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Digital Twin Generators for Disease Modeling
May 02, 2024
A patient's digital twin is a computational model that describes the evolution of their health over time. Digital twins have the potential to revolutionize medicine by enabling individual-level computer simulations of human health, which can be used to conduct more efficient clinical trials or to recommend personalized treatment options. Due to the overwhelming complexity of human biology, machine learning approaches that leverage large datasets of historical patients' longitudinal health records to generate patients' digital twins are more tractable than potential mechanistic models. In this manuscript, we describe a neural network architecture that can learn conditional generative models of clinical trajectories, which we call Digital Twin Generators (DTGs), that can create digital twins of individual patients. We show that the same neural network architecture can be trained to generate accurate digital twins for patients across 13 different indications simply by changing the training set and tuning hyperparameters. By introducing a general purpose architecture, we aim to unlock the ability to scale machine learning approaches to larger datasets and across more indications so that a digital twin could be created for any patient in the world.
Deep Learning Based Named Entity Recognition Models for Recipes
Feb 27, 2024Food touches our lives through various endeavors, including flavor, nourishment, health, and sustainability. Recipes are cultural capsules transmitted across generations via unstructured text. Automated protocols for recognizing named entities, the building blocks of recipe text, are of immense value for various applications ranging from information extraction to novel recipe generation. Named entity recognition is a technique for extracting information from unstructured or semi-structured data with known labels. Starting with manually-annotated data of 6,611 ingredient phrases, we created an augmented dataset of 26,445 phrases cumulatively. Simultaneously, we systematically cleaned and analyzed ingredient phrases from RecipeDB, the gold-standard recipe data repository, and annotated them using the Stanford NER. Based on the analysis, we sampled a subset of 88,526 phrases using a clustering-based approach while preserving the diversity to create the machine-annotated dataset. A thorough investigation of NER approaches on these three datasets involving statistical, fine-tuning of deep learning-based language models and few-shot prompting on large language models (LLMs) provides deep insights. We conclude that few-shot prompting on LLMs has abysmal performance, whereas the fine-tuned spaCy-transformer emerges as the best model with macro-F1 scores of 95.9%, 96.04%, and 95.71% for the manually-annotated, augmented, and machine-annotated datasets, respectively.
Sparse Graph Representations for Procedural Instructional Documents
Feb 06, 2024Computation of document similarity is a critical task in various NLP domains that has applications in deduplication, matching, and recommendation. Traditional approaches for document similarity computation include learning representations of documents and employing a similarity or a distance function over the embeddings. However, pairwise similarities and differences are not efficiently captured by individual representations. Graph representations such as Joint Concept Interaction Graph (JCIG) represent a pair of documents as a joint undirected weighted graph. JCIGs facilitate an interpretable representation of document pairs as a graph. However, JCIGs are undirected, and don't consider the sequential flow of sentences in documents. We propose two approaches to model document similarity by representing document pairs as a directed and sparse JCIG that incorporates sequential information. We propose two algorithms inspired by Supergenome Sorting and Hamiltonian Path that replace the undirected edges with directed edges. Our approach also sparsifies the graph to $O(n)$ edges from JCIG's worst case of $O(n^2)$. We show that our sparse directed graph model architecture consisting of a Siamese encoder and GCN achieves comparable results to the baseline on datasets not containing sequential information and beats the baseline by ten points on an instructional documents dataset containing sequential information.
Exploring Large Language Models for Code Explanation
Oct 25, 2023
Automating code documentation through explanatory text can prove highly beneficial in code understanding. Large Language Models (LLMs) have made remarkable strides in Natural Language Processing, especially within software engineering tasks such as code generation and code summarization. This study specifically delves into the task of generating natural-language summaries for code snippets, using various LLMs. The findings indicate that Code LLMs outperform their generic counterparts, and zero-shot methods yield superior results when dealing with datasets with dissimilar distributions between training and testing sets.
Data-driven decision-focused surrogate modeling
Aug 23, 2023
We introduce the concept of decision-focused surrogate modeling for solving computationally challenging nonlinear optimization problems in real-time settings. The proposed data-driven framework seeks to learn a simpler, e.g. convex, surrogate optimization model that is trained to minimize the decision prediction error, which is defined as the difference between the optimal solutions of the original and the surrogate optimization models. The learning problem, formulated as a bilevel program, can be viewed as a data-driven inverse optimization problem to which we apply a decomposition-based solution algorithm from previous work. We validate our framework through numerical experiments involving the optimization of common nonlinear chemical processes such as chemical reactors, heat exchanger networks, and material blending systems. We also present a detailed comparison of decision-focused surrogate modeling with standard data-driven surrogate modeling methods and demonstrate that our approach is significantly more data-efficient while producing simple surrogate models with high decision prediction accuracy.
Counterspeeches up my sleeve! Intent Distribution Learning and Persistent Fusion for Intent-Conditioned Counterspeech Generation
May 23, 2023
Counterspeech has been demonstrated to be an efficacious approach for combating hate speech. While various conventional and controlled approaches have been studied in recent years to generate counterspeech, a counterspeech with a certain intent may not be sufficient in every scenario. Due to the complex and multifaceted nature of hate speech, utilizing multiple forms of counter-narratives with varying intents may be advantageous in different circumstances. In this paper, we explore intent-conditioned counterspeech generation. At first, we develop IntentCONAN, a diversified intent-specific counterspeech dataset with 6831 counterspeeches conditioned on five intents, i.e., informative, denouncing, question, positive, and humour. Subsequently, we propose QUARC, a two-stage framework for intent-conditioned counterspeech generation. QUARC leverages vector-quantized representations learned for each intent category along with PerFuMe, a novel fusion module to incorporate intent-specific information into the model. Our evaluation demonstrates that QUARC outperforms several baselines by an average of 10% across evaluation metrics. An extensive human evaluation supplements our hypothesis of better and more appropriate responses than comparative systems.
