Predicting the inhibitory potency of small molecules against Tyrosyl-DNA Phosphodiesterase 1 (TDP1) -- a key target in overcoming cancer chemoresistance--remains a critical challenge in early drug discovery. We present a deep learning framework for the quantitative regression of pIC50 values from molecular Simplified Molecular Input Line Entry System (SMILES) strings using fine-tuned variants of ChemBERTa, a pre-trained chemical language model. Leveraging a large-scale consensus dataset of 177,092 compounds, we systematically evaluate two pre-training strategies--Masked Language Modeling (MLM) and Masked Token Regression (MTR)--under stratified data splits and sample weighting to address severe activity imbalance which only 2.1% are active. Our approach outperforms classical baselines Random Predictor in both regression accuracy and virtual screening utility, and has competitive performance compared to Random Forest, achieving high enrichment factor EF@1% 17.4 and precision Precision@1% 37.4 among top-ranked predictions. The resulting model, validated through rigorous ablation and hyperparameter studies, provides a robust, ready-to-deploy tool for prioritizing TDP1 inhibitors for experimental testing. By enabling accurate, 3D-structure-free pIC50 prediction directly from SMILES, this work demonstrates the transformative potential of chemical transformers in accelerating target-specific drug discovery.

Assistive robots operating in unstructured environments must understand not only what objects are, but what they can be used for. This requires grounding language-based action queries to objects that both afford the requested function and can be physically retrieved. Existing approaches often rely on black-box models or fixed affordance labels, limiting transparency, controllability, and reliability for human-facing applications. We introduce CRAFT-E, a modular neuro-symbolic framework that composes a structured verb-property-object knowledge graph with visual-language alignment and energy-based grasp reasoning. The system generates interpretable grounding paths that expose the factors influencing object selection and incorporates grasp feasibility as an integral part of affordance inference. We further construct a benchmark dataset with unified annotations for verb-object compatibility, segmentation, and grasp candidates, and deploy the full pipeline on a physical robot. CRAFT-E achieves competitive performance in static scenes, ImageNet-based functional retrieval, and real-world trials involving 20 verbs and 39 objects. The framework remains robust under perceptual noise and provides transparent, component-level diagnostics. By coupling symbolic reasoning with embodied perception, CRAFT-E offers an interpretable and customizable alternative to end-to-end models for affordance-grounded object selection, supporting trustworthy decision-making in assistive robotic systems.

Large Language Models (LLMs) have transformed natural language processing and hold growing promise for advancing science, healthcare, and decision-making. Yet their training paradigms remain dominated by affirmation-based inference, akin to \textit{modus ponens}, where accepted premises yield predicted consequents. While effective for generative fluency, this one-directional approach leaves models vulnerable to logical fallacies, adversarial manipulation, and failures in causal reasoning. This paper makes two contributions. First, it demonstrates how existing LLMs from major platforms exhibit systematic weaknesses when reasoning in scientific domains with negation, counterexamples, or faulty premises \footnote{Code to recreate these experiments are at https://github.com/hannahdavidsoncollege-maker/ScientificReasoningForEnvironment-MedicineWithLLMs. Second, it introduces a dual-reasoning training framework that integrates affirmative generation with structured counterfactual denial. Grounded in formal logic, cognitive science, and adversarial training, this training paradigm formalizes a computational analogue of ``denying the antecedent'' as a mechanism for disconfirmation and robustness. By coupling generative synthesis with explicit negation-aware objectives, the framework enables models that not only affirm valid inferences but also reject invalid ones, yielding systems that are more resilient, interpretable, and aligned with human reasoning.

Modelling the complexity and diversity of human activity scheduling behaviour is inherently challenging. We demonstrate a deep conditional-generative machine learning approach for the modelling of realistic activity schedules depending on input labels such as an individual's age, employment status, or other information relevant to their scheduling. We combine (i) a structured latent generative approach, with (ii) a conditional approach, through a novel Conditional VAE architecture. This allows for the rapid generation of precise and realistic schedules for different input labels. We extensively evaluate model capabilities using a joint density estimation framework and several case studies. We additionally show that our approach has practical data and computational requirements, and can be deployed within new and existing demand modelling frameworks. We evaluate the importance of generative capability more generally, by comparing our combined approach to (i) a purely generative model without conditionality, and (ii) a purely conditional model which outputs the most likely schedule given the input labels. This comparison highlights the usefulness of explicitly modelling the randomness of complex and diverse human behaviours using deep generative approaches.

Large Language Models (LLMs) are increasingly used in healthcare, yet ensuring their safety and trustworthiness remains a barrier to deployment. Conversational medical assistants must avoid unsafe compliance without over-refusing benign queries. We present an iterative post-deployment alignment framework that applies Kahneman-Tversky Optimization (KTO) and Direct Preference Optimization (DPO) to refine models against domain-specific safety signals. Using the CARES-18K benchmark for adversarial robustness, we evaluate four LLMs (Llama-3B/8B, Meditron-8B, Mistral-7B) across multiple cycles. Our results show up to 42% improvement in safety-related metrics for harmful query detection, alongside interesting trade-offs against erroneous refusals, thereby exposing architecture-dependent calibration biases. We also perform ablation studies to identify when self-evaluation is reliable and when external or finetuned judges are necessary to maximize performance gains. Our findings underscore the importance of adopting best practices that balance patient safety, user trust, and clinical utility in the design of conversational medical assistants.

