arXiv subjects

Joseph Paul Cohen

Publications and source records attributed to Joseph Paul Cohen.

52 records · Page 3Linked to original sources

arXiv2019

GradMask: Reduce Overfitting by Regularizing Saliency

With too few samples or too many model parameters, overfitting can inhibit the ability to generalise predictions to new data. Within medical imaging, this can occur when features are incorrectly assigned importance such as distinct hospital specific artifacts, leading to poor performance on a new dataset from a different institution without those features, which is undesirable. Most regularization methods do not explicitly penalize the incorrect association of these features to the target class and hence fail to address this issue. We propose a regularization method, GradMask, which penalizes saliency maps inferred from the classifier gradients when they are not consistent with the lesion segmentation. This prevents non-tumor related features to contribute to the classification of unhealthy samples. We demonstrate that this method can improve test accuracy between 1-3% compared to the baseline without GradMask, showing that it has an impact on reducing overfitting.

cs.CV↗

arXiv2018

Towards the Latent Transcriptome

In this work we propose a method to compute continuous embeddings for kmers from raw RNA-seq data, without the need for alignment to a reference genome. The approach uses an RNN to transform kmers of the RNA-seq reads into a 2 dimensional representation that is used to predict abundance of each kmer. We report that our model captures information of both DNA sequence similarity as well as DNA sequence abundance in the embedding latent space, that we call the Latent Transcriptome. We confirm the quality of these vectors by comparing them to known gene sub-structures and report that the latent space recovers exon information from raw RNA-Seq data from acute myeloid leukemia patients. Furthermore we show that this latent space allows the detection of genomic abnormalities such as translocations as well as patient-specific mutations, making this representation space both useful for visualization as well as analysis.

q-bio.GN↗

arXiv2018

A Survey of Mobile Computing for the Visually Impaired

The number of visually impaired or blind (VIB) people in the world is estimated at several hundred million. Based on a series of interviews with the VIB and developers of assistive technology, this paper provides a survey of machine-learning based mobile applications and identifies the most relevant applications. We discuss the functionality of these apps, how they align with the needs and requirements of the VIB users, and how they can be improved with techniques such as federated learning and model compression. As a result of this study we identify promising future directions of research in mobile perception, micro-navigation, and content-summarization.

cs.HC↗

arXiv2018

Distribution Matching Losses Can Hallucinate Features in Medical Image Translation

This paper discusses how distribution matching losses, such as those used in CycleGAN, when used to synthesize medical images can lead to mis-diagnosis of medical conditions. It seems appealing to use these new image synthesis methods for translating images from a source to a target domain because they can produce high quality images and some even do not require paired data. However, the basis of how these image translation models work is through matching the translation output to the distribution of the target domain. This can cause an issue when the data provided in the target domain has an over or under representation of some classes (e.g. healthy or sick). When the output of an algorithm is a transformed image there are uncertainties whether all known and unknown class labels have been preserved or changed. Therefore, we recommend that these translated images should not be used for direct interpretation (e.g. by doctors) because they may lead to misdiagnosis of patients based on hallucinated image features by an algorithm that matches a distribution. However there are many recent papers that seem as though this is the goal.

cs.CV↗

arXiv2018

Towards Gene Expression Convolutions using Gene Interaction Graphs

We study the challenges of applying deep learning to gene expression data. We find experimentally that there exists non-linear signal in the data, however is it not discovered automatically given the noise and low numbers of samples used in most research. We discuss how gene interaction graphs (same pathway, protein-protein, co-expression, or research paper text association) can be used to impose a bias on a deep model similar to the spatial bias imposed by convolutions on an image. We explore the usage of Graph Convolutional Neural Networks coupled with dropout and gene embeddings to utilize the graph information. We find this approach provides an advantage for particular tasks in a low data regime but is very dependent on the quality of the graph used. We conclude that more work should be done in this direction. We design experiments that show why existing methods fail to capture signal that is present in the data when features are added which clearly isolates the problem that needs to be addressed.

q-bio.GN↗

arXiv2018

Learning to rank for censored survival data

Survival analysis is a type of semi-supervised ranking task where the target output (the survival time) is often right-censored. Utilizing this information is a challenge because it is not obvious how to correctly incorporate these censored examples into a model. We study how three categories of loss functions, namely partial likelihood methods, rank methods, and our classification method based on a Wasserstein metric (WM) and the non-parametric Kaplan Meier estimate of the probability density to impute the labels of censored examples, can take advantage of this information. The proposed method allows us to have a model that predict the probability distribution of an event. If a clinician had access to the detailed probability of an event over time this would help in treatment planning. For example, determining if the risk of kidney graft rejection is constant or peaked after some time. Also, we demonstrate that this approach directly optimizes the expected C-index which is the most common evaluation metric for ranking survival models.

