arXiv subjects

Farnoush Banaei-Kashani

Publications and source records attributed to Farnoush Banaei-Kashani.

12 recordsLinked to original sources

arXiv2026

Universe of Thoughts: A Computational Framework for Creative Reasoning in Large Language Models

Recent advances in Large Language Model (LLM) reasoning have improved conventional problem solving, but creative reasoning remains comparatively underexplored. Inspired by cognitive science, we formalize combinational, exploratory, and transformational creativity as executable computational operators over structured problem and solution spaces, specifying how each mode combines, explores, or transforms those spaces. Combinational reasoning transfers ideas across domains to form unfamiliar combinations; exploratory reasoning searches for new solutions within an existing conceptual space; and transformational reasoning modifies the rules or constraints that define that space. This formalization yields distinct algorithmic procedures, which we instantiate in Universe of Thoughts (UoT), an LLM reasoning framework. Existing creativity benchmarks emphasize either open-ended ideation or highly constrained problem solving. We therefore introduce three novel creative-reasoning tasks requiring concrete solutions in low-constraint settings. Across 10 generations per method and task, T-UoT with GPT-4o performs strongest on the low-constraint, high-objective-specificity Bridge and Electricity tasks, while C-UoT shows its strongest relative performance on the low-constraint, lower-objective-specificity Society task. In addition, we evaluate UoT on HypoArena, an independent scientific hypothesis-generation benchmark with 100 tasks across biomedical, machine-learning, and social-science domains. With Qwen3-14B, Exploratory UoT ranks first among seven reasoning methods, achieving a 32.7\% pairwise win rate compared with 25.5\% for the next-best method. Our results suggest distinct performance patterns across task structures: T-UoT is strongest in low-constraint, high-specificity settings, E-UoT in more constrained, high-specificity settings, and C-UoT in low-constraint, lower-specificity settings.

cs.AI↗

arXiv2026

FRAGMENTA: Efficient End-to-end Fragmentation-based Generative Model with Agentic Tuning for Drug Lead Optimization in Small Data Regime

Molecule generation from extremely limited training data is a key challenge in drug discovery. Existing fragment-based methods are more suitable than atom-based approaches in this regime, but typically optimize fragment selection separately from downstream generation. Expert feedback is also especially valuable with limited data, yet translating such feedback into model objectives usually requires AI engineering expertise. We introduce FRAGMENTA, an end-to-end framework for small-data drug lead optimization with two components: (1) LVSEF, a fragment-based generator that jointly optimizes fragmentation and generation through a tabular reward-update mechanism, and (2) an agentic system that converts conversational expert feedback into updated generative objectives. Across three small-data datasets (11--104 molecules), LVSEF outperforms state-of-the-art methods in the smallest-data settings, matches them at larger scales, and trains ${\sim}16\times$ faster. On three public protein targets, iterative closed-loop optimization improves final-round discovery yield by up to ${\sim}16%$ over one-shot LVSEF-only on kinase, with gains depending on how well feedback matches target chemistry. In a real-world cancer drug-discovery deployment, Human-Agent FRAGMENTA identified nearly twice as many molecules with favorable docking scores ($< -6$) as baseline methods.

cs.AI↗

arXiv2026

Multi-Label Proportion Learning for Sea-Ice Type Prediction

Sea-ice type prediction is important for climate monitoring, maritime navigation, and decision-making in polar regions. The main source of label data for this task is the ice chart, produced manually by ice analysts who interpret satellite imagery to delineate ice zones into polygons. Although ice charts are valuable, their production is labor-intensive and expensive, motivating recent efforts to automate the process using deep learning. However, deep learning models require patch-level (or pixel-level) label data for training, while ice charts provide only polygon-level annotations. As a workaround, supervised approaches often create approximate patch-level labels from polygon-level ice chart labels by assigning each sample the dominant ice type of its parent polygon. This approach enables supervised training but creates an ill-posed learning problem with intrinsically approximate solution. In this paper, we redefine sea-ice type prediction as a weakly supervised multi-label proportion learning problem to be able to directly use the polygon-level ice chart labels and avoid unnecessary label approximation for improved prediction accuracy. To address this problem, we propose a two-module framework where first Multiple Instance Learning (MIL) is used for water--ice classification, and then a multi-label proportion learning (MLPL) is introduced for ice-type composition prediction. We further extend this framework with a multimodal model that integrates SAR imagery with AMSR2 brightness temperatures and ERA5 reanalysis data through modality-guided auxiliary regularization. Evaluated on the AI4Arctic dataset, the SAR-only model reduces MAE by 14.5\% and more than doubles mean ice-class F1 over the best supervised baseline. The multimodal model further reduces MAE by 21.5\% and raises mean F1 by 41.2\% over the SAR-only model, and by 52.7\% over the supervised multimodal baseline.

