Lipidomics generates large data that makes manual annotation and interpretation challenging. Lipid chemical and structural diversity with structural isomers further complicates annotation. Although, several commercial and open-source software for targeted lipid identification exists, it lacks automated method generation workflows and integration with statistical and bioinformatics tools. We have developed the Comprehensive Lipidomic Automated Workflow (CLAW) platform with integrated workflow for parsing, detailed statistical analysis and lipid annotations based on custom multiple reaction monitoring (MRM) precursor and product ion pair transitions. CLAW contains several modules including identification of carbon-carbon double bond position(s) in unsaturated lipids when combined with ozone electrospray ionization (OzESI)-MRM methodology. To demonstrate the utility of the automated workflow in CLAW, large-scale lipidomics data was collected with traditional and OzESI-MRM profiling on biological and non-biological samples. Specifically, a total of 1497 transitions organized into 10 MRM-based mass spectrometry methods were used to profile lipid droplets isolated from different brain regions of 18-24 month-old Alzheimer's disease mice and age-matched wild-type controls. Additionally, triacyclglycerols (TGs) profiles with carbon-carbon double bond specificity were generated from canola oil samples using OzESI-MRM profiling. We also developed an integrated language user interface with large language models using artificially intelligent (AI) agents that permits users to interact with the CLAW platform using a chatbot terminal to perform statistical and bioinformatic analyses. We envision CLAW pipeline to be used in high-throughput lipid structural identification tasks aiding users to generate automated lipidomics workflows ranging from data acquisition to AI agent-based bioinformatic analysis.

With the advancement in capabilities of Large Language Models (LLMs), one major step in the responsible and safe use of such LLMs is to be able to detect text generated by these models. While supervised AI-generated text detectors perform well on text generated by older LLMs, with the frequent release of new LLMs, building supervised detectors for identifying text from such new models would require new labeled training data, which is infeasible in practice. In this work, we tackle this problem and propose a domain generalization framework for the detection of AI-generated text from unseen target generators. Our proposed framework, EAGLE, leverages the labeled data that is available so far from older language models and learns features invariant across these generators, in order to detect text generated by an unknown target generator. EAGLE learns such domain-invariant features by combining the representational power of self-supervised contrastive learning with domain adversarial training. Through our experiments we demonstrate how EAGLE effectively achieves impressive performance in detecting text generated by unseen target generators, including recent state-of-the-art ones such as GPT-4 and Claude, reaching detection scores of within 4.7% of a fully supervised detector.

Language model-based code completion models have quickly grown in use, helping thousands of developers write code in many different programming languages. However, research on code completion models typically focuses on imperative languages such as Python and JavaScript, which results in a lack of representation for functional programming languages. Consequently, these models often perform poorly on functional languages such as Haskell. To investigate whether this can be alleviated, we evaluate the performance of two language models for code, CodeGPT and UniXcoder, on the functional programming language Haskell. We fine-tune and evaluate the models on Haskell functions sourced from a publicly accessible Haskell dataset on HuggingFace. Additionally, we manually evaluate the models using our novel translated HumanEval dataset. Our automatic evaluation shows that knowledge of imperative programming languages in the pre-training of LLMs may not transfer well to functional languages, but that code completion on functional languages is feasible. Consequently, this shows the need for more high-quality Haskell datasets. A manual evaluation on HumanEval-Haskell indicates CodeGPT frequently generates empty predictions and extra comments, while UniXcoder more often produces incomplete or incorrect predictions. Finally, we release HumanEval-Haskell, along with the fine-tuned models and all code required to reproduce our experiments on GitHub (https://github.com/AISE-TUDelft/HaskellCCEval).

Parameter-efficient finetuning (PEFT) is a key technique for adapting large language models (LLMs) to downstream tasks. In this paper, we study leveraging knowledge graph embeddings to improve the effectiveness of PEFT. We propose a knowledgeable adaptation method called KnowLA. It inserts an adaptation layer into an LLM to integrate the embeddings of entities appearing in the input text. The adaptation layer is trained in combination with LoRA on instruction data. Experiments on six benchmarks with two popular LLMs and three knowledge graphs demonstrate the effectiveness and robustness of KnowLA. We show that \modelname can help activate the relevant parameterized knowledge in an LLM to answer a question without changing its parameters or input prompts.

The capabilities of AI for biomedicine span a wide spectrum, from the atomic level, where it solves partial differential equations for quantum systems, to the molecular level, predicting chemical or protein structures, and further extending to societal predictions like infectious disease outbreaks. Recent advancements in large language models, exemplified by models like ChatGPT, have showcased significant prowess in natural language tasks, such as translating languages, constructing chatbots, and answering questions. When we consider biomedical data, we observe a resemblance to natural language in terms of sequences: biomedical literature and health records presented as text, biological sequences or sequencing data arranged in sequences, or sensor data like brain signals as time series. The question arises: Can we harness the potential of recent large language models to drive biomedical knowledge discoveries? In this survey, we will explore the application of large language models to three crucial categories of biomedical data: 1) textual data, 2) biological sequences, and 3) brain signals. Furthermore, we will delve into large language model challenges in biomedical research, including ensuring trustworthiness, achieving personalization, and adapting to multi-modal data representation

Event temporal relation (TempRel) is a primary subject of the event relation extraction task. However, the inherent ambiguity of TempRel increases the difficulty of the task. With the rise of prompt engineering, it is important to design effective prompt templates and verbalizers to extract relevant knowledge. The traditional manually designed templates struggle to extract precise temporal knowledge. This paper introduces a novel retrieval-augmented TempRel extraction approach, leveraging knowledge retrieved from large language models (LLMs) to enhance prompt templates and verbalizers. Our method capitalizes on the diverse capabilities of various LLMs to generate a wide array of ideas for template and verbalizer design. Our proposed method fully exploits the potential of LLMs for generation tasks and contributes more knowledge to our design. Empirical evaluations across three widely recognized datasets demonstrate the efficacy of our method in improving the performance of event temporal relation extraction tasks.

