signatures associated with discrete regions within genomes, many of which are important for a wide range of nuclear processes. The ability to profile the epigenomic landscape associated with genes, repetitive regions, transposons, transcription, differential expression, cis-regulatory elements, and 3D chromatin interactions has vastly improved our understanding of plant genomes. However, many epigenomic and single-cell genomic assays are challenging to perform in plants, leading to a wide range of data quality issues; thus, the data require rigorous evaluation prior to downstream analyses and interpretation. In this commentary, we provide considerations for the evaluation of plant epigenomics and single-cell genomics data quality with the aim of improving the quality and utility of studies using those data across diverse plant species.
more »
« less
Interpretation of deep learning in genomics and epigenomics
Abstract Machine learning methods have been widely applied to big data analysis in genomics and epigenomics research. Although accuracy and efficiency are common goals in many modeling tasks, model interpretability is especially important to these studies towards understanding the underlying molecular and cellular mechanisms. Deep neural networks (DNNs) have recently gained popularity in various types of genomic and epigenomic studies due to their capabilities in utilizing large-scale high-throughput bioinformatics data and achieving high accuracy in predictions and classifications. However, DNNs are often challenged by their potential to explain the predictions due to their black-box nature. In this review, we present current development in the model interpretation of DNNs, focusing on their applications in genomics and epigenomics. We first describe state-of-the-art DNN interpretation methods in representative machine learning fields. We then summarize the DNN interpretation methods in recent studies on genomics and epigenomics, focusing on current data- and computing-intensive topics such as sequence motif identification, genetic variations, gene expression, chromatin interactions and non-coding RNAs. We also present the biological discoveries that resulted from these interpretation methods. We finally discuss the advantages and limitations of current interpretation approaches in the context of genomic and epigenomic studies. Contact:xiaoman@mail.ucf.edu, haihu@cs.ucf.edu
more »
« less
- Award ID(s):
- 1661414
- NSF-PAR ID:
- 10233703
- Date Published:
- Journal Name:
- Briefings in Bioinformatics
- Volume:
- 22
- Issue:
- 3
- ISSN:
- 1467-5463
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
Deep neural networks (DNNs) have gained considerable attention in various real-world applications due to the strong performance on representation learning. However, a DNN needs to be trained many epochs for pursuing a higher inference accuracy, which requires storing sequential versions of DNNs and releasing the updated versions to users. As a result, large amounts of storage and network resources are required, which significantly hamper DNN utilization on resource-constrained platforms (e.g., IoT, mobile phone). In this paper, we present a novel delta compression framework called Delta-DNN, which can efficiently compress the float-point numbers in DNNs by exploiting the floats similarity existing in DNNs during training. Specifically, (1) we observe the high similarity of float-point numbers between the neighboring versions of a neural network in training; (2) inspired by delta compression technique, we only record the delta (i.e., the differences) between two neighboring versions, instead of storing the full new version for DNNs; (3) we use the error-bounded lossy compression to compress the delta data for a high compression ratio, where the error bound is strictly assessed by an acceptable loss of DNNs’ inference accuracy; (4) we evaluate Delta-DNN’s performance on two scenarios, including reducing the transmission of releasing DNNs over network and saving the storage space occupied by multiple versions of DNNs. According to experimental results on six popular DNNs, DeltaDNN achieves the compression ratio 2x~10x higher than state-ofthe-art methods, while without sacrificing inference accuracy and changing the neural network structure.more » « less
-
null (Ed.)Abstract Radiogenomics uses machine-learning (ML) to directly connect the morphologic and physiological appearance of tumors on clinical imaging with underlying genomic features. Despite extensive growth in the area of radiogenomics across many cancers, and its potential role in advancing clinical decision making, no published studies have directly addressed uncertainty in these model predictions. We developed a radiogenomics ML model to quantify uncertainty using transductive Gaussian Processes (GP) and a unique dataset of 95 image-localized biopsies with spatially matched MRI from 25 untreated Glioblastoma (GBM) patients. The model generated predictions for regional EGFR amplification status (a common and important target in GBM) to resolve the intratumoral genetic heterogeneity across each individual tumor—a key factor for future personalized therapeutic paradigms. The model used probability distributions for each sample prediction to quantify uncertainty, and used transductive learning to reduce the overall uncertainty. We compared predictive accuracy and uncertainty of the transductive learning GP model against a standard GP model using leave-one-patient-out cross validation. Additionally, we used a separate dataset containing 24 image-localized biopsies from 7 high-grade glioma patients to validate the model. Predictive uncertainty informed the likelihood of achieving an accurate sample prediction. When stratifying predictions based on uncertainty, we observed substantially higher performance in the group cohort (75% accuracy, n = 95) and amongst sample predictions with the lowest uncertainty (83% accuracy, n = 72) compared to predictions with higher uncertainty (48% accuracy, n = 23), due largely to data interpolation (rather than extrapolation). On the separate validation set, our model achieved 78% accuracy amongst the sample predictions with lowest uncertainty. We present a novel approach to quantify radiogenomics uncertainty to enhance model performance and clinical interpretability. This should help integrate more reliable radiogenomics models for improved medical decision-making.more » « less
