Biomedical researchers increasingly rely on large-scale structured databases for complex analytical tasks. However, current text-to-SQL systems often struggle to map qualitative scientific questions into executable SQL, particularly when implicit domain reasoning is required. We introduce BiomedSQL, the first benchmark explicitly designed to evaluate scientific reasoning in text-to-SQL generation over a real-world biomedical knowledge base. BiomedSQL comprises 68,000 question/SQL query/answer triples generated from templates and grounded in a harmonized BigQuery knowledge base that integrates gene-disease associations, causal inference from omics data, and drug approval records. Each question requires models to infer domain-specific criteria, such as genome-wide significance thresholds, effect directionality, or trial phase filtering, rather than rely on syntactic translation alone. We evaluate a range of open- and closed-source LLMs across prompting strategies and interaction paradigms. Our results reveal a substantial performance gap: GPT-o3-mini achieves 59.0% execution accuracy, while our custom multi-step agent, BMSQL, reaches 62.6%, both well below the expert baseline of 90.0%. BiomedSQL provides a new foundation for advancing text-to-SQL systems capable of supporting scientific discovery through robust reasoning over structured biomedical knowledge bases. Our dataset is publicly available at https://huggingface.co/datasets/NIH-CARD/BiomedSQL, and our code is open-source at https://github.com/NIH-CARD/biomedsql.

The proliferation of spectroscopic data across various scientific and engineering fields necessitates automated processing. We introduce OASIS (Omni-purpose Analysis of Spectra via Intelligent Systems), a machine learning (ML) framework for technique-independent, automated spectral analysis, encompassing denoising, baseline correction, and comprehensive peak parameter (location, intensity, FWHM) retrieval without human intervention. OASIS achieves its versatility through models trained on a strategically designed synthetic dataset incorporating features from numerous spectroscopy techniques. Critically, the development of innovative, task-specific loss functions-such as the vicinity peak response (ViPeR) for peak localization-enabled the creation of compact yet highly accurate models from this dataset, validated with experimental data from Raman, UV-vis, and fluorescence spectroscopy. OASIS demonstrates significant potential for applications including in situ experiments, high-throughput optimization, and online monitoring. This study underscores the optimization of the loss function as a key resource-efficient strategy to develop high-performance ML models.

A conventional LLM Unlearning setting consists of two subsets -"forget" and "retain", with the objectives of removing the undesired knowledge from the forget set while preserving the remaining knowledge from the retain. In privacy-focused unlearning research, a retain set is often further divided into neighbor sets, containing either directly or indirectly connected to the forget targets; and augmented by a general-knowledge set. A common practice in existing benchmarks is to employ only a single neighbor set, with general knowledge which fails to reflect the real-world data complexities and relationships. LLM Unlearning typically involves 1:1 sampling or cyclic iteration sampling. However, the efficacy and stability of these de facto standards have not been critically examined. In this study, we systematically evaluate these common practices. Our findings reveal that relying on a single neighbor set is suboptimal and that a standard sampling approach can obscure performance trade-offs. Based on this analysis, we propose and validate an initial set of best practices: (1) Incorporation of diverse neighbor sets to balance forget efficacy and model utility, (2) Standard 1:1 sampling methods are inefficient and yield poor results, (3) Our proposed Modular Entity-Level Unlearning (MELU) strategy as an alternative to cyclic sampling. We demonstrate that this modular approach, combined with robust algorithms, provides a clear and stable path towards effective unlearning.

Failure triage in design functional verification is critical but time-intensive, relying on manual specification reviews, log inspections, and waveform analyses. While machine learning (ML) has improved areas like stimulus generation and coverage closure, its application to RTL-level simulation failure triage, particularly for large designs, remains limited. VCDiag offers an efficient, adaptable approach using VCD data to classify failing waveforms and pinpoint likely failure locations. In the largest experiment, VCDiag achieves over 94% accuracy in identifying the top three most likely modules. The framework introduces a novel signal selection and statistical compression approach, achieving over 120x reduction in raw data size while preserving features essential for classification. It can also be integrated into diverse Verilog/SystemVerilog designs and testbenches.

This paper investigates false positive constructions: grammatical structures which an LLM hallucinates as distinct constructions but which human introspection does not support. Both a behavioural probing task using contextual embeddings and a meta-linguistic probing task using prompts are included, allowing us to distinguish between implicit and explicit linguistic knowledge. Both methods reveal that models do indeed hallucinate constructions. We then simulate hypothesis testing to determine what would have happened if a linguist had falsely hypothesized that these hallucinated constructions do exist. The high accuracy obtained shows that such false hypotheses would have been overwhelmingly confirmed. This suggests that construction probing methods suffer from a confirmation bias and raises the issue of what unknown and incorrect syntactic knowledge these models also possess.

