MUST-CNN: A Multilayer Shift-and-Stitch Deep Convolutional Architecture for Sequence-based Protein Structure Prediction

Predicting protein properties such as solvent accessibility and secondary structure from its primary amino acid sequence is an important task in bioinformatics. Recently, a few deep learning models have surpassed the traditional window based multilayer perceptron. Taking inspiration from the image classification domain we propose a deep convolutional neural network architecture, MUST-CNN, to predict protein properties. This architecture uses a novel multilayer shift-and-stitch (MUST) technique to generate fully dense per-position predictions on protein sequences. Our model is significantly simpler than the state-of-the-art, yet achieves better results. By combining MUST and the efficient convolution operation, we can consider far more parameters while retaining very fast prediction speeds. We beat the state-of-the-art performance on two large protein property prediction datasets.Comment: 8 pages ; 3 figures ; deep learning based sequence-sequence prediction. in AAAI 201

Reevaluating Adversarial Examples in Natural Language

State-of-the-art attacks on NLP models lack a shared definition of a what constitutes a successful attack. We distill ideas from past work into a unified framework: a successful natural language adversarial example is a perturbation that fools the model and follows some linguistic constraints. We then analyze the outputs of two state-of-the-art synonym substitution attacks. We find that their perturbations often do not preserve semantics, and 38% introduce grammatical errors. Human surveys reveal that to successfully preserve semantics, we need to significantly increase the minimum cosine similarities between the embeddings of swapped words and between the sentence encodings of original and perturbed sentences.With constraints adjusted to better preserve semantics and grammaticality, the attack success rate drops by over 70 percentage points.Comment: 15 pages; 9 Tables; 5 Figure

Black-box Generation of Adversarial Text Sequences to Evade Deep Learning Classifiers

Although various techniques have been proposed to generate adversarial samples for white-box attacks on text, little attention has been paid to black-box attacks, which are more realistic scenarios. In this paper, we present a novel algorithm, DeepWordBug, to effectively generate small text perturbations in a black-box setting that forces a deep-learning classifier to misclassify a text input. We employ novel scoring strategies to identify the critical tokens that, if modified, cause the classifier to make an incorrect prediction. Simple character-level transformations are applied to the highest-ranked tokens in order to minimize the edit distance of the perturbation, yet change the original classification. We evaluated DeepWordBug on eight real-world text datasets, including text classification, sentiment analysis, and spam detection. We compare the result of DeepWordBug with two baselines: Random (Black-box) and Gradient (White-box). Our experimental results indicate that DeepWordBug reduces the prediction accuracy of current state-of-the-art deep-learning models, including a decrease of 68\% on average for a Word-LSTM model and 48\% on average for a Char-CNN model.Comment: This is an extended version of the 6page Workshop version appearing in 1st Deep Learning and Security Workshop colocated with IEEE S&

Learning to Reason and Memorize with Self-Notes

Large language models have been shown to struggle with multi-step reasoning, and do not retain previous reasoning steps for future use. We propose a simple method for solving both of these problems by allowing the model to take Self-Notes. Unlike recent chain-of-thought or scratchpad approaches, the model can deviate from the input context at any time to explicitly think and write down its thoughts. This allows the model to perform reasoning on the fly as it reads the context and even integrate previous reasoning steps, thus enhancing its memory with useful information and enabling multi-step reasoning. Experiments across a wide variety of tasks demonstrate that our method can outperform chain-of-thought and scratchpad methods by taking Self-Notes that interleave the input text