We introduce a convolutional neural network that operates directly on graphs. These networks allow end-to-end learning of prediction pipelines whose inputs are graphs of arbitrary size and shape. The architecture we present generalizes standard molecular feature extraction methods based on circular fingerprints. We show that these data-driven features are more interpretable, and have better predictive performance on a variety of tasks.

Deep learning models for image classification have become standard tools in recent years. A well known vulnerability of these models is their susceptibility to adversarial examples. These are generated by slightly altering an image of a certain class in a way that is imperceptible to humans but causes the model to classify it wrongly as another class. Many algorithms have been proposed to address this problem, falling generally into one of two categories: (i) building robust classifiers (ii) directly detecting attacked images. Despite the good performance of these detectors, we argue that in a white-box setting, where the attacker knows the configuration and weights of the network and the detector, they can overcome the detector by running many examples on a local copy, and sending only those that were not detected to the actual model. This problem is common in security applications where even a very good model is not sufficient to ensure safety. In this paper we propose to overcome this inherent limitation of any static defence with randomization. To do so, one must generate a very large family of detectors with consistent performance, and select one or more of them randomly for each input. For the individual detectors, we suggest the method of neural fingerprints. In the training phase, for each class we repeatedly sample a tiny random subset of neurons from certain layers of the network, and if their average is sufficiently different between clean and attacked images of the focal class they are considered a fingerprint and added to the detector bank. During test time, we sample fingerprints from the bank associated with the label predicted by the model, and detect attacks using a likelihood ratio test. We evaluate our detectors on ImageNet with different attack methods and model architectures, and show near-perfect detection with low rates of false detection.

We introduce a convolutional neural network that operates directly on graphs. These networks allow end-to-end learning of prediction pipelines whose inputs are graphs of arbitrary size and shape. The architecture we present generalizes standard molecular feature extraction methods based on circular fingerprints. We show that these data-driven features are more interpretable, and have better predictive performance on a variety of tasks.

Fast screening of drug molecules based on the ligand binding affinity is an important step in the drug discovery pipeline. Graph neural fingerprint is a promising method for developing molecular docking surrogates with high throughput and great fidelity. In this study, we built a COVID-19 drug docking dataset of about 300,000 drug candidates on 23 coronavirus protein targets. With this dataset, we trained graph neural fingerprint docking models for high-throughput virtual COVID-19 drug screening. The graph neural fingerprint models yield high prediction accuracy on docking scores with the mean squared error lower than $0.21$ kcal/mol for most of the docking targets, showing significant improvement over conventional circular fingerprint methods. To make the neural fingerprints transferable for unknown targets, we also propose a transferable graph neural fingerprint method trained on multiple targets. With comparable accuracy to target-specific graph neural fingerprint models, the transferable model exhibits superb training and data efficiency. We highlight that the impact of this study extends beyond COVID-19 dataset, as our approach for fast virtual ligand screening can be easily adapted and integrated into a general machine learning-accelerated pipeline to battle future bio-threats.

Brain Computer Interface (BCI) has great potential for solving many brain signal analysis limitations, mental disorder resolutions, and restoring missing limb functionality via neural-controlled implants. However, there is no single available, and safe implant for daily life usage exists yet. Most of the proposed implants have several implementation issues, such as infection hazards and heat dissipation, which limits their usability and makes it more challenging to pass regulations and quality control production. The wireless implant does not require a chronic wound in the skull. However, the current complex clustering neuron identification algorithms inside the implant chip consume a lot of power and bandwidth, causing higher heat dissipation issues and draining the implant's battery. The spike sorting is the core unit of an invasive BCI chip, which plays a significant role in power consumption, accuracy, and area. Therefore, in this study, we propose a low-power adaptive simplified VLSI architecture, "Zydeco-Style," for BCI spike sorting that is computationally less complex with higher accuracy that performs up to 93.5% in the worst-case scenario. The architecture uses a low-power Bluetooth Wireless communication module with external IoT medical ICU devices. The proposed architecture was implemented and simulated in Verilog. In addition, we are proposing an implant conceptual design.

Chemical fingerprints [1] have long been the representation used to represent chemical structures as numbers, which are suitable inputs to machine learning models. A brief summary of chemical fingerprints is provided in another of my blog posts here. Above, we computed the fingerprint for Atorvastatin, a drug which generated over $100B in revenue over 2003–2013. At some point a few years ago, people started to realize [3] that instead of computing a non-differentiable fingerprint, we can compute a differentiable fingerprint. Then, by backpropagation, we can train not only a deep-learning model but also train the fingerprint-generating function itself. The promise would be to learn richer molecular representations.

In our study, we demonstrate the synergy effect between convolutional neural networks and the multiplicity of SMILES. The model we propose, the so-called Convolutional Neural Fingerprint (CNF) model, reaches the accuracy of traditional descriptors such as Dragon (Mauri et al. [22]), RDKit (Landrum [18]), CDK2 (Willighagen et al. [43]) and PyDescriptor (Masand and Rastija [20]). Moreover the CNF model generally performs better than highly fine-tuned traditional descriptors, especially on small data sets, which is of great interest for the chemical field where data sets are generally small due to experimental costs, the availability of molecules or accessibility to private databases. We evaluate the CNF model along with SMILES augmentation during both training and testing. To the best of our knowledge, this is the first time that such a methodology is presented. We show that using the multiplicity of SMILES during training acts as a regulariser and therefore avoids overfitting and can be seen as ensemble learning when considered for testing.

We introduce a deep learning architecture for structure-based virtual screening that generates fixed-sized fingerprints of proteins and small molecules by applying learnable atom convolution and softmax operations to each compound separately. These fingerprints are further transformed non-linearly, their inner-product is calculated and used to predict the binding potential. Moreover, we show that widely used benchmark datasets may be insufficient for testing structure-based virtual screening methods that utilize machine learning. Therefore, we introduce a new benchmark dataset, which we constructed based on DUD-E and PDBBind databases.

We introduce a convolutional neural network that operates directly on graphs. These networks allow end-to-end learning of prediction pipelines whose inputs are graphs of arbitrary size and shape. The architecture we present generalizes standard molecular feature extraction methods based on circular fingerprints. We show that these data-driven features are more interpretable, and have better predictive performanceon a variety of tasks.

We introduce a convolutional neural network that operates directly on graphs. These networks allow end-to-end learning of prediction pipelines whose inputs are graphs of arbitrary size and shape. The architecture we present generalizes standard molecular feature extraction methods based on circular fingerprints. We show that these data-driven features are more interpretable, and have better predictive performance on a variety of tasks.