cs.LG↗

arXiv2026

An Autonomous GeoAI Agent for Arctic Eco-Navigation

Arctic maritime navigation is becoming increasingly important as changing sea-ice conditions expand seasonal accessibility while simultaneously introducing substantial operational, environmental, and community risks. Arctic route planning is inherently a multi-criteria problem: routes that improve vessel safety or efficiency may increase exposure to sea ice, sensitive ecosystems, or nearby communities. Existing routing methods prioritize travel time, fuel use, and navigational risk, often overlooking ecological and community impacts. We introduce a human-in-the-loop, multi-agent GeoAI system for Arctic eco-navigation that integrates operational, physical, ecological, and community-related criteria within a unified routing framework. Multiple specialized agents coordinate geospatial data acquisition and preparation, multi-objective route generation, and skyline-based decision support. The ecological criteria explicitly account for exposure to sensitive areas, including Essential Fish Habitat and seal critical habitat. By considering these ecosystem impacts and potential community burdens while keeping consequential value judgments under human control, the framework supports safer, more transparent, and socially responsible Arctic navigation. Project page and code are publicly available. https://samiraat.github.io/Arctic-Eco-Navigation-Agent/, https://github.com/samiraat/Arctic-Eco-Navigation-Agent

cs.AI↗

arXiv2026

Uncertainty-Aware Sea-Ice Type Mapping with Multiple Ice Charts

Sea-ice stage of development (SoD) describes the age and associated thickness of sea ice and provides important information for navigation, and operational ice monitoring. SoD labels are obtained from operational ice charts, where trained analysts interpret satellite observations and assign standardized stage codes to regions with similar ice conditions. These codes often represent ranges of compatible ice thicknesses rather than exact physical values. Deep-learning methods can automate SoD mapping and commonly adopt operational ice charts as reference labels for training. These annotations are not exact, however; this is because chart interpretation relies on analyst judgement and on the observations available at the time, so different ice services may assign different SoD labels to the same conditions. We term this variation across independently produced expert annotations multi-annotator label uncertainty; collapsing the annotations into a single deterministic target discards this variation. A second source of uncertainty originates in the learned model itself. In this paper, we quantify both sources: annotation uncertainty from disagreement among independent ice-service charts and model uncertainty from the learned predictive models. We then evaluate their relationship by testing whether model uncertainty is higher where ice services disagree. We observe that supervision incorporating information from multiple annotators can improve this correspondence, with soft supervision achieving the highest overall correlation of 0.256. The relationship becomes substantially stronger near the ice edge, where model predictive uncertainty closely tracks multi-annotator disagreement, reaching a correlation of 0.704 within 0--10 km. Among the uncertainty-estimation approaches, Monte Carlo dropout provides the best-calibrated confidence estimates, with an expected calibration error of 0.050.

cs.LG↗

arXiv2026

Uncertainty-Aware Learning from Multi-Expert Interval Targets

Many machine learning (ML) applications rely on expert labels, and qualified experts may provide different but plausible interpretations of the same observation. Such variation across expert labels may reflect genuine disagreement or ambiguity rather than annotation error. When individual experts additionally report intervals rather than exact values, the supervision contains two distinct sources of label uncertainty: within-label imprecision and between-expert variation. Existing methods treat these forms separately: multi-expert approaches collapse labels to a consensus, interval-target methods often yield a single prediction, and predictive-uncertainty methods rarely validate their uncertainty estimates against observed expert disagreement. To address this problem, we propose an approach that preserves individual expert intervals, separates within-label imprecision from between-expert variation, and validates the corresponding predictive uncertainty components. First, heterogeneous label vocabularies are harmonized into a common probabilistic label space, separating encoding differences from expert judgement. Second, individual label intervals are retained and modeled with a mixture of Beta distributions trained using a proper Cramér-distance objective, preserving distinct expert-reported labels. Third, we decompose predictive uncertainty into within-component, between-component, and model uncertainty, and evaluate whether these components correspond to within-label uncertainty, between-label uncertainty, and model error, respectively. Because this correspondence is not guaranteed, we introduce decomposition matching, which aligns the predictive components to their intended label-side sources. On sea-ice concentration the model reduces MAE by 31\% over hard labels and outperforms aggregation, interval-distribution, and interval-regression baselines.

