Adithya Kulkarni

Tuo Wang, Jian Kang, Yujun Yan et al.

Conformal prediction for graph neural networks (GNNs) offers a promising framework for quantifying uncertainty, enhancing GNN reliability in high-stakes applications. However, existing methods predominantly focus on static graphs, neglecting the evolving nature of real-world graphs. Temporal dependencies in graph structure, node attributes, and ground truth labels violate the fundamental exchangeability assumption of standard conformal prediction methods, limiting their applicability. To address these challenges, in this paper, we introduce NCPNET, a novel end-to-end conformal prediction framework tailored for temporal graphs. Our approach extends conformal prediction to dynamic settings, mitigating statistical coverage violations induced by temporal dependencies. To achieve this, we propose a diffusion-based non-conformity score that captures both topological and temporal uncertainties within evolving networks. Additionally, we develop an efficiency-aware optimization algorithm that improves the conformal prediction process, enhancing computational efficiency and reducing coverage violations. Extensive experiments on diverse real-world temporal graphs, including WIKI, REDDIT, DBLP, and IBM Anti-Money Laundering dataset, demonstrate NCPNET's capability to ensure guaranteed coverage in temporal graphs, achieving up to a 31% reduction in prediction set size on the WIKI dataset, significantly improving efficiency compared to state-of-the-art methods. Our data and code are available at https://github.com/ODYSSEYWT/NCPNET.

Adithya Kulkarni, Fatimah Alotaibi, Xinyue Zeng et al.

Large Language Models (LLMs) are transforming scientific hypothesis generation and validation by enabling information synthesis, latent relationship discovery, and reasoning augmentation. This survey provides a structured overview of LLM-driven approaches, including symbolic frameworks, generative models, hybrid systems, and multi-agent architectures. We examine techniques such as retrieval-augmented generation, knowledge-graph completion, simulation, causal inference, and tool-assisted reasoning, highlighting trade-offs in interpretability, novelty, and domain alignment. We contrast early symbolic discovery systems (e.g., BACON, KEKADA) with modern LLM pipelines that leverage in-context learning and domain adaptation via fine-tuning, retrieval, and symbolic grounding. For validation, we review simulation, human-AI collaboration, causal modeling, and uncertainty quantification, emphasizing iterative assessment in open-world contexts. The survey maps datasets across biomedicine, materials science, environmental science, and social science, introducing new resources like AHTech and CSKG-600. Finally, we outline a roadmap emphasizing novelty-aware generation, multimodal-symbolic integration, human-in-the-loop systems, and ethical safeguards, positioning LLMs as agents for principled, scalable scientific discovery.

Xinyue Zeng, Tuo Wang, Adithya Kulkarni et al.

Recent advances in protein structure prediction have achieved near-atomic accuracy for well-folded proteins. However, current benchmarks inadequately assess model performance in biologically challenging contexts, especially those involving intrinsically disordered regions (IDRs), limiting their utility in applications such as drug discovery, disease variant interpretation, and protein interface design. We introduce DisProtBench, a comprehensive benchmark for evaluating protein structure prediction models (PSPMs) under structural disorder and complex biological conditions. DisProtBench spans three key axes: (1) Data complexity, covering disordered regions, G protein-coupled receptor (GPCR) ligand pairs, and multimeric complexes; (2) Task diversity, benchmarking twelve leading PSPMs across structure-based tasks with unified classification, regression, and interface metrics; and (3) Interpretability, via the DisProtBench Portal, which provides precomputed 3D structures and visual error analyses. Our results reveal significant variability in model robustness under disorder, with low-confidence regions linked to functional prediction failures. Notably, global accuracy metrics often fail to predict task performance in disordered settings, emphasizing the need for function-aware evaluation. DisProtBench establishes a reproducible, extensible, and biologically grounded framework for assessing next-generation PSPMs in realistic biomedical scenarios.

Mohna Chakraborty, Adithya Kulkarni, Qi Li

Prompt-based methods leverage the knowledge of pre-trained language models (PLMs) trained with a masked language modeling (MLM) objective; however, these methods are sensitive to template, verbalizer, and few-shot instance selection, particularly in cold-start settings with no labeled data. Existing studies overlook the dependency between instances and verbalizers, where instance-label probabilities depend on verbalizer token proximity in the embedding space. To address this, we propose COLDSELECT, a joint verbalizer and instance selection approach that models data diversity. COLDSELECT maps PLM vocabulary and $h_{[MASK]}$ embeddings into a shared space, applying dimensionality reduction and clustering to ensure efficient and diverse selection. By optimizing for minimal uncertainty and maximal diversity, COLDSELECT captures data relationships effectively. Experiments on eight benchmarks demonstrate COLDSELECT's superiority in reducing uncertainty and enhancing generalization, outperforming baselines in verbalizer and few-shot instance selection for cold-start scenarios.