We introduce an optimization framework for variational inference based on the coupled free energy, extending variational inference techniques to account for the curved geometry of the coupled exponential family. This family includes important heavy-tailed distributions such as the generalized Pareto and the Student's t. By leveraging the coupled free energy, which is equal to the coupled evidence lower bound (ELBO) of the inverted probabilities, we improve the accuracy and robustness of the learned model. The coupled generalization of Fisher Information metric and the affine connection. The method is applied to the design of a coupled variational autoencoder (CVAE). By using the coupling for both the distributions and cost functions, the reconstruction metric is derived to still be the mean-square average loss with modified constants. The novelty comes from sampling the heavy-tailed latent distribution with its associated coupled probability, which has faster decaying tails. The result is the ability to train a model robust against severe outliers, while assuring that the training process is stable. The Wasserstein-2 or Fréchet Inception Distance of the reconstructed CelebA images shows the CVAE has a 3\% improvement over the VAE after 5 epochs of training.

Large Language Models (LLMs) have recently gained attention in the life sciences due to their capacity to model, extract, and apply complex biological information. Beyond their classical use as chatbots, these systems are increasingly used for complex analysis and problem-solving in specialized fields, including bioinformatics. First, we introduce BIOPARS-BENCH, a dataset from over 10,000 scientific articles, textbooks, and medical websites. BioParsQA was also introduced to evaluate the proposed model, which consists of 5,231 Persian medical questions and answers. This study then introduces BioPars, a simple but accurate measure designed to assess LLMs for three main abilities: acquiring subject-specific knowledge, interpreting and synthesizing such knowledge, and demonstrating proper evidence. Comparing ChatGPT, Llama, and Galactica, our study highlights their ability to remember and retrieve learned knowledge but also reveals shortcomings in addressing higher-level, real-world questions and fine-grained inferences. These findings indicate the need for further fine-tuning to address the capabilities of LLM in bioinformatics tasks. To our knowledge, BioPars is the first application of LLM in Persian medical QA, especially for generating long answers. Evaluation of four selected medical QA datasets shows that BioPars has achieved remarkable results compared to comparative approaches. The model on BioParsQA achieved a ROUGE-L score of 29.99, which is an improvement over GPT-4 1.0. The model achieved a BERTScore of 90.87 with the MMR method. The MoverScore and BLEURT values were also higher in this model than the other three models. In addition, the reported scores for the model are MoverScore=60.43 and BLEURT=50.78. BioPars is an ongoing project and all resources related to its development will be made available via the following GitHub repository: https://github.com/amirap80/BioPars.

Spike sorting is a crucial step in decoding multichannel extracellular neural signals, enabling the identification of individual neuronal activity. A key challenge in brain-machine interfaces (BMIs) is achieving real-time, low-power spike sorting at the edge while keeping high neural decoding performance. This study introduces the Neuromorphic Sparse Sorter (NSS), a compact two-layer spiking neural network optimized for efficient spike sorting. NSS leverages the Locally Competitive Algorithm (LCA) for sparse coding to extract relevant features from noisy events with reduced computational demands. NSS learns to sort detected spike waveforms in an online fashion and operates entirely unsupervised. To exploit multi-bit spike coding capabilities of neuromorphic platforms like Intel's Loihi 2, a custom neuron model was implemented, enabling flexible power-performance trade-offs via adjustable spike bit-widths. Evaluations on simulated and real-world tetrode signals with biological drift showed NSS outperformed established pipelines such as WaveClus3 and PCA+KMeans. With 2-bit graded spikes, NSS on Loihi 2 outperformed NSS implemented with leaky integrate-and-fire neuron and achieved an F1-score of 77% (+10% improvement) while consuming 8.6mW (+1.65mW) when tested on a drifting recording, with a computational processing time of 0.25ms (+60 us) per inference.

An Advanced Persistent Threat (APT) is a multistage, highly sophisticated, and covert form of cyber threat that gains unauthorized access to networks to either steal valuable data or disrupt the targeted network. These threats often remain undetected for extended periods, emphasizing the critical need for early detection in networks to mitigate potential APT consequences. In this work, we propose a feature selection method for developing a lightweight intrusion detection system capable of effectively identifying APTs at the initial compromise stage. Our approach leverages the XGBoost algorithm and Explainable Artificial Intelligence (XAI), specifically utilizing the SHAP (SHapley Additive exPlanations) method for identifying the most relevant features of the initial compromise stage. The results of our proposed method showed the ability to reduce the selected features of the SCVIC-APT-2021 dataset from 77 to just four while maintaining consistent evaluation metrics for the suggested system. The estimated metrics values are 97% precision, 100% recall, and a 98% F1 score. The proposed method not only aids in preventing successful APT consequences but also enhances understanding of APT behavior at early stages.

--Machine learning (ML)-based intrusion detection systems (IDS) are vulnerable to adversarial attacks. It is crucial for an IDS to learn to recognize adversarial examples before malicious entities exploit them. In this paper, we generated adversarial samples using the Jacobian Saliency Map Attack (JSMA). We validate the generalization and scalability of the adversarial samples to tackle a broad range of real attacks on Industrial Control Systems (ICS). We evaluated the impact by assessing multiple attacks generated using the proposed method. The model trained with adversarial samples detected attacks with 95% accuracy on real-world attack data not used during training. The study was conducted using an operational secure water treatment (SWaT) testbed. Industrial control systems (ICS) comprise a significant portion of any state or nation's critical infrastructure (CI). Examples of such systems include water treatment plants and electric power grids, where an ICS regulates the physical processes. The physical processes consist of two primary parts: monitoring and controlling. The monitoring part maintains processes and ensures they are operating properly by measuring various signals acquired from sensors.