arXiv subjects

Izhak Shafran

Publications and source records attributed to Izhak Shafran.

28 records · Page 2Linked to original sources

arXiv2021

R2D2: Relational Text Decoding with Transformers

We propose a novel framework for modeling the interaction between graphical structures and the natural language text associated with their nodes and edges. Existing approaches typically fall into two categories. On group ignores the relational structure by converting them into linear sequences and then utilize the highly successful Seq2Seq models. The other side ignores the sequential nature of the text by representing them as fixed-dimensional vectors and apply graph neural networks. Both simplifications lead to information loss. Our proposed method utilizes both the graphical structure as well as the sequential nature of the texts. The input to our model is a set of text segments associated with the nodes and edges of the graph, which are then processed with a transformer encoder-decoder model, equipped with a self-attention mechanism that is aware of the graphical relations between the nodes containing the segments. This also allows us to use BERT-like models that are already trained on large amounts of text. While the proposed model has wide applications, we demonstrate its capabilities on data-to-text generation tasks. Our approach compares favorably against state-of-the-art methods in four tasks without tailoring the model architecture. We also provide an early demonstration in a novel practical application -- generating clinical notes from the medical entities mentioned during clinical visits.

cs.CL↗

arXiv2021

Understanding Medical Conversations: Rich Transcription, Confidence Scores & Information Extraction

In this paper, we describe novel components for extracting clinically relevant information from medical conversations which will be available as Google APIs. We describe a transformer-based Recurrent Neural Network Transducer (RNN-T) model tailored for long-form audio, which can produce rich transcriptions including speaker segmentation, speaker role labeling, punctuation and capitalization. On a representative test set, we compare performance of RNN-T models with different encoders, units and streaming constraints. Our transformer-based streaming model performs at about 20% WER on the ASR task, 6% WDER on the diarization task, 43% SER on periods, 52% SER on commas, 43% SER on question marks and 30% SER on capitalization. Our recognizer is paired with a confidence model that utilizes both acoustic and lexical features from the recognizer. The model performs at about 0.37 NCE. Finally, we describe a RNN-T based tagging model. The performance of the model depends on the ontologies, with F-scores of 0.90 for medications, 0.76 for symptoms, 0.75 for conditions, 0.76 for diagnosis, and 0.61 for treatments. While there is still room for improvement, our results suggest that these models are sufficiently accurate for practical applications.

cs.LG↗

arXiv2020

Google COVID-19 Search Trends Symptoms Dataset: Anonymization Process Description (version 1.0)

This report describes the aggregation and anonymization process applied to the initial version of COVID-19 Search Trends symptoms dataset (published at https://goo.gle/covid19symptomdataset on September 2, 2020), a publicly available dataset that shows aggregated, anonymized trends in Google searches for symptoms (and some related topics). The anonymization process is designed to protect the daily symptom search activity of every user with $\varepsilon$-differential privacy for $\varepsilon$ = 1.68.

cs.CR↗

arXiv2020

The Medical Scribe: Corpus Development and Model Performance Analyses

There is a growing interest in creating tools to assist in clinical note generation using the audio of provider-patient encounters. Motivated by this goal and with the help of providers and medical scribes, we developed an annotation scheme to extract relevant clinical concepts. We used this annotation scheme to label a corpus of about 6k clinical encounters. This was used to train a state-of-the-art tagging model. We report ontologies, labeling results, model performances, and detailed analyses of the results. Our results show that the entities related to medications can be extracted with a relatively high accuracy of 0.90 F-score, followed by symptoms at 0.72 F-score, and conditions at 0.57 F-score. In our task, we not only identify where the symptoms are mentioned but also map them to canonical forms as they appear in the clinical notes. Of the different types of errors, in about 19-38% of the cases, we find that the model output was correct, and about 17-32% of the errors do not impact the clinical note. Taken together, the models developed in this work are more useful than the F-scores reflect, making it a promising approach for practical applications.

cs.CL↗

arXiv2019

Learning to Infer Entities, Properties and their Relations from Clinical Conversations

Recently we proposed the Span Attribute Tagging (SAT) Model (Du et al., 2019) to infer clinical entities (e.g., symptoms) and their properties (e.g., duration). It tackles the challenge of large label space and limited training data using a hierarchical two-stage approach that identifies the span of interest in a tagging step and assigns labels to the span in a classification step. We extend the SAT model to jointly infer not only entities and their properties but also relations between them. Most relation extraction models restrict inferring relations between tokens within a few neighboring sentences, mainly to avoid high computational complexity. In contrast, our proposed Relation-SAT (R-SAT) model is computationally efficient and can infer relations over the entire conversation, spanning an average duration of 10 minutes. We evaluate our model on a corpus of clinical conversations. When the entities are given, the R-SAT outperforms baselines in identifying relations between symptoms and their properties by about 32% (0.82 vs 0.62 F-score) and by about 50% (0.60 vs 0.41 F-score) on medications and their properties. On the more difficult task of jointly inferring entities and relations, the R-SAT model achieves a performance of 0.34 and 0.45 for symptoms and medications respectively, which is significantly better than 0.18 and 0.35 for the baseline model. The contributions of different components of the model are quantified using ablation analysis.

