Abstract

Synthetic ion channels are a promising technology in the medical and materials sciences because of their ability to conduct ions. Channels based on cyclodextrin, a cyclic oligomer of glucose, are of particular interest because of their non-toxicity and bio-compatibility. Using molecular dynamics-based free energy calculations, this study identifies cyclodextrin channel types that are best suited to serve as synthetic ion channels. Free energy profiles show that the connectivity in the channel determines whether the channel is cation-selective or anion-selective. Furthermore, the energy barrier for ion transport is governed by the number of glucose molecules constituting the cyclodextrin units of the channel. A detailed mechanism is proposed for ion transport through these channels. Findings from this study will aid in designing cyclodextrinbased channels that could be either cation-selective or anion-selective, by modifying the linkages of the channel or the number of glucose molecules in the cyclodextrin rings.

Abstract

— In this paper, we address the highly challenging problem of object goal navigation. The agent, in an unseen environment, has to perceive its surroundings to identify and navigate towards potential regions where the specified goal category can occur. Rather than developing goal driven exploration policies, we aim to adapt the existing exploration policies that maximize scene coverage to be goal-conditioned. Thus, we propose a standalone scene understanding module to identify potential regions where the goal occurs. We also propose Goal-Conditioned Exploration (GCExp), an algorithm that entails the integration of our novel scene understanding module with any existing exploration policy. We test our solution in photo-realistic simulation environments using stateof-the-art exploration policy, Active Neural Slam [1], and show improved performance over the same on every evaluation metric.

Abstract

A structure-based drug design pipeline involves the development of potential drug molecules or ligands that form stable complexes with a given receptor at its binding site. A prerequisite to this is finding druggable and functionally relevant binding sites on the 3D structure of the protein. Although several methods for detecting binding sites have been developed beforehand, a majority of them surprisingly fail in the identification and ranking of binding sites accurately. The rapid adoption and success of deep learning algorithms in various sections of structural biology beckons the usage of such algorithms for accurate binding site detection. As a combination of geometry based software and deep learning, we report a novel framework, DeepPocket that utilises 3D convolutional neural networks for the rescoring of pockets identified by Fpocket and further segments these identified cavities on the protein surface. Apart from this, we also propose another dataset SC6K containing protein structures submitted in the Protein Data Bank (PDB) from 1st January, 2018 till 28th February, 2020 for ligand binding site (LBS) detection. DeepPocket’s results on various binding site datasets and SC6K highlights its better

Abstract

We introduce SynSE, a novel syntactically guided generative approach for Zero-Shot Learning (ZSL). Our end-to-end approach learns progressively refined generative embedding spaces constrained within and across the involved modalities (visual, language). The inter-modal constraints are defined between action sequence embedding and embeddings of Parts of Speech (PoS) tagged words in the corresponding action description. We deploy SynSE for the task of skeleton-based action sequence recognition. Our design choices enable SynSE to generalize compositionally, i.e., recognize sequences whose action descriptions contain words not encountered during training. We also extend our approach to the more challenging Generalized Zero-Shot Learning (GZSL) problem via a confidence-based gating mechanism. We are the first to present zero-shot skeleton action recognition results on the largescale NTU-60 and NTU-120 skeleton action datasets with multiple splits. Our results demonstrate SynSE’s state of the art performance in both ZSL and GZSL settings compared to strong baselines on the NTU-60 and NTU-120 datasets.

Abstract

Handwritten documents are often characterized by dense and uneven layout. Despite advances, standard deep network based approaches for semantic layout segmentation are not robust to complex deformations seen across semantic regions. This phenomenon is especially pronounced for the low-resource Indic palm-leaf manuscript domain. To address the issue, we first introduce Indiscapes2, a new large-scale diverse dataset of Indic manuscripts with semantic layout annotations. Indiscapes2 contains documents from four different historical collections and is 150% larger than its predecessor, Indiscapes. We also propose a novel deep network Palmira for robust, deformation-aware instance segmentation of regions in handwritten manuscripts. We also report Hausdorff distance and its variants as a boundary-aware performance measure. Our experiments demonstrate that Palmira provides robust layouts, outperforms strong baseline approaches and ablative variants. We also include qualitative results on Arabic, South-East Asian and Hebrew historical manuscripts to showcase the generalization capability of Palmira .

