Paradigms for computational nucleic acid design

The design of DNA and RNA sequences is critical for many endeavors, from DNA nanotechnology, to PCR‐based applications, to DNA hybridization arrays. Results in the literature rely on a wide variety of design criteria adapted to the particular requirements of each application. Using an extensively studied thermodynamic model, we perform a detailed study of several criteria for designing sequences intended to adopt a target secondary structure. We conclude that superior design methods should explicitly implement both a positive design paradigm (optimize affinity for the target structure) and a negative design paradigm (optimize specificity for the target structure). The commonly used approaches of sequence symmetry minimization and minimum free‐energy satisfaction primarily implement negative design and can be strengthened by introducing a positive design component. Surprisingly, our findings hold for a wide range of secondary structures and are robust to modest perturbation of the thermodynamic parameters used for evaluating sequence quality, suggesting the feasibility and ongoing utility of a unified approach to nucleic acid design as parameter sets are refined further. Finally, we observe that designing for thermodynamic stability does not determine folding kinetics, emphasizing the opportunity for extending design criteria to target kinetic features of the energy landscape

Neural Models for Information Retrieval without Labeled Data

Recent developments of machine learning models, and in particular deep neural networks, have yielded significant improvements on several computer vision, natural language processing, and speech recognition tasks. Progress with information retrieval (IR) tasks has been slower, however, due to the lack of large-scale training data as well as neural network models specifically designed for effective information retrieval. In this dissertation, we address these two issues by introducing task-specific neural network architectures for a set of IR tasks and proposing novel unsupervised or \emph{weakly supervised} solutions for training the models. The proposed learning solutions do not require labeled training data. Instead, in our weak supervision approach, neural models are trained on a large set of noisy and biased training data obtained from external resources, existing models, or heuristics. We first introduce relevance-based embedding models that learn distributed representations for words and queries. We show that the learned representations can be effectively employed for a set of IR tasks, including query expansion, pseudo-relevance feedback, and query classification. We further propose a standalone learning to rank model based on deep neural networks. Our model learns a sparse representation for queries and documents. This enables us to perform efficient retrieval by constructing an inverted index in the learned semantic space. Our model outperforms state-of-the-art retrieval models, while performing as efficiently as term matching retrieval models. We additionally propose a neural network framework for predicting the performance of a retrieval model for a given query. Inspired by existing query performance prediction models, our framework integrates several information sources, such as retrieval score distribution and term distribution in the top retrieved documents. This leads to state-of-the-art results for the performance prediction task on various standard collections. We finally bridge the gap between retrieval and recommendation models, as the two key components in most information systems. Search and recommendation often share the same goal: helping people get the information they need at the right time. Therefore, joint modeling and optimization of search engines and recommender systems could potentially benefit both systems. In more detail, we introduce a retrieval model that is trained using user-item interaction (e.g., recommendation data), with no need to query-document relevance information for training. Our solutions and findings in this dissertation smooth the path towards learning efficient and effective models for various information retrieval and related tasks, especially when large-scale training data is not available

A framework for clustering and adaptive topic tracking on evolving text and social media data streams.

