Learning Comprehensible Theories from Structured Data

This thesis is concerned with the problem of learning comprehensible theories from structured data and covers primarily classification and regression learning. The basic knowledge representation language is set around a polymorphically-typed, higher-order logic. The general setup is closely related to the learning from propositionalized knowledge and learning from interpretations settings in Inductive Logic Programming. Individuals (also called instances) are represented as terms in the logic. A grammar-like construct called a predicate rewrite system is used to define features in the form of predicates that individuals may or may not satisfy. For learning, decision-tree algorithms of various kinds are adopted.¶ The scope of the thesis spans both theory and practice. ..

Benchmark of structured machine learning methods for microbial identification from mass-spectrometry data

Microbial identification is a central issue in microbiology, in particular in the fields of infectious diseases diagnosis and industrial quality control. The concept of species is tightly linked to the concept of biological and clinical classification where the proximity between species is generally measured in terms of evolutionary distances and/or clinical phenotypes. Surprisingly, the information provided by this well-known hierarchical structure is rarely used by machine learning-based automatic microbial identification systems. Structured machine learning methods were recently proposed for taking into account the structure embedded in a hierarchy and using it as additional a priori information, and could therefore allow to improve microbial identification systems. We test and compare several state-of-the-art machine learning methods for microbial identification on a new Matrix-Assisted Laser Desorption/Ionization Time-of-Flight mass spectrometry (MALDI-TOF MS) dataset. We include in the benchmark standard and structured methods, that leverage the knowledge of the underlying hierarchical structure in the learning process. Our results show that although some methods perform better than others, structured methods do not consistently perform better than their "flat" counterparts. We postulate that this is partly due to the fact that standard methods already reach a high level of accuracy in this context, and that they mainly confuse species close to each other in the tree, a case where using the known hierarchy is not helpful

LANISTR: Multimodal Learning from Structured and Unstructured Data

Multimodal large-scale pretraining has shown impressive performance for unstructured data including language, image, audio, and video. However, a prevalent real-world scenario involves the combination of structured data types (tabular, time-series) with unstructured data which has so far been understudied. To bridge this gap, we propose LANISTR, an attention-based framework to learn from LANguage, Image, and STRuctured data. The core of LANISTR's methodology is rooted in \textit{masking-based} training applied across both unimodal and multimodal levels. In particular, we introduce a new similarity-based multimodal masking loss that enables it to learn cross-modal relations from large-scale multimodal data with missing modalities. On two real-world datastes, MIMIC-IV (healthcare) and Amazon Product Review (retail), LANISTR demonstrates remarkable absolute improvements of 6.6\% (AUROC) and up to 14\% (accuracy) when fine-tuned on 0.1\% and 0.01\% of labeled data, respectively, compared to the state-of-the-art alternatives. Notably, these improvements are observed even in the presence of considerable missingness ratios of 35.7\% and 99.8\%, in the respective datasets

Learning from Structured Data with High Dimensional Structured Input and Output Domain

Structured data is accumulated rapidly in many applications, e.g. Bioinformatics, Cheminformatics, social network analysis, natural language processing and text mining. Designing and analyzing algorithms for handling these large collections of structured data has received significant interests in data mining and machine learning communities, both in the input and output domain. However, it is nontrivial to adopt traditional machine learning algorithms, e.g. SVM, linear regression to structured data. For one thing, the structural information in the input domain and output domain is ignored if applying the normal algorithms to structured data. For another, the major challenge in learning from many high-dimensional structured data is that input/output domain can contain tens of thousands even larger number of features and labels. With the high dimensional structured input space and/or structured output space, learning a low dimensional and consistent structured predictive function is important for both robustness and interpretability of the model. In this dissertation, we will present a few machine learning models that learn from the data with structured input features and structured output tasks. For learning from the data with structured input features, I have developed structured sparse boosting for graph classification, structured joint sparse PCA for anomaly detection and localization. Besides learning from structured input, I also investigated the interplay between structured input and output under the context of multi-task learning. In particular, I designed a multi-task learning algorithms that performs structured feature selection & task relationship Inference. We will demonstrate the applications of these structured models on subgraph based graph classification, networked data stream anomaly detection/localization, multiple cancer type prediction, neuron activity prediction and social behavior prediction. Finally, through my intern work at IBM T.J. Watson Research, I will demonstrate how to leverage structural information from mobile data (e.g. call detail record and GPS data) to derive important places from people's daily life for transit optimization and urban planning

Learning the Structure for Structured Sparsity

Structured sparsity has recently emerged in statistics, machine learning and signal processing as a promising paradigm for learning in high-dimensional settings. All existing methods for learning under the assumption of structured sparsity rely on prior knowledge on how to weight (or how to penalize) individual subsets of variables during the subset selection process, which is not available in general. Inferring group weights from data is a key open research problem in structured sparsity.In this paper, we propose a Bayesian approach to the problem of group weight learning. We model the group weights as hyperparameters of heavy-tailed priors on groups of variables and derive an approximate inference scheme to infer these hyperparameters. We empirically show that we are able to recover the model hyperparameters when the data are generated from the model, and we demonstrate the utility of learning weights in synthetic and real denoising problems