Recently, the number of parameters in DNNs has explosively increased, as exemplified by LLMs (Large Language Models), making inference on small-scale computers more difficult. Model compression technology is, therefore, essential for integration into products. In this paper, we propose a method of quantization-aware training. We introduce a novel normalization (Layer-Batch Normalization) that is independent of the mini-batch size and does not require any additional computation cost during inference. Then, we quantize the weights by the scaled round-clip function with the weight standardization. We also quantize activation functions using the same function and apply surrogate gradients to train the model with both quantized weights and the quantized activation functions. We call this method Magic for the age of Quantised DNNs (MaQD). Experimental results show that our quantization method can be achieved with minimal accuracy degradation.

We present ConVOI, a novel method for autonomous robot navigation in real-world indoor and outdoor environments using Vision Language Models (VLMs). We employ VLMs in two ways: first, we leverage their zero-shot image classification capability to identify the context or scenario (e.g., indoor corridor, outdoor terrain, crosswalk, etc) of the robot's surroundings, and formulate context-based navigation behaviors as simple text prompts (e.g. ``stay on the pavement"). Second, we utilize their state-of-the-art semantic understanding and logical reasoning capabilities to compute a suitable trajectory given the identified context. To this end, we propose a novel multi-modal visual marking approach to annotate the obstacle-free regions in the RGB image used as input to the VLM with numbers, by correlating it with a local occupancy map of the environment. The marked numbers ground image locations in the real-world, direct the VLM's attention solely to navigable locations, and elucidate the spatial relationships between them and terrains depicted in the image to the VLM. Next, we query the VLM to select numbers on the marked image that satisfy the context-based behavior text prompt, and construct a reference path using the selected numbers. Finally, we propose a method to extrapolate the reference trajectory when the robot's environmental context has not changed to prevent unnecessary VLM queries. We use the reference trajectory to guide a motion planner, and demonstrate that it leads to human-like behaviors (e.g. not cutting through a group of people, using crosswalks, etc.) in various real-world indoor and outdoor scenarios.

Navigating toward specific objects in unknown environments without additional training, known as Zero-Shot object navigation, poses a significant challenge in the field of robotics, which demands high levels of auxiliary information and strategic planning. Traditional works have focused on holistic solutions, overlooking the specific challenges agents encounter during navigation such as collision, low exploration efficiency, and misidentification of targets. To address these challenges, our work proposes TriHelper, a novel framework designed to assist agents dynamically through three primary navigation challenges: collision, exploration, and detection. Specifically, our framework consists of three innovative components: (i) Collision Helper, (ii) Exploration Helper, and (iii) Detection Helper. These components work collaboratively to solve these challenges throughout the navigation process. Experiments on the Habitat-Matterport 3D (HM3D) and Gibson datasets demonstrate that TriHelper significantly outperforms all existing baseline methods in Zero-Shot object navigation, showcasing superior success rates and exploration efficiency. Our ablation studies further underscore the effectiveness of each helper in addressing their respective challenges, notably enhancing the agent's navigation capabilities. By proposing TriHelper, we offer a fresh perspective on advancing the object navigation task, paving the way for future research in the domain of Embodied AI and visual-based navigation.

Pretrained large language models (LLMs) are currently state-of-the-art for solving the vast majority of natural language processing tasks. While many real-world applications still require fine-tuning to reach satisfactory levels of performance, many of them are in the low-data regime, making fine-tuning challenging. To address this, we propose LLM2LLM, a targeted and iterative data augmentation strategy that uses a teacher LLM to enhance a small seed dataset by augmenting additional data that can be used for fine-tuning on a specific task. LLM2LLM (1) fine-tunes a baseline student LLM on the initial seed data, (2) evaluates and extracts data points that the model gets wrong, and (3) uses a teacher LLM to generate synthetic data based on these incorrect data points, which are then added back into the training data. This approach amplifies the signal from incorrectly predicted data points by the LLM during training and reintegrates them into the dataset to focus on more challenging examples for the LLM. Our results show that LLM2LLM significantly enhances the performance of LLMs in the low-data regime, outperforming both traditional fine-tuning and other data augmentation baselines. LLM2LLM reduces the dependence on labor-intensive data curation and paves the way for more scalable and performant LLM solutions, allowing us to tackle data-constrained domains and tasks. We achieve improvements up to 24.2% on the GSM8K dataset, 32.6% on CaseHOLD, 32.0% on SNIPS, 52.6% on TREC and 39.8% on SST-2 over regular fine-tuning in the low-data regime using a LLaMA2-7B student model.