We present SciRIFF (Scientific Resource for Instruction-Following and Finetuning), a dataset of 137K instruction-following demonstrations for 54 tasks covering five essential scientific literature understanding capabilities: information extraction, summarization, question answering, claim verification, and classification. SciRIFF demonstrations are notable for their long input contexts, detailed task specifications, and complex structured outputs. While instruction-following resources are available in specific domains such as clinical medicine and chemistry, SciRIFF is the first dataset focused on extracting and synthesizing information from research literature across a wide range of scientific fields. To demonstrate the utility of SciRIFF, we develop a sample-efficient strategy to adapt a general instruction-following model for science by performing additional finetuning on a mix of general-domain and SciRIFF demonstrations. In evaluations on nine held-out scientific tasks, our model -- called SciTulu -- improves over a strong LLM baseline by 28.1% and 6.5% at the 7B and 70B scales respectively, while maintaining general instruction-following performance within 2% of the baseline. We are optimistic that SciRIFF will facilitate the development and evaluation of LLMs to help researchers navigate the ever-growing body of scientific literature. We release our dataset, model checkpoints, and data processing and evaluation code to enable further research.

Calculating mealtime insulin doses poses a significant challenge for individuals with Type 1 Diabetes (T1D). Doses should perfectly compensate for expected post-meal glucose excursions, requiring a profound understanding of the individual's insulin sensitivity and the meal macronutrients'. Usually, people rely on intuition and experience to develop this understanding. In this work, we demonstrate how a reinforcement learning agent, employing a self-attention encoder network, can effectively mimic and enhance this intuitive process. Trained on 80 virtual subjects from the FDA-approved UVA/Padova T1D adult cohort and tested on twenty, self-attention demonstrates superior performance compared to other network architectures. Results reveal a significant reduction in glycemic risk, from 16.5 to 9.6 in scenarios using sensor-augmented pump and from 9.1 to 6.7 in scenarios using automated insulin delivery. This new paradigm bypasses conventional therapy parameters, offering the potential to simplify treatment and promising improved quality of life and glycemic outcomes for people with T1D.

Recent advancements in structure-based drug design (SBDD) have significantly enhanced the efficiency and precision of drug discovery by generating molecules tailored to bind specific protein pockets. Despite these technological strides, their practical application in real-world drug development remains challenging due to the complexities of synthesizing and testing these molecules. The reliability of the Vina docking score, the current standard for assessing binding abilities, is increasingly questioned due to its susceptibility to overfitting. To address these limitations, we propose a comprehensive evaluation framework that includes assessing the similarity of generated molecules to known active compounds, introducing a virtual screening-based metric for practical deployment capabilities, and re-evaluating binding affinity more rigorously. Our experiments reveal that while current SBDD models achieve high Vina scores, they fall short in practical usability metrics, highlighting a significant gap between theoretical predictions and real-world applicability. Our proposed metrics and dataset aim to bridge this gap, enhancing the practical applicability of future SBDD models and aligning them more closely with the needs of pharmaceutical research and development.

The global cost of drug discovery and development exceeds $200 billion annually. The main results of drug discovery and development are the outcomes of clinical trials, which directly influence the regulatory approval of new drug candidates and ultimately affect patient outcomes. Despite their significance, large-scale, high-quality clinical trial outcome data are not readily available to the public. Suppose a large clinical trial outcome dataset is provided; machine learning researchers can potentially develop accurate prediction models using past trials and outcome labels, which could help prioritize and optimize therapeutic programs, ultimately benefiting patients. This paper introduces Clinical Trial Outcome (CTO) dataset, the largest trial outcome dataset with around 479K clinical trials, aggregating outcomes from multiple sources of weakly supervised labels, minimizing the noise from individual sources, and eliminating the need for human annotation. These sources include large language model (LLM) decisions on trial-related documents, news headline sentiments, stock prices of trial sponsors, trial linkages across phases, and other signals such as patient dropout rates and adverse events. CTO's labels show unprecedented agreement with supervised clinical trial outcome labels from test split of the supervised TOP dataset, with a 91 F1.

Optical continuous glucose monitoring (CGM) systems are emerging for personalized glucose management owing to their lower cost and prolonged durability compared to conventional electrochemical CGMs. Here, we report a computational CGM system, which integrates a biocompatible phosphorescence-based insertable biosensor and a custom-designed phosphorescence lifetime imager (PLI). This compact and cost-effective PLI is designed to capture phosphorescence lifetime images of an insertable sensor through the skin, where the lifetime of the emitted phosphorescence signal is modulated by the local concentration of glucose. Because this phosphorescence signal has a very long lifetime compared to tissue autofluorescence or excitation leakage processes, it completely bypasses these noise sources by measuring the sensor emission over several tens of microseconds after the excitation light is turned off. The lifetime images acquired through the skin are processed by neural network-based models for misalignment-tolerant inference of glucose levels, accurately revealing normal, low (hypoglycemia) and high (hyperglycemia) concentration ranges. Using a 1-mm thick skin phantom mimicking the optical properties of human skin, we performed in vitro testing of the PLI using glucose-spiked samples, yielding 88.8% inference accuracy, also showing resilience to random and unknown misalignments within a lateral distance of ~4.7 mm with respect to the position of the insertable sensor underneath the skin phantom. Furthermore, the PLI accurately identified larger lateral misalignments beyond 5 mm, prompting user intervention for re-alignment. The misalignment-resilient glucose concentration inference capability of this compact and cost-effective phosphorescence lifetime imager makes it an appealing wearable diagnostics tool for real-time tracking of glucose and other biomarkers.

