arXiv subjects

Cicero dos Santos

Publications and source records attributed to Cicero dos Santos.

5 recordsLinked to original sources

arXiv2021

Accelerating Antimicrobial Discovery with Controllable Deep Generative Models and Molecular Dynamics

De novo therapeutic design is challenged by a vast chemical repertoire and multiple constraints, e.g., high broad-spectrum potency and low toxicity. We propose CLaSS (Controlled Latent attribute Space Sampling) - an efficient computational method for attribute-controlled generation of molecules, which leverages guidance from classifiers trained on an informative latent space of molecules modeled using a deep generative autoencoder. We screen the generated molecules for additional key attributes by using deep learning classifiers in conjunction with novel features derived from atomistic simulations. The proposed approach is demonstrated for designing non-toxic antimicrobial peptides (AMPs) with strong broad-spectrum potency, which are emerging drug candidates for tackling antibiotic resistance. Synthesis and testing of only twenty designed sequences identified two novel and minimalist AMPs with high potency against diverse Gram-positive and Gram-negative pathogens, including one multidrug-resistant and one antibiotic-resistant K. pneumoniae, via membrane pore formation. Both antimicrobials exhibit low in vitro and in vivo toxicity and mitigate the onset of drug resistance. The proposed approach thus presents a viable path for faster and efficient discovery of potent and selective broad-spectrum antimicrobials.

cs.LG↗

arXiv2017

Improved Neural Relation Detection for Knowledge Base Question Answering

Relation detection is a core component for many NLP applications including Knowledge Base Question Answering (KBQA). In this paper, we propose a hierarchical recurrent neural network enhanced by residual learning that detects KB relations given an input question. Our method uses deep residual bidirectional LSTMs to compare questions and relation names via different hierarchies of abstraction. Additionally, we propose a simple KBQA system that integrates entity linking and our proposed relation detector to enable one enhance another. Experimental results evidence that our approach achieves not only outstanding relation detection performance, but more importantly, it helps our KBQA system to achieve state-of-the-art accuracy for both single-relation (SimpleQuestions) and multi-relation (WebQSP) QA benchmarks.

cs.CL↗

arXiv2016

Boosting Docking-based Virtual Screening with Deep Learning

In this work, we propose a deep learning approach to improve docking-based virtual screening. The introduced deep neural network, DeepVS, uses the output of a docking program and learns how to extract relevant features from basic data such as atom and residues types obtained from protein-ligand complexes. Our approach introduces the use of atom and amino acid embeddings and implements an effective way of creating distributed vector representations of protein-ligand complexes by modeling the compound as a set of atom contexts that is further processed by a convolutional layer. One of the main advantages of the proposed method is that it does not require feature engineering. We evaluate DeepVS on the Directory of Useful Decoys (DUD), using the output of two docking programs: AutodockVina1.1.2 and Dock6.6. Using a strict evaluation with leave-one-out cross-validation, DeepVS outperforms the docking programs in both AUC ROC and enrichment factor. Moreover, using the output of AutodockVina1.1.2, DeepVS achieves an AUC ROC of 0.81, which, to the best of our knowledge, is the best AUC reported so far for virtual screening using the 40 receptors from DUD.

q-bio.QM↗

arXiv2016

LSTM-based Deep Learning Models for Non-factoid Answer Selection

In this paper, we apply a general deep learning (DL) framework for the answer selection task, which does not depend on manually defined features or linguistic tools. The basic framework is to build the embeddings of questions and answers based on bidirectional long short-term memory (biLSTM) models, and measure their closeness by cosine similarity. We further extend this basic model in two directions. One direction is to define a more composite representation for questions and answers by combining convolutional neural network with the basic framework. The other direction is to utilize a simple but efficient attention mechanism in order to generate the answer representation according to the question context. Several variations of models are provided. The models are examined by two datasets, including TREC-QA and InsuranceQA. Experimental results demonstrate that the proposed models substantially outperform several strong baselines.

cs.CL↗

arXiv2016

Attentive Pooling Networks

In this work, we propose Attentive Pooling (AP), a two-way attention mechanism for discriminative model training. In the context of pair-wise ranking or classification with neural networks, AP enables the pooling layer to be aware of the current input pair, in a way that information from the two input items can directly influence the computation of each other's representations. Along with such representations of the paired inputs, AP jointly learns a similarity measure over projected segments (e.g. trigrams) of the pair, and subsequently, derives the corresponding attention vector for each input to guide the pooling. Our two-way attention mechanism is a general framework independent of the underlying representation learning, and it has been applied to both convolutional neural networks (CNNs) and recurrent neural networks (RNNs) in our studies. The empirical results, from three very different benchmark tasks of question answering/answer selection, demonstrate that our proposed models outperform a variety of strong baselines and achieve state-of-the-art performance in all the benchmarks.

cs.CL↗