Surpassing the Human Accuracy: Detecting Gallbladder Cancer from USG Images with Curriculum Learning

We explore the potential of CNN-based models for gallbladder cancer (GBC) detection from ultrasound (USG) images as no prior study is known. USG is the most common diagnostic modality for GB diseases due to its low cost and accessibility. However, USG images are challenging to analyze due to low image quality, noise, and varying viewpoints due to the handheld nature of the sensor. Our exhaustive study of state-of-the-art (SOTA) image classification techniques for the problem reveals that they often fail to learn the salient GB region due to the presence of shadows in the USG images. SOTA object detection techniques also achieve low accuracy because of spurious textures due to noise or adjacent organs. We propose GBCNet to tackle the challenges in our problem. GBCNet first extracts the regions of interest (ROIs) by detecting the GB (and not the cancer), and then uses a new multi-scale, second-order pooling architecture specializing in classifying GBC. To effectively handle spurious textures, we propose a curriculum inspired by human visual acuity, which reduces the texture biases in GBCNet. Experimental results demonstrate that GBCNet significantly outperforms SOTA CNN models, as well as the expert radiologists. Our technical innovations are generic to other USG image analysis tasks as well. Hence, as a validation, we also show the efficacy of GBCNet in detecting breast cancer from USG images. Project page with source code, trained models, and data is available at https://gbc-iitd.github.io/gbcnet

Multi-source Neural Topic Modeling in Multi-view Embedding Spaces

Though word embeddings and topics are complementary representations, several past works have only used pretrained word embeddings in (neural) topic modeling to address data sparsity in short-text or small collection of documents. This work presents a novel neural topic modeling framework using multi-view embedding spaces: (1) pretrained topic-embeddings, and (2) pretrained word-embeddings (context insensitive from Glove and context-sensitive from BERT models) jointly from one or many sources to improve topic quality and better deal with polysemy. In doing so, we first build respective pools of pretrained topic (i.e., TopicPool) and word embeddings (i.e., WordPool). We then identify one or more relevant source domain(s) and transfer knowledge to guide meaningful learning in the sparse target domain. Within neural topic modeling, we quantify the quality of topics and document representations via generalization (perplexity), interpretability (topic coherence) and information retrieval (IR) using short-text, long-text, small and large document collections from news and medical domains. Introducing the multi-source multi-view embedding spaces, we have shown state-of-the-art neural topic modeling using 6 source (high-resource) and 5 target (low-resource) corpora.

TopicBERT for Energy Efficient Document Classification

Prior research notes that BERT's computational cost grows quadratically with sequence length thus leading to longer training times, higher GPU memory constraints and carbon emissions. While recent work seeks to address these scalability issues at pre-training, these issues are also prominent in fine-tuning especially for long sequence tasks like document classification. Our work thus focuses on optimizing the computational cost of fine-tuning for document classification. We achieve this by complementary learning of both topic and language models in a unified framework, named TopicBERT. This significantly reduces the number of self-attention operations - a main performance bottleneck. Consequently, our model achieves a 1.4x ($\sim40\%$) speedup with $\sim40\%$ reduction in $CO_2$ emission while retaining $99.9\%$ performance over 5 datasets.

Explainable and Discourse Topic-aware Neural Language Understanding

Marrying topic models and language models exposes language understanding to a broader source of document-level context beyond sentences via topics. While introducing topical semantics in language models, existing approaches incorporate latent document topic proportions and ignore topical discourse in sentences of the document. This work extends the line of research by additionally introducing an explainable topic representation in language understanding, obtained from a set of key terms correspondingly for each latent topic of the proportion. Moreover, we retain sentence-topic associations along with document-topic association by modeling topical discourse for every sentence in the document. We present a novel neural composite language model that exploits both the latent and explainable topics along with topical discourse at sentence-level in a joint learning framework of topic and language models. Experiments over a range of tasks such as language modeling, word sense disambiguation, document classification, retrieval and text generation demonstrate ability of the proposed model in improving language understanding.

Neural Topic Modeling with Continual Lifelong Learning

Lifelong learning has recently attracted attention in building machine learning systems that continually accumulate and transfer knowledge to help future learning. Unsupervised topic modeling has been popularly used to discover topics from document collections. However, the application of topic modeling is challenging due to data sparsity, e.g., in a small collection of (short) documents and thus, generate incoherent topics and sub-optimal document representations. To address the problem, we propose a lifelong learning framework for neural topic modeling that can continuously process streams of document collections, accumulate topics and guide future topic modeling tasks by knowledge transfer from several sources to better deal with the sparse data. In the lifelong process, we particularly investigate jointly: (1) sharing generative homologies (latent topics) over lifetime to transfer prior knowledge, and (2) minimizing catastrophic forgetting to retain the past learning via novel selective data augmentation, co-training and topic regularization approaches. Given a stream of document collections, we apply the proposed Lifelong Neural Topic Modeling (LNTM) framework in modeling three sparse document collections as future tasks and demonstrate improved performance quantified by perplexity, topic coherence and information retrieval task.