The microscopic examination of surgical tissue remains a cornerstone of disease classification but relies on subjective interpretations and access to highly specialized experts, which can compromise accuracy and clinical care. While emerging breakthroughs in artificial intelligence (AI) offer promise for automated histological analysis, the growing number of proprietary digital pathology solutions has created barriers to real-world deployment. To address these challenges, we introduce OnSight Pathology, a platform-agnostic computer vision software that uses continuous custom screen captures to provide real-time AI inferences to users as they review digital slide images. Accessible as a single, self-contained executable file (https://onsightpathology.github.io/ ), OnSight Pathology operates locally on consumer-grade personal computers without complex software integration, enabling cost-effective and secure deployment in research and clinical workflows. Here we demonstrate the utility of OnSight Pathology using over 2,500 publicly available whole slide images across different slide viewers, as well as cases from our clinical digital pathology setup. The software's robustness is highlighted across routine histopathological tasks, including the classification of common brain tumor types, mitosis detection, and the quantification of immunohistochemical stains. A built-in multi-modal chat assistant provides verifiable descriptions of images, free of rigid class labels, for added quality control. Lastly, we show compatibility with live microscope camera feeds, including from personal smartphones, offering potential for deployment in more analog, inter-operative, and telepathology settings. Together, we highlight how OnSight Pathology can deliver real-time AI inferences across a broad range of pathology pipelines, removing key barriers to the adoption of AI tools in histopathology.

Next token prediction is an attractive pre-training task for jet foundation models, in that it is simulation free and enables excellent generative capabilities that can transfer across datasets. Here we study multiple improvements to next token prediction, building on the initial work of OmniJet-$α$. Instead of tokenizing particles and subsequently only using the token-ID as the model input for both the generative and the classification task, we adopt a hybrid setup, which allows us to use continuous feature vectors as model input while only using token-IDs in the next token prediction target. Secondly, we explore a combined pre-training strategy that combines masked particle modeling and generative learning objectives. Taken together, these changes greatly improve the performance in downstream classification tasks without any loss in generative performance.

As computational demands continue to rise, assessing the environmental footprint of AI requires moving beyond energy and water consumption to include the material demands of specialized hardware. This study quantifies the material footprint of AI training by linking computational workloads to physical hardware needs. The elemental composition of the Nvidia A100 SXM 40 GB graphics processing unit (GPU) was analyzed using inductively coupled plasma optical emission spectroscopy, which identified 32 elements. The results show that AI hardware consists of about 90% heavy metals and only trace amounts of precious metals. The elements copper, iron, tin, silicon, and nickel dominate the GPU composition by mass. In a multi-step methodology, we integrate these measurements with computational throughput per GPU across varying lifespans, accounting for the computational requirements of training specific AI models at different training efficiency regimes. Scenario-based analyses reveal that, depending on Model FLOPs Utilization (MFU) and hardware lifespan, training GPT-4 requires between 1,174 and 8,800 A100 GPUs, corresponding to the extraction and eventual disposal of up to 7 tons of toxic elements. Combined software and hardware optimization strategies can reduce material demands: increasing MFU from 20% to 60% lowers GPU requirements by 67%, while extending lifespan from 1 to 3 years yields comparable savings; implementing both measures together reduces GPU needs by up to 93%. Our findings highlight that incremental performance gains, such as those observed between GPT-3.5 and GPT-4, come at disproportionately high material costs. The study underscores the necessity of incorporating material resource considerations into discussions of AI scalability, emphasizing that future progress in AI must align with principles of resource efficiency and environmental responsibility.

Large Language Diffusion Models (LLDMs) benefit from a flexible decoding mechanism that enables parallelized inference and controllable generations over autoregressive models. Yet such flexibility introduces a critical challenge: inference performance becomes highly sensitive to the decoding order of tokens. Existing heuristic methods, however, focus mainly on local effects while overlooking long-term impacts. To address this limitation, we propose the Foreseeing Decoding Method (FDM), a novel approach that integrates both local and global considerations to unlock the full potential, employing a search-based strategy to enable effective optimization in discrete spaces. Furthermore, by analyzing the consistency of chosen tokens in the full decoding process, we develop a variant, FDM with Acceleration (FDM-A), which restricts deep exploration to critical steps identified as the exploration and balance circumantences. Extensive experiments across diverse benchmarks and model architectures validate the scalability of FDM and demonstrate the superior efficiency-performance trade-off achieved by FDM-A. Our work might potentially provide a principled step toward more powerful decoding methods for LLDMs.

Large language models (LLMs) have demonstrated several emergent behaviors with scale, including reasoning and fluency in long-form text generation. However, they continue to struggle with tasks requiring precise spatial and positional reasoning. ASCII art, a symbolic medium where characters encode structure and form, provides a unique probe of this limitation. We introduce ASCIIBench, a novel benchmark for evaluating both the generation and classification of ASCII-text images. ASCIIBench consists of a filtered dataset of 5,315 class-labeled ASCII images and is, to our knowledge, the first publicly available benchmark of its kind. Alongside the dataset, we release weights for a fine-tuned CLIP model adapted to capture ASCII structure, enabling the evaluation of LLM-generated ASCII art. Our analysis shows that cosine similarity over CLIP embeddings fails to separate most ASCII categories, yielding chance-level performance even for low-variance classes. In contrast, classes with high internal mean similarity exhibit clear discriminability, revealing that the bottleneck lies in representation rather than generational variance. These findings position ASCII art as a stress test for multimodal representations and motivate the development of new embedding methods or evaluation metrics tailored to symbolic visual modalities. All resources are available at https://github.com/ASCIIBench/ASCIIBench.