Reliable prediction of protein variant effects is crucial for both protein optimization and for advancing biological understanding. For practical use in protein engineering, it is important that we can also provide reliable uncertainty estimates for our predictions, and while prediction accuracy has seen much progress in recent years, uncertainty metrics are rarely reported. We here provide a Gaussian process regression model, Kermut, with a novel composite kernel for modelling mutation similarity, which obtains state-of-the-art performance for protein variant effect prediction while also offering estimates of uncertainty through its posterior. An analysis of the quality of the uncertainty estimates demonstrates that our model provides meaningful levels of overall calibration, but that instance-specific uncertainty calibration remains more challenging. We hope that this will encourage future work in this promising direction.

A novel approach for comparing sequences of observations using an explicit-expansion kernel is demonstrated. The kernel is derived using the assumption of the independence of the sequence of observations and a mean-squared error training criterion. The use of an explicit expan- sion kernel reduces classifier model size and computation dramatically, resulting in model sizes and computation one-hundred times smaller in our application. The explicit expansion also preserves the computational advantages of an earlier architecture based on mean-squared error train- ing. Training using standard support vector machine methodology gives accuracy that significantly exceeds the performance of state-of-the-art mean-squared error training for a speaker recognition task.

The area of argumentation theory is an increasingly important area of artificial intelligence and mechanisms that are able to automatically detect the argument structure provide a novel area of research. This paper considers the use of kernel methods for argumentation detection and classification. It shows that a classification accuracy of 65%, can be attained using Natural Language Processing based kernel approaches, which do not require any heuristic choice of features.

We propose Tree Sequence Kernel (TSK), which implicitly exhausts the structure features of a sequence of subtrees embedded in the phrasal parse tree. By incorporating the capability of sequence kernel, TSK enriches tree kernel with tree sequence features so that it may provide additional useful patterns for machine learning applications. Two approaches of penalizing the substructures are proposed and both can be accomplished by efficient algorithms via dynamic programming. Evaluations are performed on two natural language tasks, i.e. Question Classification and Relation Extraction. Experimental results suggest that TSK outperforms tree kernel for both tasks, which also reveals that the structure features made up of multiple subtrees are effective and play a complementary role to the single tree structure.

This paper proposes a new approach to feature selection based on a statistical featuremining technique for sequence and tree kernels. Since natural language data take discrete structures, convolution kernels, such as sequence and tree kernels, are advantageous for both the concept and accuracy of many natural language processing tasks. However, experiments haveshown that the best results can only be achieved when limited small substructures are dealt with by these kernels. This paper discusses thisissue of convolution kernels and then proposes a statistical feature selection that enable us to use larger substructures effectively. The proposed method, in order to execute efficiently, can be embedded into an original kernel calculation process by using substructure mining algorithms.Experiments on real NLP tasks confirm the problem in the conventional method and compare the performance of a conventional method to that of the proposed method.

This paper proposes a new approach to feature selection based on a statistical feature mining technique for sequence and tree kernels. Since natural language data take discrete structures, convolution kernels, such as sequence and tree kernels, are advantageous for both the concept and accuracy of many natural language processing tasks. However, experiments have shown that the best results can only be achieved when limited small substructures are dealt with by these kernels. This paper discusses this issue of convolution kernels and then proposes a statistical feature selection that enable us to use larger substructures effectively. The proposed method, in order to execute efficiently, can be embedded into an original kernel calculation process by using substructure mining algorithms. Experiments on real NLP tasks confirm the problem in the conventional method and compare the performance of a conventional method to that of the proposed method.

This paper proposes a new approach to feature selection based on a statistical feature mining technique for sequence and tree kernels. Since natural language data take discrete structures, convolution kernels, such as sequence and tree kernels, are advantageous for both the concept and accuracy of many natural language processing tasks. However, experiments have shown that the best results can only be achieved when limited small substructures are dealt with by these kernels. This paper discusses this issue of convolution kernels and then proposes a statistical feature selection that enable us to use larger substructures effectively. The proposed method, in order to execute efficiently, can be embedded into an original kernel calculation process by using substructure mining algorithms. Experiments on real NLP tasks confirm the problem in the conventional method and compare the performance of a conventional method to that of the proposed method.