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Although the expenses associated with DNA sequencing have been rapidly decreasing, the current cost stands at roughly \$1.3K/TB, which is dramatically more expensive than reading from existing archival storage solutions today. In this work, we aim to reduce not only the cost but also the latency of DNA storage by studying the DNA coverage depth problem, which aims to reduce the required number of reads to retrieve information from the storage system. Under this framework, our main goal is to understand how to optimally pair an error-correcting code with a given retrieval algorithm to minimize the sequencing coverage depth, while guaranteeing retrieval of the information with high probability. Additionally, we study the DNA coverage depth problem under the random-access setup.

Cross-modal contrastive learning in vision language pretraining (VLP) faces the challenge of (partial) false negatives. In this paper, we study this problem from the perspective of Mutual Information (MI) optimization. It is common sense that InfoNCE loss used in contrastive learning will maximize the lower bound of MI between anchors and their positives, while we theoretically prove that MI involving negatives also matters when noises commonly exist. Guided by a more general lower bound form for optimization, we propose a contrastive learning strategy regulated by progressively refined cross-modal similarity, to more accurately optimize MI between an image/text anchor and its negative texts/images instead of improperly minimizing it. Our method performs competitively on four downstream cross-modal tasks and systematically balances the beneficial and harmful effects of (partial) false negative samples under theoretical guidance.

'Mahabharata' is the most popular among many Indian pieces of literature referred to in many domains for completely different purposes. This text itself is having various dimension and aspects which is useful for the human being in their personal life and professional life. This Indian Epic is originally written in the Sanskrit Language. Now in the era of Natural Language Processing, Artificial Intelligence, Machine Learning, and Human-Computer interaction this text can be processed according to the domain requirement. It is interesting to process this text and get useful insights from Mahabharata. The limitation of the humans while analyzing Mahabharata is that they always have a sentiment aspect towards the story narrated by the author. Apart from that, the human cannot memorize statistical or computational details, like which two words are frequently coming in one sentence? What is the average length of the sentences across the whole literature? Which word is the most popular word across the text, what are the lemmas of the words used across the sentences? Thus, in this paper, we propose an NLP pipeline to get some statistical and computational insights along with the most relevant word searching method from the largest epic 'Mahabharata'. We stacked the different text-processing approaches to articulate the best results which can be further used in the various domain where Mahabharata needs to be referred.

Leveraging medical record information in the era of big data and machine learning comes with the caveat that data must be cleaned and deidentified. Facilitating data sharing and harmonization for multi-center collaborations are particularly difficult when protected health information (PHI) is contained or embedded in image meta-data. We propose a novel library in the Python framework, called PyLogik, to help alleviate this issue for ultrasound images, which are particularly challenging because of the frequent inclusion of PHI directly on the images. PyLogik processes the image volumes through a series of text detection/extraction, filtering, thresholding, morphological and contour comparisons. This methodology deidentifies the images, reduces file sizes, and prepares image volumes for applications in deep learning and data sharing. To evaluate its effectiveness in the identification of regions of interest (ROI), a random sample of 50 cardiac ultrasounds (echocardiograms) were processed through PyLogik, and the outputs were compared with the manual segmentations by an expert user. The Dice coefficient of the two approaches achieved an average value of 0.976. Next, an investigation was conducted to ascertain the degree of information compression achieved using the algorithm. Resultant data was found to be on average approximately 72% smaller after processing by PyLogik. Our results suggest that PyLogik is a viable methodology for ultrasound data cleaning and deidentification, determining ROI, and file compression which will facilitate efficient storage, use, and dissemination of ultrasound data.

Recently, significant advancements have been made in time-series forecasting research, with an increasing focus on analyzing the inherent characteristics of time-series data, rather than solely focusing on designing forecasting models.In this paper, we follow this trend and carefully examine previous work to propose an efficient time series forecasting model based on linear models. The model consists of two important core components: (1) the integration of different semantics brought by single-channel and multi-channel data for joint forecasting; (2) the use of a novel loss function that replaces the traditional MSE loss and MAE loss to achieve higher forecasting accuracy.On widely-used benchmark time series datasets, our model not only outperforms the current SOTA, but is also 10 $\times$ speedup and has fewer parameters than the latest SOTA model.

