Cicero Dos Santos

Youssef Mroueh, Tom Sercu, Mattia Rigotti et al.

We propose the Sobolev Independence Criterion (SIC), an interpretable dependency measure between a high dimensional random variable X and a response variable Y . SIC decomposes to the sum of feature importance scores and hence can be used for nonlinear feature selection. SIC can be seen as a gradient regularized Integral Probability Metric (IPM) between the joint distribution of the two random variables and the product of their marginals. We use sparsity inducing gradient penalties to promote input sparsity of the critic of the IPM. In the kernel version we show that SIC can be cast as a convex optimization problem by introducing auxiliary variables that play an important role in feature selection as they are normalized feature importance scores. We then present a neural version of SIC where the critic is parameterized as a homogeneous neural network, improving its representation power as well as its interpretability. We conduct experiments validating SIC for feature selection in synthetic and real-world experiments. We show that SIC enables reliable and interpretable discoveries, when used in conjunction with the holdout randomization test and knockoffs to control the False Discovery Rate. Code is available at http://github.com/ibm/sic.

Payel Das, Tom Sercu, Kahini Wadhawan et al.

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.

Pierre Dognin, Igor Melnyk, Youssef Mroueh et al.

In this paper we propose to perform model ensembling in a multiclass or a multilabel learning setting using Wasserstein (W.) barycenters. Optimal transport metrics, such as the Wasserstein distance, allow incorporating semantic side information such as word embeddings. Using W. barycenters to find the consensus between models allows us to balance confidence and semantics in finding the agreement between the models. We show applications of Wasserstein ensembling in attribute-based classification, multilabel learning and image captioning generation. These results show that the W. ensembling is a viable alternative to the basic geometric or arithmetic mean ensembling.

Payel Das, Kahini Wadhawan, Oscar Chang et al.

Given the emerging global threat of antimicrobial resistance, new methods for next-generation antimicrobial design are urgently needed. We report a peptide generation framework PepCVAE, based on a semi-supervised variational autoencoder (VAE) model, for designing novel antimicrobial peptide (AMP) sequences. Our model learns a rich latent space of the biological peptide context by taking advantage of abundant, unlabeled peptide sequences. The model further learns a disentangled antimicrobial attribute space by using the feedback from a jointly trained AMP classifier that uses limited labeled instances. The disentangled representation allows for controllable generation of AMPs. Extensive analysis of the PepCVAE-generated sequences reveals superior performance of our model in comparison to a plain VAE, as PepCVAE generates novel AMP sequences with higher long-range diversity, while being closer to the training distribution of biological peptides. These features are highly desired in next-generation antimicrobial design.

Mo Yu, Wenpeng Yin, Kazi Saidul Hasan et al.

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.

Cicero dos Santos, Ming Tan, Bing Xiang et al.

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.

Ming Tan, Cicero dos Santos, Bing Xiang et al.

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.