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.

Having an LLM that aligns with human preferences is essential for accommodating individual needs, such as maintaining writing style or generating specific topics of interest. The majority of current alignment methods rely on fine-tuning or prompting, which can be either costly or difficult to control. Model steering algorithms, which modify the model output by constructing specific steering directions, are typically easy to implement and optimization-free. However, their capabilities are typically limited to steering the model into one of the two directions (i.e., bidirectional steering), and there has been no theoretical understanding to guarantee their performance. In this work, we propose a theoretical framework to understand and quantify the model steering methods. Inspired by the framework, we propose a confident direction steering method (CONFST) that steers LLMs via modifying their activations at inference time. More specifically, CONFST builds a confident direction that is closely aligned with users' preferences, and this direction is then added to the activations of the LLMs to effectively steer the model output. Our approach offers three key advantages over popular bidirectional model steering methods: 1) It is more powerful, since multiple (i.e. more than two) users' preferences can be aligned simultaneously; 2) It is simple to implement, since there is no need to determine which layer to add the steering vector to; 3) No explicit user instruction is required. We validate our method on GPT-2 XL (1.5B), Mistral (7B) and Gemma-it (9B) models for tasks that require shifting the output of LLMs across various topics and styles, achieving superior performance over competing methods.

Network tomography is a crucial problem in network monitoring, where the observable path performance metric values are used to infer the unobserved ones, making it essential for tasks such as route selection, fault diagnosis, and traffic control. However, most existing methods either assume complete knowledge of network topology and metric formulas-an unrealistic expectation in many real-world scenarios with limited observability-or rely entirely on black-box end-to-end models. To tackle this, in this paper, we argue that a good network tomography requires synergizing the knowledge from both data and appropriate inductive bias from (partial) prior knowledge. To see this, we propose Deep Network Tomography (DeepNT), a novel framework that leverages a path-centric graph neural network to predict path performance metrics without relying on predefined hand-crafted metrics, assumptions, or the real network topology. The path-centric graph neural network learns the path embedding by inferring and aggregating the embeddings of the sequence of nodes that compose this path. Training path-centric graph neural networks requires learning the neural netowrk parameters and network topology under discrete constraints induced by the observed path performance metrics, which motivates us to design a learning objective that imposes connectivity and sparsity constraints on topology and path performance triangle inequality on path performance. Extensive experiments on real-world and synthetic datasets demonstrate the superiority of DeepNT in predicting performance metrics and inferring graph topology compared to state-of-the-art methods.

Gene expression classification is a pivotal yet challenging task in bioinformatics, primarily due to the high dimensionality of genomic data and the risk of overfitting. To bridge this gap, we propose BOLIMES, a novel feature selection algorithm designed to enhance gene expression classification by systematically refining the feature subset. Unlike conventional methods that rely solely on statistical ranking or classifier-specific selection, we integrate the robustness of Boruta with the interpretability of LIME, ensuring that only the most relevant and influential genes are retained. BOLIMES first employs Boruta to filter out non-informative genes by comparing each feature against its randomized counterpart, thus preserving valuable information. It then uses LIME to rank the remaining genes based on their local importance to the classifier. Finally, an iterative classification evaluation determines the optimal feature subset by selecting the number of genes that maximizes predictive accuracy. By combining exhaustive feature selection with interpretability-driven refinement, our solution effectively balances dimensionality reduction with high classification performance, offering a powerful solution for high-dimensional gene expression analysis.

Phishing has long been a common tactic used by cybercriminals and continues to pose a significant threat in today's digital world. When phishing attacks become more advanced and sophisticated, there is an increasing need for effective methods to detect and prevent them. To address the challenging problem of detecting phishing emails, researchers have developed numerous solutions, in particular those based on machine learning (ML) algorithms. In this work, we take steps to study the efficacy of large language models (LLMs) in detecting phishing emails. The experiments show that the LLM achieves a high accuracy rate at high precision; importantly, it also provides interpretable evidence for the decisions.