Abstract

We present CCO-VOXEL: the very first chance-constrained optimization (CCO) algorithm that can compute trajectory plans with probabilistic safety guarantees in real-time directly on the voxel-grid representation of the world. CCO-VOXEL maps the distribution over the distance to the closest obstacle to a distribution over collision-constraint violation and computes an optimal trajectory that minimizes the violation probability. Importantly, unlike existing works, we never assume the nature of the sensor uncertainty or the probability distribution of the resulting collision-constraint violations. We leverage the notion of Hilbert Space embedding of distributions and Maximum Mean Discrepancy (MMD) to compute a tractable surrogate for the original chance-constrained optimization problem and employ a combination of A* based graph-search and Cross-Entropy Method for obtaining its minimum. We show tangible performance gain in terms of collision avoidance and trajectory smoothness as a consequence of our probabilistic formulation vis a vis state-of-the-art planning methods that do not account for such nonparametric noise. Finally, we also show how a combination of low-dimensional feature embedding and pre-caching of Kernel Matrices of MMD allows us to achieve real-time performance in simulations as well as in implementations on on-board commodity hardware that controls the quadrotor flight

Abstract

Images in the medical domain are fundamentally different from the general domain images. Consequently, it is infeasible to directly employ general domain Visual Question Answering (VQA) models for the medical domain. Additionally, medical image annotation is a costly and time-consuming process. To overcome these limitations, we propose a solution inspired by self-supervised pretraining of Transformer-style architectures for NLP, Vision, and Language tasks. Our method involves learning richer medical image and text semantic representations using Masked Vision-Language Modeling as the pretext task on a large medical image+caption dataset. The proposed solution achieves new state-of-the-art performance on two VQA datasets for radiology images – VQA-Med 2019 and VQA-RAD, outperforming even the ensemble models of previous best solutions. Moreover, our solution provides attention maps which help in model interpretability.

Abstract

Protein-ligand complex structures have been utilised to design benchmark machine learning methods that perform important tasks related to drug design such as receptor binding site detection, small molecule docking and binding affinity prediction. However, these methods are usually trained on only ligand bound (or holo) conformations of the protein and therefore are not guaranteed to perform well when the protein structure is in its native unbound conformation (or apo), which is usually the conformation available for a newly identified receptor. A primary reason for this is that the local structure of the binding site usually changes upon ligand binding. To facilitate solutions for this problem, we propose a dataset called APObind that aims to provide apo conformations of proteins present in the PDBbind dataset, a popular dataset used in drug design. Furthermore, we explore the performance of methods specific to three use cases on this dataset, through which, the importance of validating them on the APObind dataset is demonstrated.

Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) manifests a broad spectrum of clinical presentations, varying in severity from asymptomatic to mortality. As the viral infection spread, it evolved and developed into many variants of concern. Understanding the impact of mutations in the SARS-CoV-2 genome on the clinical phenotype and associated co-morbidities is important for treatment and preventionas the pandemic progresses. Based on the mild, moderate, and severe clinical phenotypes, we analyzed the possible association between both, the clinical sub-phenotypes and genomic mutations with respect to the severity and outcome of the patients. We found a significant association between the requirement of respiratory support and co-morbidities. We also identified six SARS-CoV-2 genome mutations that were significantly correlated with severity and mortality in our cohort. We examined structural alterations at the RNA and protein levels as a result of three of these mutations: A26194T, T28854T, and C25611A, present in the Orf3a and N protein. The RNA secondary structure change due to the above mutations can be one of the modulators of the disease outcome. Our findings highlight the importance of integrative analysis in which clinical and genetic components of the disease are co-analyzed. In combination with genomic surveillance, the clinical outcome-associated mutations could help identify individuals for priority medical support.

Abstract

The step-by-step workflow adopted for the analysis of water molecules in the binding sites of small molecules of our interest bound to protein crystal structures. (Note: We examined the local water network around O and S atoms of carbonyl (>C=O) and thiocarbonyl (>C=S) in small molecule ligands that are non-covalently bound to protein crystal structures (≤2.5Å) deposited in the Protein Data Bank (PDB). To minimize the influence of heterogeneous chemical micro-environment on the hydration profile of O and S atoms, we chose to confine our analyses to ligands that possess both carbonyl and thiocarbonyl moieties (in thioamides, thioureas, thiocarbamates, and dithiocarbamates). A subset of protein-ligand pairs where the ligand has at least one water molecule in its First Solvation Shell (FSS is defined as a sphere containing any point that lies within 4.5 Å of a ligand atom) was selected for further analysis.

