Recent advancements have positioned AI, and particularly Large Language Models (LLMs), as transformative tools for scientific research, capable of addressing complex tasks that require reasoning, problem-solving, and decision-making. Their exceptional capabilities suggest their potential as scientific research assistants but also highlight the need for holistic, rigorous, and domain-specific evaluation to assess effectiveness in real-world scientific applications. This paper describes a multifaceted methodology for Evaluating AI models as scientific Research Assistants (EAIRA) developed at Argonne National Laboratory. This methodology incorporates four primary classes of evaluations. 1) Multiple Choice Questions to assess factual recall; 2) Open Response to evaluate advanced reasoning and problem-solving skills; 3) Lab-Style Experiments involving detailed analysis of capabilities as research assistants in controlled environments; and 4) Field-Style Experiments to capture researcher-LLM interactions at scale in a wide range of scientific domains and applications. These complementary methods enable a comprehensive analysis of LLM strengths and weaknesses with respect to their scientific knowledge, reasoning abilities, and adaptability. Recognizing the rapid pace of LLM advancements, we designed the methodology to evolve and adapt so as to ensure its continued relevance and applicability. This paper describes the methodology state at the end of February 2025. Although developed within a subset of scientific domains, the methodology is designed to be generalizable to a wide range of scientific domains.

Large language models (LLMs) have demonstrated immense capabilities in understanding textual data and are increasingly being adopted to help researchers accelerate scientific discovery through knowledge extraction (information retrieval), knowledge distillation (summarizing key findings and methodologies into concise forms), and knowledge synthesis (aggregating information from multiple scientific sources to address complex queries, generate hypothesis and formulate experimental plans). However, scientific data often exists in both visual and textual modalities. Vision language models (VLMs) address this by incorporating a pretrained vision backbone for processing images and a cross-modal projector that adapts image tokens into the LLM dimensional space, thereby providing richer multimodal comprehension. Nevertheless, off-the-shelf VLMs show limited capabilities in handling domain-specific data and are prone to hallucinations. We developed intelligent assistants finetuned from LLaVA models to enhance multimodal understanding in low-dose radiation therapy (LDRT)-a benign approach used in the treatment of cancer-related illnesses. Using multilingual data from 42,673 articles, we devise complex reasoning and detailed description tasks for visual question answering (VQA) benchmarks. Our assistants, trained on 50,882 image-text pairs, demonstrate superior performance over base models as evaluated using LLM-as-a-judge approach, particularly in reducing hallucination and improving domain-specific comprehension.

The number of international benchmarking competitions is steadily increasing in various fields of machine learning (ML) research and practice. So far, however, little is known about the common practice as well as bottlenecks faced by the community in tackling the research questions posed. To shed light on the status quo of algorithm development in the specific field of biomedical imaging analysis, we designed an international survey that was issued to all participants of challenges conducted in conjunction with the IEEE ISBI 2021 and MICCAI 2021 conferences (80 competitions in total). The survey covered participants' expertise and working environments, their chosen strategies, as well as algorithm characteristics. A median of 72% challenge participants took part in the survey. According to our results, knowledge exchange was the primary incentive (70%) for participation, while the reception of prize money played only a minor role (16%). While a median of 80 working hours was spent on method development, a large portion of participants stated that they did not have enough time for method development (32%). 25% perceived the infrastructure to be a bottleneck. Overall, 94% of all solutions were deep learning-based. Of these, 84% were based on standard architectures. 43% of the respondents reported that the data samples (e.g., images) were too large to be processed at once. This was most commonly addressed by patch-based training (69%), downsampling (37%), and solving 3D analysis tasks as a series of 2D tasks. K-fold cross-validation on the training set was performed by only 37% of the participants and only 50% of the participants performed ensembling based on multiple identical models (61%) or heterogeneous models (39%). 48% of the respondents applied postprocessing steps.

The field of neuromorphic computing is in a period of active exploration. While many tools have been developed to simulate neuronal dynamics or convert deep networks to spiking models, general software libraries for learning rules remain underexplored. This is partly due to the diverse, challenging nature of efforts to design new learning rules, which range from encoding methods to gradient approximations, from population approaches that mimic the Bayesian brain to constrained learning algorithms deployed on memristor crossbars. To address this gap, we present Neko, a modular, extensible library with a focus on aiding the design of new learning algorithms. We demonstrate the utility of Neko in three exemplar cases: online local learning, probabilistic learning, and analog on-device learning. Our results show that Neko can replicate the state-of-the-art algorithms and, in one case, lead to significant outperformance in accuracy and speed. Further, it offers tools including gradient comparison that can help develop new algorithmic variants. Neko is an open source Python library that supports PyTorch and TensorFlow backends.