Adithya Kulkarni, Oliver Eulenstein, Qi Li

Dependency parsing is an essential task in NLP, and the quality of dependency parsers is crucial for many downstream tasks. Parsers' quality often varies depending on the domain and the language involved. Therefore, it is essential to combat the issue of varying quality to achieve stable performance. In various NLP tasks, aggregation methods are used for post-processing aggregation and have been shown to combat the issue of varying quality. However, aggregation methods for post-processing aggregation have not been sufficiently studied in dependency parsing tasks. In an extensive empirical study, we compare different unsupervised post-processing aggregation methods to identify the most suitable dependency tree structure aggregation method.

Mohna Chakraborty, Adithya Kulkarni, Qi Li

Recent studies have demonstrated that natural-language prompts can help to leverage the knowledge learned by pre-trained language models for the binary sentence-level sentiment classification task. Specifically, these methods utilize few-shot learning settings to fine-tune the sentiment classification model using manual or automatically generated prompts. However, the performance of these methods is sensitive to the perturbations of the utilized prompts. Furthermore, these methods depend on a few labeled instances for automatic prompt generation and prompt ranking. This study aims to find high-quality prompts for the given task in a zero-shot setting. Given a base prompt, our proposed approach automatically generates multiple prompts similar to the base prompt employing positional, reasoning, and paraphrasing techniques and then ranks the prompts using a novel metric. We empirically demonstrate that the top-ranked prompts are high-quality and significantly outperform the base prompt and the prompts generated using few-shot learning for the binary sentence-level sentiment classification task.

Adithya Kulkarni, Nasim Sabetpour, Alexey Markin et al.

Diverse Natural Language Processing tasks employ constituency parsing to understand the syntactic structure of a sentence according to a phrase structure grammar. Many state-of-the-art constituency parsers are proposed, but they may provide different results for the same sentences, especially for corpora outside their training domains. This paper adopts the truth discovery idea to aggregate constituency parse trees from different parsers by estimating their reliability in the absence of ground truth. Our goal is to consistently obtain high-quality aggregated constituency parse trees. We formulate the constituency parse tree aggregation problem in two steps, structure aggregation and constituent label aggregation. Specifically, we propose the first truth discovery solution for tree structures by minimizing the weighted sum of Robinson-Foulds (RF) distances, a classic symmetric distance metric between two trees. Extensive experiments are conducted on benchmark datasets in different languages and domains. The experimental results show that our method, CPTAM, outperforms the state-of-the-art aggregation baselines. We also demonstrate that the weights estimated by CPTAM can adequately evaluate constituency parsers in the absence of ground truth.

Nasim Sabetpour, Adithya Kulkarni, Sihong Xie et al.

Annotation quality and quantity positively affect the learning performance of sequence labeling, a vital task in Natural Language Processing. Hiring domain experts to annotate a corpus is very costly in terms of money and time. Crowdsourcing platforms, such as Amazon Mechanical Turk (AMT), have been deployed to assist in this purpose. However, the annotations collected this way are prone to human errors due to the lack of expertise of the crowd workers. Existing literature in annotation aggregation assumes that annotations are independent and thus faces challenges when handling the sequential label aggregation tasks with complex dependencies. To conquer the challenges, we propose an optimization-based method that infers the ground truth labels using annotations provided by workers for sequential labeling tasks. The proposed Aggregation method for Sequential Labels from Crowds ($AggSLC$) jointly considers the characteristics of sequential labeling tasks, workers' reliabilities, and advanced machine learning techniques. Theoretical analysis on the algorithm's convergence further demonstrates that the proposed $AggSLC$ halts after a finite number of iterations. We evaluate $AggSLC$ on different crowdsourced datasets for Named Entity Recognition (NER) tasks and Information Extraction tasks in biomedical (PICO), as well as a simulated dataset. Our results show that the proposed method outperforms the state-of-the-art aggregation methods. To achieve insights into the framework, we study the effectiveness of $AggSLC$'s components through ablation studies.