cs.LG↗

arXiv2017

XTreePath: A generalization of XPath to handle real world structural variation

We discuss a key problem in information extraction which deals with wrapper failures due to changing content templates. A good proportion of wrapper failures are due to HTML templates changing to cause wrappers to become incompatible after element inclusion or removal in a DOM (Tree representation of HTML). We perform a large-scale empirical analyses of the causes of shift and mathematically quantify the levels of domain difficulty based on entropy. We propose the XTreePath annotation method to captures contextual node information from the training DOM. We then utilize this annotation in a supervised manner at test time with our proposed Recursive Tree Matching method which locates nodes most similar in context recursively using the tree edit distance. The search is based on a heuristic function that takes into account the similarity of a tree compared to the structure that was present in the training data. We evaluate XTreePath using 117,422 pages from 75 diverse websites in 8 vertical markets. Our XTreePath method consistently outperforms XPath and a current commercial system in terms of successful extractions in a blackbox test. We make our code and datasets publicly available online.

cs.IR↗

arXiv2017

GibbsNet: Iterative Adversarial Inference for Deep Graphical Models

Directed latent variable models that formulate the joint distribution as $p(x,z) = p(z) p(x \mid z)$ have the advantage of fast and exact sampling. However, these models have the weakness of needing to specify $p(z)$, often with a simple fixed prior that limits the expressiveness of the model. Undirected latent variable models discard the requirement that $p(z)$ be specified with a prior, yet sampling from them generally requires an iterative procedure such as blocked Gibbs-sampling that may require many steps to draw samples from the joint distribution $p(x, z)$. We propose a novel approach to learning the joint distribution between the data and a latent code which uses an adversarially learned iterative procedure to gradually refine the joint distribution, $p(x, z)$, to better match with the data distribution on each step. GibbsNet is the best of both worlds both in theory and in practice. Achieving the speed and simplicity of a directed latent variable model, it is guaranteed (assuming the adversarial game reaches the virtual training criteria global minimum) to produce samples from $p(x, z)$ with only a few sampling iterations. Achieving the expressiveness and flexibility of an undirected latent variable model, GibbsNet does away with the need for an explicit $p(z)$ and has the ability to do attribute prediction, class-conditional generation, and joint image-attribute modeling in a single model which is not trained for any of these specific tasks. We show empirically that GibbsNet is able to learn a more complex $p(z)$ and show that this leads to improved inpainting and iterative refinement of $p(x, z)$ for dozens of steps and stable generation without collapse for thousands of steps, despite being trained on only a few steps.

stat.ML↗

arXiv2017

Count-ception: Counting by Fully Convolutional Redundant Counting

Counting objects in digital images is a process that should be replaced by machines. This tedious task is time consuming and prone to errors due to fatigue of human annotators. The goal is to have a system that takes as input an image and returns a count of the objects inside and justification for the prediction in the form of object localization. We repose a problem, originally posed by Lempitsky and Zisserman, to instead predict a count map which contains redundant counts based on the receptive field of a smaller regression network. The regression network predicts a count of the objects that exist inside this frame. By processing the image in a fully convolutional way each pixel is going to be accounted for some number of times, the number of windows which include it, which is the size of each window, (i.e., 32x32 = 1024). To recover the true count we take the average over the redundant predictions. Our contribution is redundant counting instead of predicting a density map in order to average over errors. We also propose a novel deep neural network architecture adapted from the Inception family of networks called the Count-ception network. Together our approach results in a 20% relative improvement (2.9 to 2.3 MAE) over the state of the art method by Xie, Noble, and Zisserman in 2016.

cs.CV↗

arXiv2017

ShortScience.org - Reproducing Intuition

We present ShortScience.org, a platform for post-publication discussion of research papers. On ShortScience.org, the research community can read and write summaries of papers in order to increase accessible and reproducibility. Summaries contain the perspective and insight of other readers, why they liked or disliked it, and their attempt to demystify complicated sections. ShortScience.org has over 600 paper summaries, all of which are searchable and organized by paper, conference, and year. Many regular contributors are expert machine learning researchers. We present statistics from the last year of operation, user demographics, and responses from a usage survey. Results indicate that ShortScience benefits students most, by providing short, understandable summaries reflecting expert opinions.

