Rapid Bayesian optimisation for synthesis of short polymer fiber materials

The discovery of processes for the synthesis of new materials involves many decisions about process design, operation, and material properties. Experimentation is crucial but as complexity increases, exploration of variables can become impractical using traditional combinatorial approaches. We describe an iterative method which uses machine learning to optimise process development, incorporating multiple qualitative and quantitative objectives. We demonstrate the method with a novel fluid processing platform for synthesis of short polymer fibers, and show how the synthesis process can be efficiently directed to achieve material and process objectives.

High Dimensional Bayesian Optimization Using Dropout

Scaling Bayesian optimization to high dimensions is challenging task as the global optimization of high-dimensional acquisition function can be expensive and often infeasible. Existing methods depend either on limited active variables or the additive form of the objective function. We propose a new method for high-dimensional Bayesian optimization, that uses a dropout strategy to optimize only a subset of variables at each iteration. We derive theoretical bounds for the regret and show how it can inform the derivation of our algorithm. We demonstrate the efficacy of our algorithms for optimization on two benchmark functions and two real-world applications- training cascade classifiers and optimizing alloy composition.

Dual Control Memory Augmented Neural Networks for Treatment Recommendations

Machine-assisted treatment recommendations hold a promise to reduce physician time and decision errors. We formulate the task as a sequence-to-sequence prediction model that takes the entire time-ordered medical history as input, and predicts a sequence of future clinical procedures and medications. It is built on the premise that an effective treatment plan may have long-term dependencies from previous medical history. We approach the problem by using a memory-augmented neural network, in particular, by leveraging the recent differentiable neural computer that consists of a neural controller and an external memory module. But differing from the original model, we use dual controllers, one for encoding the history followed by another for decoding the treatment sequences. In the encoding phase, the memory is updated as new input is read; at the end of this phase, the memory holds not only the medical history but also the information about the current illness. During the decoding phase, the memory is write-protected. The decoding controller generates a treatment sequence, one treatment option at a time. The resulting dual controller write-protected memory-augmented neural network is demonstrated on the MIMIC-III dataset on two tasks: procedure prediction and medication prescription. The results show improved performance over both traditional bag-of-words and sequence-to-sequence methods.

Dual Memory Neural Computer for Asynchronous Two-view Sequential Learning

One of the core tasks in multi-view learning is to capture relations among views. For sequential data, the relations not only span across views, but also extend throughout the view length to form long-term intra-view and inter-view interactions. In this paper, we present a new memory augmented neural network model that aims to model these complex interactions between two asynchronous sequential views. Our model uses two encoders for reading from and writing to two external memories for encoding input views. The intra-view interactions and the long-term dependencies are captured by the use of memories during this encoding process. There are two modes of memory accessing in our system: late-fusion and early-fusion, corresponding to late and early inter-view interactions. In the late-fusion mode, the two memories are separated, containing only view-specific contents. In the early-fusion mode, the two memories share the same addressing space, allowing cross-memory accessing. In both cases, the knowledge from the memories will be combined by a decoder to make predictions over the output space. The resulting dual memory neural computer is demonstrated on a comprehensive set of experiments, including a synthetic task of summing two sequences and the tasks of drug prescription and disease progression in healthcare. The results demonstrate competitive performance over both traditional algorithms and deep learning methods designed for multi-view problems.

Learning Deep Matrix Representations

We present a new distributed representation in deep neural nets wherein the information is represented in native form as a matrix. This differs from current neural architectures that rely on vector representations. We consider matrices as central to the architecture and they compose the input, hidden and output layers. The model representation is more compact and elegant -- the number of parameters grows only with the largest dimension of the incoming layer rather than the number of hidden units. We derive several new deep networks: (i) feed-forward nets that map an input matrix into an output matrix, (ii) recurrent nets which map a sequence of input matrices into a sequence of output matrices. We also reinterpret existing models for (iii) memory-augmented networks and (iv) graphs using matrix notations. For graphs we demonstrate how the new notations lead to simple but effective extensions with multiple attentions. Extensive experiments on handwritten digits recognition, face reconstruction, sequence to sequence learning, EEG classification, and graph-based node classification demonstrate the efficacy and compactness of the matrix architectures.

Resset: A Recurrent Model for Sequence of Sets with Applications to Electronic Medical Records

Modern healthcare is ripe for disruption by AI. A game changer would be automatic understanding the latent processes from electronic medical records, which are being collected for billions of people worldwide. However, these healthcare processes are complicated by the interaction between at least three dynamic components: the illness which involves multiple diseases, the care which involves multiple treatments, and the recording practice which is biased and erroneous. Existing methods are inadequate in capturing the dynamic structure of care. We propose Resset, an end-to-end recurrent model that reads medical record and predicts future risk. The model adopts the algebraic view in that discrete medical objects are embedded into continuous vectors lying in the same space. We formulate the problem as modeling sequences of sets, a novel setting that have rarely, if not, been addressed. Within Resset, the bag of diseases recorded at each clinic visit is modeled as function of sets. The same hold for the bag of treatments. The interaction between the disease bag and the treatment bag at a visit is modeled in several, one of which as residual of diseases minus the treatments. Finally, the health trajectory, which is a sequence of visits, is modeled using a recurrent neural network. We report results on over a hundred thousand hospital visits by patients suffered from two costly chronic diseases -- diabetes and mental health. Resset shows promises in multiple predictive tasks such as readmission prediction, treatments recommendation and diseases progression.