Recent advances and widespread usage of online web services and social media platforms, coupled with ubiquitous low cost devices, mobile technologies, and increasing capacity of lower cost storage, has led to a proliferation of Big data, ranging from, news, e-commerce clickstreams, and online business transactions to continuous event logs and social media expressions. These large amounts of online data, often referred to as data streams, because they get generated at extremely high throughputs or velocity, can make conventional and classical data analytics methodologies obsolete. For these reasons, the issues of management and analysis of data streams have been researched extensively in recent years. The special case of social media Big Data brings additional challenges, particularly because of the unstructured nature of the data, specifically free text. One classical approach to mine text data has been Topic Modeling. Topic Models are statistical models that can be used for discovering the abstract ``topics\u27\u27 that may occur in a corpus of documents. Topic models have emerged as a powerful technique in machine learning and data science, providing a great balance between simplicity and complexity. They also provide sophisticated insight without the need for real natural language understanding. However they have not been designed to cope with the type of text data that is abundant on social media platforms, but rather for traditional medium size corpora consisting of longer documents, adhering to a specific language and typically spanning a stable set of topics. Unlike traditional document corpora, social media messages tend to be very short, sparse, noisy, and do not adhere to a standard vocabulary, linguistic patterns, or stable topic distributions. They are also generated at high velocity that impose high demands on topic modeling; and their evolving or dynamic nature, makes any set of results from topic modeling quickly become stale in the face of changes in the textual content and topics discussed within social media streams. In this dissertation, we propose an integrated topic modeling framework built on top of an existing stream-clustering framework called Stream-Dashboard, which can extract, isolate, and track topics over any given time period. In this new framework, Stream Dashboard first clusters the data stream points into homogeneous groups. Then data from each group is ushered to the topic modeling framework which extracts finer topics from the group. The proposed framework tracks the evolution of the clusters over time to detect milestones corresponding to changes in topic evolution, and to trigger an adaptation of the learned groups and topics at each milestone. The proposed approach to topic modeling is different from a generic Topic Modeling approach because it works in a compartmentalized fashion, where the input document stream is split into distinct compartments, and Topic Modeling is applied on each compartment separately. Furthermore, we propose extensions to existing topic modeling and stream clustering methods, including: an adaptive query reformulation approach to help focus on the topic discovery with time; a topic modeling extension with adaptive hyper-parameter and with infinite vocabulary; an adaptive stream clustering algorithm incorporating the automated estimation of dynamic, cluster-specific temporal scales for adaptive forgetting to help facilitate clustering in a fast evolving data stream. Our experimental results show that the proposed adaptive forgetting clustering algorithm can mine better quality clusters; that our proposed compartmentalized framework is able to mine topics of better quality compared to competitive baselines; and that the proposed framework can automatically adapt to focus on changing topics using the proposed query reformulation strategy

Information Retrieval: Recent Advances and Beyond

In this paper, we provide a detailed overview of the models used for information retrieval in the first and second stages of the typical processing chain. We discuss the current state-of-the-art models, including methods based on terms, semantic retrieval, and neural. Additionally, we delve into the key topics related to the learning process of these models. This way, this survey offers a comprehensive understanding of the field and is of interest for for researchers and practitioners entering/working in the information retrieval domain

Multi-expert synthesis for versatile locomotion and manipulation skills

This work focuses on generating multiple coordinated motor skills for intelligent systems and studies a Multi-Expert Synthesis (MES) approach to achieve versatile robotic skills for locomotion and manipulation. MES embeds and uses expert skills to solve new composite tasks, and is able to synthesise and coordinate different and multiple skills smoothly. We proposed essential and effective design guidelines for training successful MES policies in simulation, which were deployed on both floating- and fixed-base robots. We formulated new algorithms to systematically determine task-relevant state variables for each individual experts which improved robustness and learning efficiency, and an explicit enforcement objective to diversify skills among different experts. The capabilities of MES policies were validated in both simulation and real experiments for locomotion and bi-manual manipulation. We demonstrated that the MES policies achieved robust locomotion on the quadruped ANYmal by fusing the gait recovery and trotting skills. For object manipulation, the MES policies learned to first reconfigure an object in an ungraspable pose and then grasp it through cooperative dual-arm manipulation

A Survey on Metric Learning for Feature Vectors and Structured Data

The need for appropriate ways to measure the distance or similarity between data is ubiquitous in machine learning, pattern recognition and data mining, but handcrafting such good metrics for specific problems is generally difficult. This has led to the emergence of metric learning, which aims at automatically learning a metric from data and has attracted a lot of interest in machine learning and related fields for the past ten years. This survey paper proposes a systematic review of the metric learning literature, highlighting the pros and cons of each approach. We pay particular attention to Mahalanobis distance metric learning, a well-studied and successful framework, but additionally present a wide range of methods that have recently emerged as powerful alternatives, including nonlinear metric learning, similarity learning and local metric learning. Recent trends and extensions, such as semi-supervised metric learning, metric learning for histogram data and the derivation of generalization guarantees, are also covered. Finally, this survey addresses metric learning for structured data, in particular edit distance learning, and attempts to give an overview of the remaining challenges in metric learning for the years to come.Comment: Technical report, 59 pages. Changes in v2: fixed typos and improved presentation. Changes in v3: fixed typos. Changes in v4: fixed typos and new method