cs.DL↗

arXiv2017

RandomOut: Using a convolutional gradient norm to rescue convolutional filters

Filters in convolutional neural networks are sensitive to their initialization. The random numbers used to initialize filters are a bias and determine if you will "win" and converge to a satisfactory local minimum so we call this The Filter Lottery. We observe that the 28x28 Inception-V3 model without Batch Normalization fails to train 26% of the time when varying the random seed alone. This is a problem that affects the trial and error process of designing a network. Because random seeds have a large impact it makes it hard to evaluate a network design without trying many different random starting weights. This work aims to reduce the bias imposed by the initial weights so a network converges more consistently. We propose to evaluate and replace specific convolutional filters that have little impact on the prediction. We use the gradient norm to evaluate the impact of a filter on error, and re-initialize filters when the gradient norm of its weights falls below a specific threshold. This consistently improves accuracy on the 28x28 Inception-V3 with a median increase of +3.3%. In effect our method RandomOut increases the number of filters explored without increasing the size of the network. We observe that the RandomOut method has more consistent generalization performance, having a standard deviation of 1.3% instead of 2% when varying random seeds, and does so faster and with fewer parameters.

cs.CV↗

arXiv2016

Rapid building detection using machine learning

This work describes algorithms for performing discrete object detection, specifically in the case of buildings, where usually only low quality RGB-only geospatial reflective imagery is available. We utilize new candidate search and feature extraction techniques to reduce the problem to a machine learning (ML) classification task. Here we can harness the complex patterns of contrast features contained in training data to establish a model of buildings. We avoid costly sliding windows to generate candidates; instead we innovatively stitch together well known image processing techniques to produce candidates for building detection that cover 80-85% of buildings. Reducing the number of possible candidates is important due to the scale of the problem. Each candidate is subjected to classification which, although linear, costs time and prohibits large scale evaluation. We propose a candidate alignment algorithm to boost classification performance to 80-90% precision with a linear time algorithm and show it has negligible cost. Also, we propose a new concept called a Permutable Haar Mesh (PHM) which we use to form and traverse a search space to recover candidate buildings which were lost in the initial preprocessing phase.

cs.CV↗

arXiv2016

Academic Torrents: Scalable Data Distribution

As competitions get more popular, transferring ever-larger data sets becomes infeasible and costly. For example, downloading the 157.3 GB 2012 ImageNet data set incurs about $4.33 in bandwidth costs per download. Downloading the full ImageNet data set takes 33 days. ImageNet has since become popular beyond the competition, and many papers and models now revolve around this data set. For sharing such an important resource to the machine learning community, the sharers of ImageNet must shoulder a large bandwidth burden. Academic Torrents reduces this burden for disseminating competition data, and also increases download speeds for end users. Academic Torrents is run by a pending nonprofit.. By augmenting an existing HTTP server with a peer-to-peer swarm, requests get re-routed to get data from downloaders. While existing systems slow down with more users, the benefits of Academic Torrents grow, with noticeable effects even when only one other person is downloading.

cs.NI↗

arXiv2016

Crater Detection via Convolutional Neural Networks

Craters are among the most studied geomorphic features in the Solar System because they yield important information about the past and present geological processes and provide information about the relative ages of observed geologic formations. We present a method for automatic crater detection using advanced machine learning to deal with the large amount of satellite imagery collected. The challenge of automatically detecting craters comes from their is complex surface because their shape erodes over time to blend into the surface. Bandeira provided a seminal dataset that embodied this challenge that is still an unsolved pattern recognition problem to this day. There has been work to solve this challenge based on extracting shape and contrast features and then applying classification models on those features. The limiting factor in this existing work is the use of hand crafted filters on the image such as Gabor or Sobel filters or Haar features. These hand crafted methods rely on domain knowledge to construct. We would like to learn the optimal filters and features based on training examples. In order to dynamically learn filters and features we look to Convolutional Neural Networks (CNNs) which have shown their dominance in computer vision. The power of CNNs is that they can learn image filters which generate features for high accuracy classification.

cs.CV↗

arXiv2015

The cost of reading research. A study of Computer Science publication venues

What does the cost of academic publishing look like to the common researcher today? Our goal is to convey the current state of academic publishing, specifically in regards to the field of computer science and provide analysis and data to be used as a basis for future studies. We will focus on author and reader costs as they are the primary points of interaction within the publishing world. In this work, we restrict our focus to only computer science in order to make the data collection more feasible (the authors are computer scientists) and hope future work can analyze and collect data across all academic fields.

cs.DL↗

arXiv2013

Wireless Message Dissemination via Selective Relay over Bluetooth (MDSRoB)

This paper presents a wireless message dissemination method designed with no need to trust other users. This method utilizes modern wireless adaptors ability to broadcast device name and identification information. Using the scanning features built into Bluetooth and Wifi, messages can be exchanged via their device names. This paper outlines a method of interchanging multiple messages to discoverable and nondiscoverable devices using a user defined scanning interval method along with a response based system. By selectively relaying messages each user is in control of their involvement in the ad-hoc network.

cs.NI↗