cs.LG↗

arXiv2026

TCA-SIR: Learning Target-Conditioned Abstractions for Scientific Inspiration Retrieval

Scientific hypothesis generation for AI for Science typically involves Scientific Inspiration Retrieval (SIR) followed by hypothesis composition. Existing SIR methods rank papers by topical similarity and do not explicitly represent how a candidate inspiration transfers to a target problem. This is especially limiting for remote inspirations, whose value often lies in reusable problem-solving principles rather than topical overlap. Motivated by how humans abstract transferable aspects of a source and remap them to a new target, we reformulate SIR as target-conditioned abstraction (TCA). The retrieval object is a transferable abstract principle extracted from a candidate specifically for the target. We present TCA-SIR, which learns to generate target-conditioned abstractions and uses their representations to predict transferability. On ResearchBench, TCA-SIR outperforms prior SIR methods and direct LLM retrieval, improving HitRate@top4% over MOOSE-Chem by more than 10 percentage points. Learned abstractions also recover target-relevant mechanisms more clearly than an untrained TCA prompt, yielding both stronger retrieval and an interpretable rationale for scientific inspiration.

cs.IR↗

arXiv2026

Ice-FMBench: A Foundation Model Benchmark for Sea Ice Type Segmentation

Accurate segmentation and mapping of sea ice types is crucial for safe polar navigation, offshore operations, and climate monitoring. While deep learning has demonstrated strong potential for automating sea ice type segmentation, its success often relies on access to extensive expert labeled datasets, which is both resource intensive and time consuming to create. However, foundation models (FMs), recently developed through self-supervised training on large-scale datasets, have demonstrated impressive performance. Nevertheless, their applicability to sea ice type segmentation based on Synthetic Aperture Radar (SAR) imagery remains uncertain due to the unique challenges posed by sea ice such as intricate geophysical patterns, pronounced seasonal variability, and SAR-specific artifacts like banding, scalloping, and heterogeneous backscatter as well as the fact that SAR data in polar regions are often acquired using specialized sensor modes that differ markedly from those used to collect FM training data at lower latitudes, limiting their direct transferability to polar environments. To address this gap, we contribute: (1) IceFMBench, a comprehensive benchmark framework for evaluation of the state-of-the-art remote sensing FMs on the sea ice type segmentation task using Sentinel1 SAR imagery, where IceFMBench is composed of a widely used standardized dataset, diverse evaluation metrics, and a representative set of selected remote sensing FM models suitable for sea ice type segmentation, with the ability to include new models side by side the existing models; (2) an extensive comparative evaluation of the representative FMs using IceFMBench, with additional case studies to assess performance of the top-performing model in terms of transferability across temporal and spatial domains and (3) a multi teacher knowledge distillation approach to address lack of spatiotemporal transferability.

cs.LG↗

arXiv2025

BioNeuralNet: A Graph Neural Network based Multi-Omics Network Data Analysis Tool

Multi-omics data offer unprecedented insights into complex biological systems, yet their high dimensionality, sparsity, and intricate interactions pose significant analytical challenges. Network-based approaches have advanced multi-omics research by effectively capturing biologically relevant relationships among molecular entities. While these methods are powerful for representing molecular interactions, there remains a need for tools specifically designed to effectively utilize these network representations across diverse downstream analyses. To fulfill this need, we introduce BioNeuralNet, a flexible and modular Python framework tailored for end-to-end network-based multi-omics data analysis. BioNeuralNet leverages Graph Neural Networks (GNNs) to learn biologically meaningful low-dimensional representations from multi-omics networks, converting these complex molecular networks into versatile embeddings. BioNeuralNet supports all major stages of multi-omics network analysis, including several network construction techniques, generation of low-dimensional representations, and a broad range of downstream analytical tasks. Its extensive utilities, including diverse GNN architectures, and compatibility with established Python packages (e.g., scikit-learn, PyTorch, NetworkX), enhance usability and facilitate quick adoption. BioNeuralNet is an open-source, user-friendly, and extensively documented framework designed to support flexible and reproducible multi-omics network analysis in precision medicine.