-
null (Ed.)Security of machine learning is increasingly becoming a major concern due to the ubiquitous deployment of deep learning in many security-sensitive domains. Many prior studies have shown external attacks such as adversarial examples that tamper the integrity of DNNs using maliciously crafted inputs. However, the security implication of internal threats (i.e., hardware vulnerabilities) to DNN models has not yet been well understood. In this paper, we demonstrate the first hardware-based attack on quantized deep neural networks–DeepHammer–that deterministically induces bit flips in model weights to compromise DNN inference by exploiting the rowhammer vulnerability. DeepHammer performs an aggressive bit search in the DNN model to identify the most vulnerable weight bits that are flippable under system constraints. To trigger deterministic bit flips across multiple pages within a reasonable amount of time, we develop novel system-level techniques that enable fast deployment of victim pages, memory-efficient rowhammering and precise flipping of targeted bits. DeepHammer can deliberately degrade the inference accuracy of the victim DNN system to a level that is only as good as random guess, thus completely depleting the intelligence of targeted DNN systems. We systematically demonstrate our attacks on real systems against 11 DNN architectures with 4 datasets corresponding to different application domains. Our evaluation shows that DeepHammer is able to successfully tamper DNN inference behavior at run-time within a few minutes. We further discuss several mitigation techniques from both algorithm and system levels to protect DNNs against such attacks. Our work highlights the need to incorporate security mechanisms in future deep learning systems to enhance the robustness against hardware-based deterministic fault injections.more » « less
-
Model compression is an important technique to facilitate efficient embedded and hardware implementations of deep neural networks (DNNs), a number of prior works are dedicated to model compression techniques. The target is to simultaneously reduce the model storage size and accelerate the computation, with minor effect on accuracy. Two important categories of DNN model compression techniques are weight pruning and weight quantization. The former leverages the redundancy in the number of weights, whereas the latter leverages the redundancy in bit representation of weights. These two sources of redundancy can be combined, thereby leading to a higher degree of DNN model compression. However, a systematic framework of joint weight pruning and quantization of DNNs is lacking, thereby limiting the available model compression ratio. Moreover, the computation reduction, energy efficiency improvement, and hardware performance overhead need to be accounted besides simply model size reduction, and the hardware performance overhead resulted from weight pruning method needs to be taken into consideration. To address these limitations, we present ADMM-NN, the first algorithm-hardware co-optimization framework of DNNs using Alternating Direction Method of Multipliers (ADMM), a powerful technique to solve non-convex optimization problems with possibly combinatorial constraints. The first part of ADMM-NN is a systematic, joint framework of DNN weight pruning and quantization using ADMM. It can be understood as a smart regularization technique with regularization target dynamically updated in each ADMM iteration, thereby resulting in higher performance in model compression than the state-of-the-art. The second part is hardware-aware DNN optimizations to facilitate hardware-level implementations. We perform ADMM-based weight pruning and quantization considering (i) the computation reduction and energy efficiency improvement, and (ii) the hardware performance overhead due to irregular sparsity. The first requirement prioritizes the convolutional layer compression over fully-connected layers, while the latter requires a concept of the break-even pruning ratio, defined as the minimum pruning ratio of a specific layer that results in no hardware performance degradation. Without accuracy loss, ADMM-NN achieves 85× and 24× pruning on LeNet-5 and AlexNet models, respectively, --- significantly higher than the state-of-the-art. The improvements become more significant when focusing on computation reduction. Combining weight pruning and quantization, we achieve 1,910× and 231× reductions in overall model size on these two benchmarks, when focusing on data storage. Highly promising results are also observed on other representative DNNs such as VGGNet and ResNet-50. We release codes and models at https://github.com/yeshaokai/admm-nn.more » « less
- Free Publicly Accessible Full Text
-
Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.1093/bib/bbaa177
