How can we effectively generate missing data transformations among tables in a data repository? Multiple versions of the same tables are generated from the iterative process when data scientists and machine learning engineers fine-tune their ML pipelines, making incremental improvements. This process often involves data transformation and augmentation that produces an augmented table based on its base version and related tables. However, data transformations are often not well-documented or completely missing, resulting in poor traceability, reproducibility and explainability of ML pipelines. In this paper, we propose DATALoRE, a framework that explains data changes between an initial dataset and its augmented version to improves traceability. Given a base table, DATALoRE first discovers its potentially related tables from the data repository using a variety of data discovery techniques. DATALoRE then effectively leverages a large language model (LLM) to generate a variety of data transformations that lead to the augmented table. DATALoRE validates these transformations and selects the minimum number of related tables to ensure traceability and reproducibility of the ML pipelines. A preliminary experiment shows that DATALoRE is able to effectively recovery data transformations on two benchmark datasets.

Foundation models (FMs) learn from large volumes of unlabeled data to demonstrate superior performance across a wide range of tasks. However, FMs developed for biomedical domains have largely remained unimodal, i.e., independently trained and used for tasks on protein sequences alone, small molecule structures alone, or clinical data alone. To overcome this limitation, we present BioBridge, a parameter-efficient learning framework, to bridge independently trained unimodal FMs to establish multimodal behavior. BioBridge achieves it by utilizing Knowledge Graphs (KG) to learn transformations between one unimodal FM and another without fine-tuning any underlying unimodal FMs. Our results demonstrate that BioBridge can beat the best baseline KG embedding methods (on average by ~ 76.3%) in cross-modal retrieval tasks. We also identify BioBridge demonstrates out-of-domain generalization ability by extrapolating to unseen modalities or relations. Additionally, we also show that BioBridge presents itself as a general-purpose retriever that can aid biomedical multimodal question answering as well as enhance the guided generation of novel drugs. Code is at https://github.com/RyanWangZf/BioBridge.

Miguel Ballesteros, Rishita Anubhai, Shuai Wang, Nima Pourdamghani, Yogarshi Vyas, Jie Ma, Parminder Bhatia, Kathleen McKeown, Yaser Al-Onaizan. Proceedings of the 2020 Conference on Empirical Methods in Natural Language Processing (EMNLP). 2020.

Kasturi Bhattacharjee, Miguel Ballesteros, Rishita Anubhai, Smaranda Muresan, Jie Ma, Faisal Ladhak, Yaser Al-Onaizan. Proceedings of the 2020 Conference on Empirical Methods in Natural Language Processing (EMNLP). 2020.

We show that an end-to-end deep learning approach can be used to recognize either English or Mandarin Chinese speech–two vastly different languages. Because it replaces entire pipelines of hand-engineered components with neural networks, end-to-end learning allows us to handle a diverse variety of speech including noisy environments, accents and different languages. Key to our approach is our application of HPC techniques, enabling experiments that previously took weeks to now run in days. This allows us to iterate more quickly to identify superior architectures and algorithms. As a result, in several cases, our system is competitive with the transcription of human workers when benchmarked on standard datasets. Finally, using a technique called Batch Dispatch with GPUs in the data center, we show that our system can be inexpensively deployed in an online setting, delivering low latency when serving users at scale.

SSL (Secure Sockets Layer) is the de facto standard for secure Internet communications. Security of SSL connections against an active network attacker depends on correctly validating public-key certificates presented when the connection is established.