Graph Memory Networks for Molecular Activity Prediction

Molecular activity prediction is critical in drug design. Machine learning techniques such as kernel methods and random forests have been successful for this task. These models require fixed-size feature vectors as input while the molecules are variable in size and structure. As a result, fixed-size fingerprint representation is poor in handling substructures for large molecules. In addition, molecular activity tests, or a so-called BioAssays, are relatively small in the number of tested molecules due to its complexity. Here we approach the problem through deep neural networks as they are flexible in modeling structured data such as grids, sequences and graphs. We train multiple BioAssays using a multi-task learning framework, which combines information from multiple sources to improve the performance of prediction, especially on small datasets. We propose Graph Memory Network (GraphMem), a memory-augmented neural network to model the graph structure in molecules. GraphMem consists of a recurrent controller coupled with an external memory whose cells dynamically interact and change through a multi-hop reasoning process. Applied to the molecules, the dynamic interactions enable an iterative refinement of the representation of molecular graphs with multiple bond types. GraphMem is capable of jointly training on multiple datasets by using a specific-task query fed to the controller as an input. We demonstrate the effectiveness of the proposed model for separately and jointly training on more than 100K measurements, spanning across 9 BioAssay activity tests.

Knowledge Graph Embedding with Multiple Relation Projections

Knowledge graphs contain rich relational structures of the world, and thus complement data-driven machine learning in heterogeneous data. One of the most effective methods in representing knowledge graphs is to embed symbolic relations and entities into continuous spaces, where relations are approximately linear translation between projected images of entities in the relation space. However, state-of-the-art relation projection methods such as TransR, TransD or TransSparse do not model the correlation between relations, and thus are not scalable to complex knowledge graphs with thousands of relations, both in computational demand and in statistical robustness. To this end we introduce TransF, a novel translation-based method which mitigates the burden of relation projection by explicitly modeling the basis subspaces of projection matrices. As a result, TransF is far more light weight than the existing projection methods, and is robust when facing a high number of relations. Experimental results on the canonical link prediction task show that our proposed model outperforms competing rivals by a large margin and achieves state-of-the-art performance. Especially, TransF improves by 9%/5% in the head/tail entity prediction task for N-to-1/1-to-N relations over the best performing translation-based method.

Finding Algebraic Structure of Care in Time: A Deep Learning Approach

Understanding the latent processes from Electronic Medical Records could be a game changer in modern healthcare. However, the processes are complex due to the interaction between at least three dynamic components: the illness, the care and the recording practice. Existing methods are inadequate in capturing the dynamic structure of care. We propose an end-to-end model that reads medical record and predicts future risk. The model adopts the algebraic view in that discrete medical objects are embedded into continuous vectors lying in the same space. The bag of disease and comorbidities recorded at each hospital visit are modeled as function of sets. The same holds for the bag of treatments. The interaction between diseases and treatments at a visit is modeled as the residual of the diseases minus the treatments. Finally, the health trajectory, which is a sequence of visits, is modeled using a recurrent neural network. We report preliminary results on chronic diseases - diabetes and mental health - for predicting unplanned readmission.

Nonnegative Restricted Boltzmann Machines for Parts-based Representations Discovery and Predictive Model Stabilization

The success of any machine learning system depends critically on effective representations of data. In many cases, it is desirable that a representation scheme uncovers the parts-based, additive nature of the data. Of current representation learning schemes, restricted Boltzmann machines (RBMs) have proved to be highly effective in unsupervised settings. However, when it comes to parts-based discovery, RBMs do not usually produce satisfactory results. We enhance such capacity of RBMs by introducing nonnegativity into the model weights, resulting in a variant called nonnegative restricted Boltzmann machine (NRBM). The NRBM produces not only controllable decomposition of data into interpretable parts but also offers a way to estimate the intrinsic nonlinear dimensionality of data, and helps to stabilize linear predictive models. We demonstrate the capacity of our model on applications such as handwritten digit recognition, face recognition, document classification and patient readmission prognosis. The decomposition quality on images is comparable with or better than what produced by the nonnegative matrix factorization (NMF), and the thematic features uncovered from text are qualitatively interpretable in a similar manner to that of the latent Dirichlet allocation (LDA). The stability performance of feature selection on medical data is better than RBM and competitive with NMF. The learned features, when used for classification, are more discriminative than those discovered by both NMF and LDA and comparable with those by RBM.