FDA Medical Device recalls are critical and time-sensitive events, requiring swift identification of impacted devices to inform the public of a recall event and ensure patient safety. The OpenFDA device recall dataset contains valuable information about ongoing device recall actions, but manually extracting relevant device information from the recall action summaries is a time-consuming task. Named Entity Recognition (NER) is a task in Natural Language Processing (NLP) that involves identifying and categorizing named entities in unstructured text. Existing NER models, including domain-specific models like BioBERT, struggle to correctly identify medical device trade names, part numbers and component terms within these summaries. To address this, we propose DeviceBERT, a medical device annotation, pre-processing and enrichment pipeline, which builds on BioBERT to identify and label medical device terminology in the device recall summaries with improved accuracy. Furthermore, we demonstrate that our approach can be applied effectively for performing entity recognition tasks where training data is limited or sparse.

Driven by the ever-growing volume and decentralized nature of data, coupled with the need to harness this data and generate knowledge from it, has led to the extensive use of distributed deep learning (DDL) techniques for training. These techniques rely on local training that is performed at the distributed nodes based on locally collected data, followed by a periodic synchronization process that combines these models to create a global model. However, frequent synchronization of DL models, encompassing millions to many billions of parameters, creates a communication bottleneck, severely hindering scalability. Worse yet, DDL algorithms typically waste valuable bandwidth, and make themselves less practical in bandwidth-constrained federated settings, by relying on overly simplistic, periodic, and rigid synchronization schedules. These drawbacks also have a direct impact on the time required for the training process, necessitating excessive time for data communication. To address these shortcomings, we propose Federated Dynamic Averaging (FDA), a communication-efficient DDL strategy that dynamically triggers synchronization based on the value of the model variance. In essence, the costly synchronization step is triggered only if the local models, which are initialized from a common global model after each synchronization, have significantly diverged. This decision is facilitated by the communication of a small local state from each distributed node/worker. Through extensive experiments across a wide range of learning tasks we demonstrate that FDA reduces communication cost by orders of magnitude, compared to both traditional and cutting-edge communication-efficient algorithms. Additionally, we show that FDA maintains robust performance across diverse data heterogeneity settings.

Large language models (LLMs) have transformed AI and achieved breakthrough performance on a wide range of tasks that require human intelligence. In science, perhaps the most interesting application of LLMs is for hypothesis formation. A feature of LLMs, which results from their probabilistic structure, is that the output text is not necessarily a valid inference from the training text. These are 'hallucinations', and are a serious problem in many applications. However, in science, hallucinations may be useful: they are novel hypotheses whose validity may be tested by laboratory experiments. Here we experimentally test the use of LLMs as a source of scientific hypotheses using the domain of breast cancer treatment. We applied the LLM GPT4 to hypothesize novel pairs of FDA-approved non-cancer drugs that target the MCF7 breast cancer cell line relative to the non-tumorigenic breast cell line MCF10A. In the first round of laboratory experiments GPT4 succeeded in discovering three drug combinations (out of 12 tested) with synergy scores above the positive controls. These combinations were itraconazole + atenolol, disulfiram + simvastatin and dipyridamole + mebendazole. GPT4 was then asked to generate new combinations after considering its initial results. It then discovered three more combinations with positive synergy scores (out of four tested), these were disulfiram + fulvestrant, mebendazole + quinacrine and disulfiram + quinacrine. A limitation of GPT4 as a generator of hypotheses was that its explanations for them were formulaic and unconvincing. We conclude that LLMs are an exciting novel source of scientific hypotheses.

Recent progress in Graph Neural Networks (GNNs) has greatly enhanced the ability to model complex molecular structures for predicting properties. Nevertheless, molecular data encompasses more than just graph structures, including textual and visual information that GNNs do not handle well. To bridge this gap, we present an innovative framework that utilizes multimodal molecular data to extract insights from Large Language Models (LLMs). We introduce GALLON (Graph Learning from Large Language Model Distillation), a framework that synergizes the capabilities of LLMs and GNNs by distilling multimodal knowledge into a unified Multilayer Perceptron (MLP). This method integrates the rich textual and visual data of molecules with the structural analysis power of GNNs. Extensive experiments reveal that our distilled MLP model notably improves the accuracy and efficiency of molecular property predictions.

Natural language processing (NLP) is utilized in a wide range of fields, where words in text are typically transformed into feature vectors called embeddings. BioConceptVec is a specific example of embeddings tailored for biology, trained on approximately 30 million PubMed abstracts using models such as skip-gram. Generally, word embeddings are known to solve analogy tasks through simple vector arithmetic. For instance, $\mathrm{\textit{king}} - \mathrm{\textit{man}} + \mathrm{\textit{woman}}$ predicts $\mathrm{\textit{queen}}$. In this study, we demonstrate that BioConceptVec embeddings, along with our own embeddings trained on PubMed abstracts, contain information about drug-gene relations and can predict target genes from a given drug through analogy computations. We also show that categorizing drugs and genes using biological pathways improves performance. Furthermore, we illustrate that vectors derived from known relations in the past can predict unknown future relations in datasets divided by year.