Speaker Profiling in Multiparty Conversations
Apr 19, 2023
In conversational settings, individuals exhibit unique behaviors, rendering a one-size-fits-all approach insufficient for generating responses by dialogue agents. Although past studies have aimed to create personalized dialogue agents using speaker persona information, they have relied on the assumption that the speaker's persona is already provided. However, this assumption is not always valid, especially when it comes to chatbots utilized in industries like banking, hotel reservations, and airline bookings. This research paper aims to fill this gap by exploring the task of Speaker Profiling in Conversations (SPC). The primary objective of SPC is to produce a summary of persona characteristics for each individual speaker present in a dialogue. To accomplish this, we have divided the task into three subtasks: persona discovery, persona-type identification, and persona-value extraction. Given a dialogue, the first subtask aims to identify all utterances that contain persona information. Subsequently, the second task evaluates these utterances to identify the type of persona information they contain, while the third subtask identifies the specific persona values for each identified type. To address the task of SPC, we have curated a new dataset named SPICE, which comes with specific labels. We have evaluated various baselines on this dataset and benchmarked it with a new neural model, SPOT, which we introduce in this paper. Furthermore, we present a comprehensive analysis of SPOT, examining the limitations of individual modules both quantitatively and qualitatively.
Dimension reduction and redundancy removal through successive Schmidt decompositions
Feb 09, 2023
Quantum computers are believed to have the ability to process huge data sizes which can be seen in machine learning applications. In these applications, the data in general is classical. Therefore, to process them on a quantum computer, there is a need for efficient methods which can be used to map classical data on quantum states in a concise manner. On the other hand, to verify the results of quantum computers and study quantum algorithms, we need to be able to approximate quantum operations into forms that are easier to simulate on classical computers with some errors. Motivated by these needs, in this paper we study the approximation of matrices and vectors by using their tensor products obtained through successive Schmidt decompositions. We show that data with distributions such as uniform, Poisson, exponential, or similar to these distributions can be approximated by using only a few terms which can be easily mapped onto quantum circuits. The examples include random data with different distributions, the Gram matrices of iris flower, handwritten digits, 20newsgroup, and labeled faces in the wild. And similarly, some quantum operations such as quantum Fourier transform and variational quantum circuits with a small depth also may be approximated with a few terms that are easier to simulate on classical computers. Furthermore, we show how the method can be used to simplify quantum Hamiltonians: In particular, we show the application to randomly generated transverse field Ising model Hamiltonians. The reduced Hamiltonians can be mapped into quantum circuits easily and therefore can be simulated more efficiently.
Coherence and Diversity through Noise: Self-Supervised Paraphrase Generation via Structure-Aware Denoising
Feb 06, 2023
In this paper, we propose SCANING, an unsupervised framework for paraphrasing via controlled noise injection. We focus on the novel task of paraphrasing algebraic word problems having practical applications in online pedagogy as a means to reduce plagiarism as well as ensure understanding on the part of the student instead of rote memorization. This task is more complex than paraphrasing general-domain corpora due to the difficulty in preserving critical information for solution consistency of the paraphrased word problem, managing the increased length of the text and ensuring diversity in the generated paraphrase. Existing approaches fail to demonstrate adequate performance on at least one, if not all, of these facets, necessitating the need for a more comprehensive solution. To this end, we model the noising search space as a composition of contextual and syntactic aspects and sample noising functions consisting of either one or both aspects. This allows for learning a denoising function that operates over both aspects and produces semantically equivalent and syntactically diverse outputs through grounded noise injection. The denoising function serves as a foundation for learning a paraphrasing function which operates solely in the input-paraphrase space without carrying any direct dependency on noise. We demonstrate SCANING considerably improves performance in terms of both semantic preservation and producing diverse paraphrases through extensive automated and manual evaluation across 4 datasets.
A Privacy-Preserving Outsourced Data Model in Cloud Environment
Nov 24, 2022
Nowadays, more and more machine learning applications, such as medical diagnosis, online fraud detection, email spam filtering, etc., services are provided by cloud computing. The cloud service provider collects the data from the various owners to train or classify the machine learning system in the cloud environment. However, multiple data owners may not entirely rely on the cloud platform that a third party engages. Therefore, data security and privacy problems are among the critical hindrances to using machine learning tools, particularly with multiple data owners. In addition, unauthorized entities can detect the statistical input data and infer the machine learning model parameters. Therefore, a privacy-preserving model is proposed, which protects the privacy of the data without compromising machine learning efficiency. In order to protect the data of data owners, the epsilon-differential privacy is used, and fog nodes are used to address the problem of the lower bandwidth and latency in this proposed scheme. The noise is produced by the epsilon-differential mechanism, which is then added to the data. Moreover, the noise is injected at the data owner site to protect the owners data. Fog nodes collect the noise-added data from the data owners, then shift it to the cloud platform for storage, computation, and performing the classification tasks purposes.