cs.LG↗

arXiv2025

IceBench: A Benchmark for Deep Learning based Sea Ice Type Classification

Sea ice plays a critical role in the global climate system and maritime operations, making timely and accurate classification essential. However, traditional manual methods are time-consuming, costly, and have inherent biases. Automating sea ice type classification addresses these challenges by enabling faster, more consistent, and scalable analysis. While both traditional and deep learning approaches have been explored, deep learning models offer a promising direction for improving efficiency and consistency in sea ice classification. However, the absence of a standardized benchmark and comparative study prevents a clear consensus on the best-performing models. To bridge this gap, we introduce \textit{IceBench}, a comprehensive benchmarking framework for sea ice type classification. Our key contributions are threefold: First, we establish the IceBench benchmarking framework which leverages the existing AI4Arctic Sea Ice Challenge dataset as a standardized dataset, incorporates a comprehensive set of evaluation metrics, and includes representative models from the entire spectrum of sea ice type classification methods categorized in two distinct groups, namely, pixel-based classification methods and patch-based classification methods. IceBench is open-source and allows for convenient integration and evaluation of other sea ice type classification methods; hence, facilitating comparative evaluation of new methods and improving reproducibility in the field. Second, we conduct an in-depth comparative study on representative models to assess their strengths and limitations, providing insights for both practitioners and researchers. Third, we leverage IceBench for systematic experiments addressing key research questions on model transferability across seasons (time) and locations (space), data downscaling, and preprocessing strategies.

cs.CV↗

arXiv2024

Partial Label Learning with Focal Loss for Sea Ice Classification Based on Ice Charts

Sea ice, crucial to the Arctic and Earth's climate, requires consistent monitoring and high-resolution mapping. Manual sea ice mapping, however, is time-consuming and subjective, prompting the need for automated deep learning-based classification approaches. However, training these algorithms is challenging because expert-generated ice charts, commonly used as training data, do not map single ice types but instead map polygons with multiple ice types. Moreover, the distribution of various ice types in these charts is frequently imbalanced, resulting in a performance bias towards the dominant class. In this paper, we present a novel GeoAI approach to training sea ice classification by formalizing it as a partial label learning task with explicit confidence scores to address multiple labels and class imbalance. We treat the polygon-level labels as candidate partial labels, assign the corresponding ice concentrations as confidence scores to each candidate label, and integrate them with focal loss to train a Convolutional Neural Network (CNN). Our proposed approach leads to enhanced performance for sea ice classification in Sentinel-1 dual-polarized SAR images, improving classification accuracy (from 87% to 92%) and weighted average F-1 score (from 90% to 93%) compared to the conventional training approach of using one-hot encoded labels and Categorical Cross-Entropy loss. It also improves the F-1 score in 4 out of the 6 sea ice classes.

cs.CV↗

arXiv2022

Bridging the Gap between Artificial Intelligence and Artificial General Intelligence: A Ten Commandment Framework for Human-Like Intelligence

The field of artificial intelligence has seen explosive growth and exponential success. The last phase of development showcased deep learnings ability to solve a variety of difficult problems across a multitude of domains. Many of these networks met and exceeded human benchmarks by becoming experts in the domains in which they are trained. Though the successes of artificial intelligence have begun to overshadow its failures, there is still much that separates current artificial intelligence tools from becoming the exceptional general learners that humans are. In this paper, we identify the ten commandments upon which human intelligence is systematically and hierarchically built. We believe these commandments work collectively to serve as the essential ingredients that lead to the emergence of higher-order cognition and intelligence. This paper discusses a computational framework that could house these ten commandments and suggests new architectural modifications that could lead to the development of smarter, more explainable, and generalizable artificial systems inspired by a neuromorphic approach.

cs.AI↗