Abstract

Datasets for training crowd counting deep networks are typically heavy-tailed in count distribution and exhibit discontinuities across the count range. As a result, the de facto statistical measures (MSE, MAE) exhibit large variance and tend to be unreliable indicators of performance across the count range. To address these concerns in a holistic manner, we revise processes at various stages of the standard crowd counting pipeline. To enable principled and balanced

Abstract

Localizing structured layout components such as tables is an important task in document image analysis. Numerous layout datasets with document images from various domains exist. However, healthcare and medical documents represent a crucial domain that has not been included so far. To address this gap, we contribute MediTables, a new dataset of 200 diverse medical document images with multi-category table annotations. Meditables contains a wide range of medical document images with variety in capture quality, layouts, skew, occlusion and illumination. The dataset images include pathology, diagnostic and hospital-related reports. In addition to document diversity, the dataset includes implicitly structured tables that are typically not present in other datasets. We benchmark state of the art table localization approaches on the MediTables dataset and introduce a custom-designed U-Net which exhibits robust performance while being drastically smaller in size compared to strong baselines. Our annotated dataset and models represent a useful first step towards the development of focused systems for medical document image analytics, a domain that mandates robust systems for reliable information retrieval. The dataset and models can be accessed at https://github.com/atmacvit/meditables

Abstract

Quantum states that possess negative conditional von Neumann entropy provide quantum advantage in several information-theoretic protocols including superdense coding, state merging, distributed private randomness distillation and one-way entanglement distillation. While entanglement is an important resource, only a subset of entangled states have negative conditional von Neumann entropy. In this work, we characterize the class of density matrices having non-negative conditional von Neumann entropy as convex and compact. This allows us to prove the existence of a Hermitian operator (a witness) for the detection of states having negative conditional entropy for bipartite systems in arbitrary dimensions. We show two constructions of such witnesses. For one of the constructions, the expectation value of the witness in a state is an upper bound to the conditional entropy of the state. We pose the problem of obtaining a tight upper bound to the set of conditional entropies of states in which an operator gives the same expectation value. We solve this convex optimization problem numerically for a two qubit case and find that this enhances the usefulness of our witnesses. We also find that for a particular witness, the estimated tight upper bound matches the value of conditional entropy for Werner states. We explicate the utility of our work in the detection of useful states in several protocols.

Abstract

The ACM Hypertext and Social Media Conference is a premium venue for high quality peerreviewed research on hypertext theory, systems and applications. It is concerned with all aspects of modern hypertext research including social media, semantic web, dynamic and computed hypertext and hypermedia as well as narrative systems and applications. ACM Hypertext 2021, the 32nd ACM Conference on Hypertext and Social Media was organized as a virtual event, hosted by the ADAPT Centre and Trinity College Dublin, Ireland. The theme of HT'21 is: "Hypertext in a Multimodal World". The hypertext paradigm has transformed the way we store and transfer knowledge and how we think about information and access it. We access the same sources via multiple devices, ranging from smart watches and smart phones to laptops. Information and transactions have become ever more visual, with video increasingly replacing traditional text-based web pages. Particularly, we use interactive hypertext, news feeds and videos for getting things done: planning a trip, managing our finances, interacting with colleagues, friends and family, being productive and creative. The Covid-19 situation has put a sharp focus on the interwoven disciplines needed to realise such rich applications. The research of the Hypertext community has never been more relevant. The main tracks for ACM Hypertext 2021 are: Adaptive Web and Recommender Systems, Social Web, Semantic Web and NLP, Human-information Interaction, Search and Retrieval, and Digital Humanities, Games, and Culture. In addition, the conference features a Late Breaking Results track, in which visionary Blue Sky papers were also invited, and a Doctoral Consortium.

Abstract

In drug discovery applications, high throughput virtual screening exercises are routinely performed to determine an initial set of candidate molecules referred to as “hits”. In such an experiment, each molecule from a large small-molecule drug library is evaluated in terms of physical properties such as the docking score against a target receptor. In real-life drug discovery experiments, drug libraries are extremely large but still there is only a minor representation of the essentially infinite chemical space, and evaluation of physical properties for each molecule in the library is not computationally feasible. In the current study, a novel Machine learning framework for Enhanced MolEcular Screening (MEMES) based on Bayesian optimization is proposed for efficient sampling of the chemical space. The proposed framework is demonstrated to identify 90% of the top-1000 molecules from a molecular library of size about 100 million, while calculating the docking score only for about 6% of the complete library. We believe that such a framework would tremendously help to reduce the computational effort in not only drug-discovery but also areas that require such high-throughput experiments.