Achieving high-quality semantic segmentation predictions using only image-level labels enables a new level of real-world applicability. Although state-of-the-art networks deliver reliable predictions, the amount of handcrafted pixel-wise annotations to enable these results are not feasible in many real-world applications. Hence, several works have already targeted this bottleneck, using classifier-based networks like Class Activation Maps~\cite{CAM} (CAMs) as a base. Addressing CAM's weaknesses of fuzzy borders and incomplete predictions, state-of-the-art approaches rely only on adding regulations to the classifier loss or using pixel-similarity-based refinement after the fact. We propose a framework that introduces an additional module using object perimeters for improved saliency. We define object perimeter information as the line separating the object and background. Our new PerimeterFit module will be applied to pre-refine the CAM predictions before using the pixel-similarity-based network. In this way, our PerimeterFit increases the quality of the CAM prediction while simultaneously improving the false negative rate. We investigated a wide range of state-of-the-art unsupervised semantic segmentation networks and edge detection techniques to create useful perimeter maps, which enable our framework to predict object locations with sharper perimeters. We achieved up to 1.5% improvement over frameworks without our PerimeterFit module. We conduct an exhaustive analysis to illustrate that SILOP enhances existing state-of-the-art frameworks for image-level-based semantic segmentation. The framework is open-source and accessible online at //github.com/ErikOstrowski/SILOP.

Since the inception of human research studies, researchers often need to interact with participants on a set schedule to collect data. While some human research is automated, most is not; which costs researchers both time and money. Usually, user-provided data collection consists of surveys administered via telephone or email. While these methods are simplest, they are tedious for the survey administrators, which could incur fatigue and potentially lead to collection mistakes. A solution to this was the creation of "chatbots". Early developments relied on mostly rule-based tactics (e.g. ELIZA), which were suitable for uniform input. However, as the complexity of interactions increases, rule-based systems begin breaking down since there exist a variety of ways for a user to express the same intention. This is especially true when tracking states within a research study (or protocol). Recently, natural language processing (NLP) models and, subsequently, virtual assistants have become increasingly more sophisticated when communicating with users. Examples of these efforts range from research studies to commercial health products. This project leverages recent advancements in conversational artificial intelligence (AI), speech-to-text, natural language understanding (NLU), and finite-state machines to automate protocols, specifically in research settings. This application must be generalized, fully customizable, and irrespective of any research study. These parameters allow new research protocols to be created quickly once envisioned. With this in mind, I present SmartState, a fully-customizable, state-driven protocol manager combined with supporting AI components to autonomously manage user data and intelligently determine the intention of users through chat and end device interactions to drive protocols.

For invasive breast cancer, immunohistochemical (IHC) techniques are often used to detect the expression level of human epidermal growth factor receptor-2 (HER2) in breast tissue to formulate a precise treatment plan. From the perspective of saving manpower, material and time costs, directly generating IHC-stained images from hematoxylin and eosin (H&E) stained images is a valuable research direction. Therefore, we held the breast cancer immunohistochemical image generation challenge, aiming to explore novel ideas of deep learning technology in pathological image generation and promote research in this field. The challenge provided registered H&E and IHC-stained image pairs, and participants were required to use these images to train a model that can directly generate IHC-stained images from corresponding H&E-stained images. We selected and reviewed the five highest-ranking methods based on their PSNR and SSIM metrics, while also providing overviews of the corresponding pipelines and implementations. In this paper, we further analyze the current limitations in the field of breast cancer immunohistochemical image generation and forecast the future development of this field. We hope that the released dataset and the challenge will inspire more scholars to jointly study higher-quality IHC-stained image generation.

It is always well believed that modeling relationships between objects would be helpful for representing and eventually describing an image. Nevertheless, there has not been evidence in support of the idea on image description generation. In this paper, we introduce a new design to explore the connections between objects for image captioning under the umbrella of attention-based encoder-decoder framework. Specifically, we present Graph Convolutional Networks plus Long Short-Term Memory (dubbed as GCN-LSTM) architecture that novelly integrates both semantic and spatial object relationships into image encoder. Technically, we build graphs over the detected objects in an image based on their spatial and semantic connections. The representations of each region proposed on objects are then refined by leveraging graph structure through GCN. With the learnt region-level features, our GCN-LSTM capitalizes on LSTM-based captioning framework with attention mechanism for sentence generation. Extensive experiments are conducted on COCO image captioning dataset, and superior results are reported when comparing to state-of-the-art approaches. More remarkably, GCN-LSTM increases CIDEr-D performance from 120.1% to 128.7% on COCO testing set.

This paper discusses and demonstrates the outcomes from our experimentation on Image Captioning. Image captioning is a much more involved task than image recognition or classification, because of the additional challenge of recognizing the interdependence between the objects/concepts in the image and the creation of a succinct sentential narration. Experiments on several labeled datasets show the accuracy of the model and the fluency of the language it learns solely from image descriptions. As a toy application, we apply image captioning to create video captions, and we advance a few hypotheses on the challenges we encountered.