cs.CL↗

arXiv2019

Joint Speech Recognition and Speaker Diarization via Sequence Transduction

Speech applications dealing with conversations require not only recognizing the spoken words, but also determining who spoke when. The task of assigning words to speakers is typically addressed by merging the outputs of two separate systems, namely, an automatic speech recognition (ASR) system and a speaker diarization (SD) system. The two systems are trained independently with different objective functions. Often the SD systems operate directly on the acoustics and are not constrained to respect word boundaries and this deficiency is overcome in an ad hoc manner. Motivated by recent advances in sequence to sequence learning, we propose a novel approach to tackle the two tasks by a joint ASR and SD system using a recurrent neural network transducer. Our approach utilizes both linguistic and acoustic cues to infer speaker roles, as opposed to typical SD systems, which only use acoustic cues. We evaluated the performance of our approach on a large corpus of medical conversations between physicians and patients. Compared to a competitive conventional baseline, our approach improves word-level diarization error rate from 15.8% to 2.2%.

cs.CL↗

arXiv2019

Extracting Symptoms and their Status from Clinical Conversations

This paper describes novel models tailored for a new application, that of extracting the symptoms mentioned in clinical conversations along with their status. Lack of any publicly available corpus in this privacy-sensitive domain led us to develop our own corpus, consisting of about 3K conversations annotated by professional medical scribes. We propose two novel deep learning approaches to infer the symptom names and their status: (1) a new hierarchical span-attribute tagging (\SAT) model, trained using curriculum learning, and (2) a variant of sequence-to-sequence model which decodes the symptoms and their status from a few speaker turns within a sliding window over the conversation. This task stems from a realistic application of assisting medical providers in capturing symptoms mentioned by patients from their clinical conversations. To reflect this application, we define multiple metrics. From inter-rater agreement, we find that the task is inherently difficult. We conduct comprehensive evaluations on several contrasting conditions and observe that the performance of the models range from an F-score of 0.5 to 0.8 depending on the condition. Our analysis not only reveals the inherent challenges of the task, but also provides useful directions to improve the models.

cs.CL↗

arXiv2019

Complex Evolution Recurrent Neural Networks (ceRNNs)

Unitary Evolution Recurrent Neural Networks (uRNNs) have three attractive properties: (a) the unitary property, (b) the complex-valued nature, and (c) their efficient linear operators. The literature so far does not address -- how critical is the unitary property of the model? Furthermore, uRNNs have not been evaluated on large tasks. To study these shortcomings, we propose the complex evolution Recurrent Neural Networks (ceRNNs), which is similar to uRNNs but drops the unitary property selectively. On a simple multivariate linear regression task, we illustrate that dropping the constraints improves the learning trajectory. In copy memory task, ceRNNs and uRNNs perform identically, demonstrating that their superior performance over LSTMs is due to complex-valued nature and their linear operators. In a large scale real-world speech recognition, we find that pre-pending a uRNN degrades the performance of our baseline LSTM acoustic models, while pre-pending a ceRNN improves the performance over the baseline by 0.8% absolute WER.

cs.LG↗

arXiv2019

Audio De-identification: A New Entity Recognition Task

Named Entity Recognition (NER) has been mostly studied in the context of written text. Specifically, NER is an important step in de-identification (de-ID) of medical records, many of which are recorded conversations between a patient and a doctor. In such recordings, audio spans with personal information should be redacted, similar to the redaction of sensitive character spans in de-ID for written text. The application of NER in the context of audio de-identification has yet to be fully investigated. To this end, we define the task of audio de-ID, in which audio spans with entity mentions should be detected. We then present our pipeline for this task, which involves Automatic Speech Recognition (ASR), NER on the transcript text, and text-to-audio alignment. Finally, we introduce a novel metric for audio de-ID and a new evaluation benchmark consisting of a large labeled segment of the Switchboard and Fisher audio datasets and detail our pipeline's results on it.

cs.CL↗

arXiv2016

Fuzzy Statistical Matrices for Cell Classification

In this paper, we generalize image (texture) statistical descriptors and propose algorithms that improve their efficacy. Recently, a new method showed how the popular Co-Occurrence Matrix (COM) can be modified into a fuzzy version (FCOM) which is more effective and robust to noise. Here, we introduce new fuzzy versions of two additional higher order statistical matrices: the Run Length Matrix (RLM) and the Size Zone Matrix (SZM). We define the fuzzy zones and propose an efficient algorithm to compute the descriptors. We demonstrate the advantage of the proposed improvements over several state-of-the-art methods on three tasks from quantitative cell biology: analyzing and classifying Human Epithelial type 2 (HEp-2) cells using Indirect Immunofluorescence protocol (IFF).

cs.CV↗