Linguistically Informed Relation Extraction and Neural Architectures for Nested Named Entity Recognition in BioNLP-OST 2019

Named Entity Recognition (NER) and Relation Extraction (RE) are essential tools in distilling knowledge from biomedical literature. This paper presents our findings from participating in BioNLP Shared Tasks 2019. We addressed Named Entity Recognition including nested entities extraction, Entity Normalization and Relation Extraction. Our proposed approach of Named Entities can be generalized to different languages and we have shown it's effectiveness for English and Spanish text. We investigated linguistic features, hybrid loss including ranking and Conditional Random Fields (CRF), multi-task objective and token-level ensembling strategy to improve NER. We employed dictionary based fuzzy and semantic search to perform Entity Normalization. Finally, our RE system employed Support Vector Machine (SVM) with linguistic features. Our NER submission (team:MIC-CIS) ranked first in BB-2019 norm+NER task with standard error rate (SER) of 0.7159 and showed competitive performance on PharmaCo NER task with F1-score of 0.8662. Our RE system ranked first in the SeeDev-binary Relation Extraction Task with F1-score of 0.3738.

BioNLP-OST 2019 RDoC Tasks: Multi-grain Neural Relevance Ranking Using Topics and Attention Based Query-Document-Sentence Interactions

This paper presents our system details and results of participation in the RDoC Tasks of BioNLP-OST 2019. Research Domain Criteria (RDoC) construct is a multi-dimensional and broad framework to describe mental health disorders by combining knowledge from genomics to behaviour. Non-availability of RDoC labelled dataset and tedious labelling process hinders the use of RDoC framework to reach its full potential in Biomedical research community and Healthcare industry. Therefore, Task-1 aims at retrieval and ranking of PubMed abstracts relevant to a given RDoC construct and Task-2 aims at extraction of the most relevant sentence from a given PubMed abstract. We investigate (1) attention based supervised neural topic model and SVM for retrieval and ranking of PubMed abstracts and, further utilize BM25 and other relevance measures for re-ranking, (2) supervised and unsupervised sentence ranking models utilizing multi-view representations comprising of query-aware attention-based sentence representation (QAR), bag-of-words (BoW) and TF-IDF. Our best systems achieved 1st rank and scored 0.86 mean average precision (mAP) and 0.58 macro average accuracy (MAA) in Task-1 and Task-2 respectively.

Lifelong Neural Topic Learning in Contextualized Autoregressive Topic Models of Language via Informative Transfers

Topic models such as LDA, DocNADE, iDocNADEe have been popular in document analysis. However, the traditional topic models have several limitations including: (1) Bag-of-words (BoW) assumption, where they ignore word ordering, (2) Data sparsity, where the application of topic models is challenging due to limited word co-occurrences, leading to incoherent topics and (3) No Continuous Learning framework for topic learning in lifelong fashion, exploiting historical knowledge (or latent topics) and minimizing catastrophic forgetting. This thesis focuses on addressing the above challenges within neural topic modeling framework. We propose: (1) Contextualized topic model that combines a topic and a language model and introduces linguistic structures (such as word ordering, syntactic and semantic features, etc.) in topic modeling, (2) A novel lifelong learning mechanism into neural topic modeling framework to demonstrate continuous learning in sequential document collections and minimizing catastrophic forgetting. Additionally, we perform a selective data augmentation to alleviate the need for complete historical corpora during data hallucination or replay.

Multi-view and Multi-source Transfers in Neural Topic Modeling with Pretrained Topic and Word Embeddings

Though word embeddings and topics are complementary representations, several past works have only used pre-trained word embeddings in (neural) topic modeling to address data sparsity problem in short text or small collection of documents. However, no prior work has employed (pre-trained latent) topics in transfer learning paradigm. In this paper, we propose an approach to (1) perform knowledge transfer using latent topics obtained from a large source corpus, and (2) jointly transfer knowledge via the two representations (or views) in neural topic modeling to improve topic quality, better deal with polysemy and data sparsity issues in a target corpus. In doing so, we first accumulate topics and word representations from one or many source corpora to build a pool of topics and word vectors. Then, we identify one or multiple relevant source domain(s) and take advantage of corresponding topics and word features via the respective pools to guide meaningful learning in the sparse target domain. We quantify the quality of topic and document representations via generalization (perplexity), interpretability (topic coherence) and information retrieval (IR) using short-text, long-text, small and large document collections from news and medical domains. We have demonstrated the state-of-the-art results on topic modeling with the proposed framework.