Abstract

The quest for stabilizing planar forms of tetracoordinate carbon started five decades ago and intends to achieve interconversion between [R]- and [S]-stereoisomers without breaking covalent bonds. Several strategies are successful in making the planar tetracoordinate form a minimum on its potential energy surface. However, the first examples of systems where stereomutation is possible were reported only recently. In this study, the possibility of neutral and dications of simple hydrocarbons (cyclopentane, cyclopentene, spiropentane, and spiropentadiene) and their counterparts with the central carbon atom replaced by elements from groups 13, 14, and 15 are explored using ab initio MP2 calculations. The energy difference between the tetrahedral and planar forms decreases from row II to row III or IV substituents. Additionally, aromaticity involving the delocalization of the lone pair on the central atom appears to help in further stabilizing the planar form compared to the tetrahedral form, especially for the row II substituents. We identified 11 systems where the tetrahedral state is a minimum on the potential energy surface, and the planar form is a transition state corresponding to stereomutation. Interestingly, the planar structures of three systems were found to be minimum, and the corresponding tetrahedral states were transition states. The energy profiles corresponding to such transitions involving both planar and tetrahedral states without the breaking of covalent bonds were examined. The systems showcased in this study and research in this direction are expected to realize molecules that experimentally exhibit stereomutation.

Abstract

In the left-right symmetric models, a heavy charged gauge boson can decay to a lepton and a right-handed neutrino (RHN). If the neutrino masses are generated through the standard type-I seesaw mechanism, the Yukawa couplings controlling two-body decays of the RHN become very small. As a result, the RHN decays to another lepton and a pair of jets via an off-shell . This is the basis of the Keung-Senjanovi'{c} (KS) process, which was originally proposed as a probe of lepton number violation at the LHC. However, if a different mechanism like the inverse seesaw generates the neutrino masses, a TeV-scale RHN can have large Yukawa couplings and hence, dominantly decay to a lepton and a boson, leading to a kinematically different process from the KS one. We investigate the prospect of this unexplored process as a probe of the inverse seesaw mechanism in the left-right symmetric models at the HL-LHC. Our signal arises from the Drell-Yan production of a and leads to two high- same-flavour-opposite-sign leptons and a boosted -like fatjet in the final state. We find that a sequential with mass up to ~TeV along with a TeV-scale RHN can be discovered at the HL-LHC.

Abstract

We explore the possibility of CP violation in baryonic Λb → ðΛþ c ; pþÞπþμ−μ− decays which are mediated by two Majorana sterile neutrinos and are jΔLj ¼ 2 lepton-number-violating processes. Appreciable CP asymmetry can be obtained if there are two on-shell Majorana neutrinos that are quasidegenerate in mass with the mass difference of the order of average decay widths. We find that, given the present constraints on the heavy to light mixing element jVμNj, the Λb → pþπþμ−μ− and Λb → Λþ c πþμ−μ− decay rates are suppressed but could be within the experimental reach at the LHC. If searches of the modes are performed, then experimental limits on the rates can be translated to constraints on the Majorana neutrino mass mN and heavy to light mixing element squared jVμNj 2. We show that the constraints on the ðmN; jVμNj 2Þ parameter space coming from the jΔLj ¼ 2 baryonic decays are complementary to the bounds coming from other processes.

Abstract

The recent anomalies in b → slþl− transitions could originate from some new physics beyond the Standard Model. Either to confirm or to rule out this assumption, more tests of b → slþl− transition are needed. Polarized Λb decay to a Λ and a dilepton pair offers a plethora of observables that are suitable to discriminate new physics from the Standard Model. In this paper, we present a full angular analysis of a polarized Λb decay to a Λð→ pπÞlþl− final state. The study is performed in a set of the operator where the Standard Model operator basis is supplemented with its chirality flipped counterparts, and new scalar and pseudoscalar operators. The full angular distribution is calculated by retaining the mass of the final state leptons. At the low hadronic recoil, we use the heavy quark effective theory framework to relate the hadronic form factors which lead to simplified expression of the angular observables where short- and longdistance physics factorize. Using the factorized expressions of the observables, we construct a number of test of short- and long-distance physics including null tests of the Standard Model and its chirality flipped counterparts that can be carried out using experimental data.

Abstract

Communication with the deaf community relies profoundly on the interpretation of sign languages performed by the signers. In light of the recent breakthroughs in sign language translations, we propose a pipeline that we term "Translating Sign Language Videos to Talking Faces". In this context, we improve the existing sign language translation systems by using POS tags to improve language modeling. We further extend the challenge to develop a system that can interpret a video from a signer to an avatar speaking in spoken languages. We focus on the translation systems that attempt to translate sign languages to text without glosses,