Anatomic tracing data provides detailed information on brain circuitry essential for addressing some of the common errors in diffusion MRI tractography. However, automated detection of fiber bundles on tracing data is challenging due to sectioning distortions, presence of noise and artifacts and intensity/contrast variations. In this work, we propose a deep learning method with a self-supervised loss function that takes anatomy-based constraints into account for accurate segmentation of fiber bundles on the tracer sections from macaque brains. Also, given the limited availability of manual labels, we use a semi-supervised training technique for efficiently using unlabeled data to improve the performance, and location constraints for further reduction of false positives. Evaluation of our method on unseen sections from a different macaque yields promising results with a true positive rate of 0.90. The code for our method is available at https://github.com/v-sundaresan/

Human leukocyte antigen (HLA) is an important molecule family in the field of human immunity, which recognizes foreign threats and triggers immune responses by presenting peptides to T cells. In recent years, the synthesis of tumor vaccines to induce specific immune responses has become the forefront of cancer treatment. Computationally modeling the binding patterns between peptide and HLA can greatly accelerate the development of tumor vaccines. However, most of the prediction methods performance is very limited and they cannot fully take advantage of the analysis of existing biological knowledge as the basis of modeling. In this paper, we propose TripHLApan, a novel pan-specific prediction model, for HLA molecular peptide binding prediction. TripHLApan exhibits powerful prediction ability by integrating triple coding matrix, BiGRU + Attention models, and transfer learning strategy. The comprehensive evaluations demonstrate the effectiveness of TripHLApan in predicting HLA-I and HLA-II peptide binding in different test environments. The predictive power of HLA-I is further demonstrated in the latest data set. In addition, we show that TripHLApan has strong binding reconstitution ability in the samples of a melanoma patient. In conclusion, TripHLApan is a powerful tool for predicting the binding of HLA-I and HLA-II molecular peptides for the synthesis of tumor vaccines.

Pancreatic cancer is one of the global leading causes of cancer-related deaths. Despite the success of Deep Learning in computer-aided diagnosis and detection (CAD) methods, little attention has been paid to the detection of Pancreatic Cancer. We propose a method for detecting pancreatic tumor that utilizes clinically-relevant features in the surrounding anatomical structures, thereby better aiming to exploit the radiologist's knowledge compared to other, conventional deep learning approaches. To this end, we collect a new dataset consisting of 99 cases with pancreatic ductal adenocarcinoma (PDAC) and 97 control cases without any pancreatic tumor. Due to the growth pattern of pancreatic cancer, the tumor may not be always visible as a hypodense lesion, therefore experts refer to the visibility of secondary external features that may indicate the presence of the tumor. We propose a method based on a U-Net-like Deep CNN that exploits the following external secondary features: the pancreatic duct, common bile duct and the pancreas, along with a processed CT scan. Using these features, the model segments the pancreatic tumor if it is present. This segmentation for classification and localization approach achieves a performance of 99% sensitivity (one case missed) and 99% specificity, which realizes a 5% increase in sensitivity over the previous state-of-the-art method. The model additionally provides location information with reasonable accuracy and a shorter inference time compared to previous PDAC detection methods. These results offer a significant performance improvement and highlight the importance of incorporating the knowledge of the clinical expert when developing novel CAD methods.

Recognizing objects in dense clutter accurately plays an important role to a wide variety of robotic manipulation tasks including grasping, packing, rearranging and many others. However, conventional visual recognition models usually miss objects because of the significant occlusion among instances and causes incorrect prediction due to the visual ambiguity with the high object crowdedness. In this paper, we propose an interactive exploration framework called Smart Explorer for recognizing all objects in dense clutters. Our Smart Explorer physically interacts with the clutter to maximize the recognition performance while minimize the number of motions, where the false positives and negatives can be alleviated effectively with the optimal accuracy-efficiency trade-offs. Specifically, we first collect the multi-view RGB-D images of the clutter and reconstruct the corresponding point cloud. By aggregating the instance segmentation of RGB images across views, we acquire the instance-wise point cloud partition of the clutter through which the existed classes and the number of objects for each class are predicted. The pushing actions for effective physical interaction are generated to sizably reduce the recognition uncertainty that consists of the instance segmentation entropy and multi-view object disagreement. Therefore, the optimal accuracy-efficiency trade-off of object recognition in dense clutter is achieved via iterative instance prediction and physical interaction. Extensive experiments demonstrate that our Smart Explorer acquires promising recognition accuracy with only a few actions, which also outperforms the random pushing by a large margin.

