Physics-Informed Neural Networks (PINNs) leverage machine learning with differential equations to solve direct and inverse problems, ensuring predictions follow physical laws. Physiologically based pharmacokinetic (PBPK) modeling advances beyond classical compartmental approaches by using a mechanistic, physiology focused framework. A PBPK model is based on a system of ODEs, with each equation representing the mass balance of a drug in a compartment, such as an organ or tissue. These ODEs include parameters that reflect physiological, biochemical, and drug-specific characteristics to simulate how the drug moves through the body. In this paper, we introduce PBPK-iPINN, a method to estimate drug-specific or patient-specific parameters and drug concentration profiles in PBPK brain compartment models using inverse PINNs. We demonstrate that, for the inverse problem to converge to the correct solution, the loss function components (data loss, initial conditions loss, and residual loss) must be appropriately weighted, and parameters (including number of layers, number of neurons, activation functions, learning rate, optimizer, and collocation points) must be carefully tuned. The performance of the PBPK-iPINN approach is then compared with established traditional numerical and statistical methods.

The current state-of-the-art (SOTA) for automated text-to-SQL still falls well short of expert human performance as measured by execution accuracy (EX) on the BIRD-SQL benchmark. The most accurate methods are also slow and expensive. To advance the SOTA for text-to-SQL while reducing cost and improving speed, we explore the combination of low-cost fine tuning, novel methods for diverse retrieval-augmented generation (RAG) and new input and output formats that help large language models (LLMs) achieve higher EX. We introduce two new methods, Dubo-SQL v1 and v2. Dubo-SQL v1 sets a new record for EX on the holdout test set of BIRD-SQL. Dubo-SQL v2 achieves even higher performance on the BIRD-SQL dev set. Dubo-SQL v1 relies on LLMs from OpenAI, but uses the low-cost GPT-3.5 Turbo while exceeding the performance of the next-best model using OpenAI, which instead uses the more expensive GPT-4. Dubo-SQL v1 exceeds the performance of the next-best model using GPT-3.5 by over 20%. Dubo-SQL v2 uses GPT-4 Turbo and RAG in place of fine tuning to push EX higher.

We introduce a new open information extraction (OIE) benchmark for pre-trained language models (LM). Recent studies have demonstrated that pre-trained LMs, such as BERT and GPT, may store linguistic and relational knowledge. In particular, LMs are able to answer ``fill-in-the-blank'' questions when given a pre-defined relation category. Instead of focusing on pre-defined relations, we create an OIE benchmark aiming to fully examine the open relational information present in the pre-trained LMs. We accomplish this by turning pre-trained LMs into zero-shot OIE systems. Surprisingly, pre-trained LMs are able to obtain competitive performance on both standard OIE datasets (CaRB and Re-OIE2016) and two new large-scale factual OIE datasets (TAC KBP-OIE and Wikidata-OIE) that we establish via distant supervision. For instance, the zero-shot pre-trained LMs outperform the F1 score of the state-of-the-art supervised OIE methods on our factual OIE datasets without needing to use any training sets. Our code and datasets are available at https://github.com/cgraywang/IELM

This paper shows how to construct knowledge graphs (KGs) from pre-trained language models (e.g., BERT, GPT-2/3), without human supervision. Popular KGs (e.g, Wikidata, NELL) are built in either a supervised or semi-supervised manner, requiring humans to create knowledge. Recent deep language models automatically acquire knowledge from large-scale corpora via pre-training. The stored knowledge has enabled the language models to improve downstream NLP tasks, e.g., answering questions, and writing code and articles. In this paper, we propose an unsupervised method to cast the knowledge contained within language models into KGs. We show that KGs are constructed with a single forward pass of the pre-trained language models (without fine-tuning) over the corpora. We demonstrate the quality of the constructed KGs by comparing to two KGs (Wikidata, TAC KBP) created by humans. Our KGs also provide open factual knowledge that is new in the existing KGs. Our code and KGs will be made publicly available.