Fatal diseases, as Critical Health Episodes (CHEs), represent real dangers for patients hospitalized in Intensive Care Units. These episodes can lead to irreversible organ damage and death. Nevertheless, diagnosing them in time would greatly reduce their inconvenience. This study therefore focused on building a highly effective early warning system for CHEs such as Acute Hypotensive Episodes and Tachycardia Episodes. To facilitate the precocity of the prediction, a gap of one hour was considered between the observation periods (Observation Windows) and the periods during which a critical event can occur (Target Windows). The MIMIC II dataset was used to evaluate the performance of the proposed system. This system first includes extracting additional features using three different modes. Then, the feature selection process allowing the selection of the most relevant features was performed using the Mutual Information Gain feature importance. Finally, the high-performance predictive model LightGBM was used to perform episode classification. This approach called MIG-LightGBM was evaluated using five different metrics: Event Recall (ER), Reduced Precision (RP), average Anticipation Time (aveAT), average False Alarms (aveFA), and Event F1-score (EF1-score). A method is therefore considered highly efficient for the early prediction of CHEs if it exhibits not only a large aveAT but also a large EF1-score and a low aveFA. Compared to systems using Extreme Gradient Boosting, Support Vector Classification or Naive Bayes as a predictive model, the proposed system was found to be highly dominant. It also confirmed its superiority over the Layered Learning approach.

The real-time segmentation of drivable areas plays a vital role in accomplishing autonomous perception in cars. Recently there have been some rapid strides in the development of image segmentation models using deep learning. However, most of the advancements have been made in model architecture design. In solving any supervised deep learning problem related to segmentation, the success of the model that one builds depends upon the amount and quality of input training data we use for that model. This data should contain well-annotated varied images for better working of the segmentation model. Issues like this pertaining to annotations in a dataset can lead the model to conclude with overwhelming Type I and II errors in testing and validation, causing malicious issues when trying to tackle real world problems. To address this problem and to make our model more accurate, dynamic, and robust, data augmentation comes into usage as it helps in expanding our sample training data and making it better and more diversified overall. Hence, in our study, we focus on investigating the benefits of data augmentation by analyzing pre-existing image datasets and performing augmentations accordingly. Our results show that the performance and robustness of existing state of the art (or SOTA) models can be increased dramatically without any increase in model complexity or inference time. The augmentations decided on and used in this paper were decided only after thorough research of several other augmentation methodologies and strategies and their corresponding effects that are in widespread usage today. All our results are being reported on the widely used Cityscapes Dataset.

Globally, the number of obese patients has doubled due to sedentary lifestyles and improper dieting. The tremendous increase altered human genetics, and health. According to the world health organization, Life expectancy dropped from 80 to 75 years, as obese people struggle with different chronic diseases. This report will address the problems of obesity in children and adults using ML datasets to feature, predict, and analyze the causes of obesity. By engaging neural ML networks, we will explore neural control using diffusion tensor imaging to consider body fats, BMI, waist \& hip ratio circumference of obese patients. To predict the present and future causes of obesity with ML, we will discuss ML techniques like decision trees, SVM, RF, GBM, LASSO, BN, and ANN and use datasets implement the stated algorithms. Different theoretical literature from experts ML \& Bioinformatics experiments will be outlined in this report while making recommendations on how to advance ML for predicting obesity and other chronic diseases.

We develop a Bayesian approach to predict a continuous or binary outcome from data that are collected from multiple sources with a multi-way (i.e.. multidimensional tensor) structure. As a motivating example we consider molecular data from multiple 'omics sources, each measured over multiple developmental time points, as predictors of early-life iron deficiency (ID) in a rhesus monkey model. We use a linear model with a low-rank structure on the coefficients to capture multi-way dependence and model the variance of the coefficients separately across each source to infer their relative contributions. Conjugate priors facilitate an efficient Gibbs sampling algorithm for posterior inference, assuming a continuous outcome with normal errors or a binary outcome with a probit link. Simulations demonstrate that our model performs as expected in terms of misclassification rates and correlation of estimated coefficients with true coefficients, with large gains in performance by incorporating multi-way structure and modest gains when accounting for differing signal sizes across the different sources. Moreover, it provides robust classification of ID monkeys for our motivating application. Software in the form of R code is available at https://github.com/BiostatsKim/BayesMSMW .

Recent advances in the fingerprinting of deep neural networks detect instances of models, placed in a black-box interaction scheme. Inputs used by the fingerprinting protocols are specifically crafted for each precise model to be checked for. While efficient in such a scenario, this nevertheless results in a lack of guarantee after a mere modification (like retraining, quantization) of a model. This paper tackles the challenges to propose i) fingerprinting schemes that are resilient to significant modifications of the models, by generalizing to the notion of model families and their variants, ii) an extension of the fingerprinting task encompassing scenarios where one wants to fingerprint not only a precise model (previously referred to as a detection task) but also to identify which model family is in the black-box (identification task). We achieve both goals by demonstrating that benign inputs, that are unmodified images, for instance, are sufficient material for both tasks. We leverage an information-theoretic scheme for the identification task. We devise a greedy discrimination algorithm for the detection task. Both approaches are experimentally validated over an unprecedented set of more than 1,000 networks.

Bloom filters are widely used data structures that compactly represent sets of elements. Querying a Bloom filter reveals if an element is not included in the underlying set or is included with a certain error rate. This membership testing can be modeled as a binary classification problem and solved through deep learning models, leading to what is called learned Bloom filters. We have identified that the benefits of learned Bloom filters are apparent only when considering a vast amount of data, and even then, there is a possibility to further reduce their memory consumption. For that reason, we introduce a lossless input compression technique that improves the memory consumption of the learned model while preserving a comparable model accuracy. We evaluate our approach and show significant memory consumption improvements over learned Bloom filters.