Madhusudan Ghosh

Madhusudan Ghosh, Shrimon Mukherjee, Asmit Ganguly et al.

In recent years, there has been a surge in the publication of clinical trial reports, making it challenging to conduct systematic reviews. Automatically extracting Population, Intervention, Comparator, and Outcome (PICO) from clinical trial studies can alleviate the traditionally time-consuming process of manually scrutinizing systematic reviews. Existing approaches of PICO frame extraction involves supervised approach that relies on the existence of manually annotated data points in the form of BIO label tagging. Recent approaches, such as In-Context Learning (ICL), which has been shown to be effective for a number of downstream NLP tasks, require the use of labeled examples. In this work, we adopt ICL strategy by employing the pretrained knowledge of Large Language Models (LLMs), gathered during the pretraining phase of an LLM, to automatically extract the PICO-related terminologies from clinical trial documents in unsupervised set up to bypass the availability of large number of annotated data instances. Additionally, to showcase the highest effectiveness of LLM in oracle scenario where large number of annotated samples are available, we adopt the instruction tuning strategy by employing Low Rank Adaptation (LORA) to conduct the training of gigantic model in low resource environment for the PICO frame extraction task. Our empirical results show that our proposed ICL-based framework produces comparable results on all the version of EBM-NLP datasets and the proposed instruction tuned version of our framework produces state-of-the-art results on all the different EBM-NLP datasets. Our project is available at \url{https://github.com/shrimonmuke0202/AlpaPICO.git}.

Madhusudan Ghosh, Debasis Ganguly, Partha Basuchowdhuri et al.

Research in scientific disciplines evolves, often rapidly, over time with the emergence of novel methodologies and their associated terminologies. While methodologies themselves being conceptual in nature and rather difficult to automatically extract and characterise, in this paper, we seek to develop supervised models for automatic extraction of the names of the various constituents of a methodology, e.g., `R-CNN', `ELMo' etc. The main research challenge for this task is effectively modeling the contexts around these methodology component names in a few-shot or even a zero-shot setting. The main contributions of this paper towards effectively identifying new evolving scientific methodology names are as follows: i) we propose a factored approach to sequence modeling, which leverages a broad-level category information of methodology domains, e.g., `NLP', `RL' etc.; ii) to demonstrate the feasibility of our proposed approach of identifying methodology component names under a practical setting of fast evolving AI literature, we conduct experiments following a simulated chronological setup (newer methodologies not seen during the training process); iii) our experiments demonstrate that the factored approach outperforms state-of-the-art baselines by margins of up to 9.257\% for the methodology extraction task with the few-shot setup.

Shrimon Mukherjee, Madhusudan Ghosh, Partha Basuchowdhuri

Application of artificial intelligence (AI) has been ubiquitous in the growth of research in the areas of basic sciences. Frequent use of machine learning (ML) and deep learning (DL) based methodologies by researchers has resulted in significant advancements in the last decade. These techniques led to notable performance enhancements in different tasks such as protein structure prediction, drug-target binding affinity prediction, and molecular property prediction. In material science literature, it is well-known that crystalline materials exhibit topological structures. Such topological structures may be represented as graphs and utilization of graph neural network (GNN) based approaches could help encoding them into an augmented representation space. Primarily, such frameworks adopt supervised learning techniques targeted towards downstream property prediction tasks on the basis of electronic properties (formation energy, bandgap, total energy, etc.) and crystalline structures. Generally, such type of frameworks rely highly on the handcrafted atom feature representations along with the structural representations. In this paper, we propose an unsupervised framework namely, CrysAtom, using untagged crystal data to generate dense vector representation of atoms, which can be utilized in existing GNN-based property predictor models to accurately predict important properties of crystals. Empirical results show that our dense representation embeds chemical properties of atoms and enhance the performance of the baseline property predictor models significantly.

Madhusudan Ghosh, Rishabh Gupta

The rapid advancement of large language models (LLMs) has led to a significant increase in automated tools in the software engineering, capable of performing various code-related tasks such as code generation, completion, and translation. Despite these advancements, its effectiveness is constrained by fixed context lengths, limiting its ability to generalize across long, domain-specific code sequences. To address this challenge, we investigate zero-shot, inference-only methods aimed at improving position encodings and optimizing attention mechanisms. Our goal is to provide a thorough analysis of current approaches that facilitate context length extrapolation in code, particularly in the context of long code completion tasks.

Payel Santra, Lavisha Sharma, Madhusudan Ghosh et al.

The rapid spread of misinformation on social media highlights the need for robust, automated fact correction frameworks. However, existing works rely on supervised learning from manually annotated claim-evidence pairs, which are scarce and prone to biases, limiting their generalization across domains. Moreover, these methods overlook semantic faithfulness in their correction process. To address these challenges, we propose Mask-to-Correct (M$_2$C), a training-free, inference-only Retrieval Augmented Generation (RAG) based framework that leverages diversity-aware masking to identify erroneous spans of claims and evaluate the faithfulness of corrections using retrieved evidence. However, the effectiveness of RAG heavily depends on the choice of retriever, which may vary across queries. To mitigate this, we further introduce M$_2$C$^+$, an ensemble-based framework that combines corrections across multiple rankers to reduce retrieval bias and improve robustness. Extensive experiments on the benchmark datasets demonstrate that our proposed frameworks consistently outperform all baselines, achieving up to 14% improvement in SARI scores, without using gold evidence.

Manojit Chakraborty, Madhusudan Ghosh, Rishabh Gupta

In the domain of software development, LLMs have been utilized to automate tasks such as code translation, where source code from one programming language is translated to another while preserving its functionality. However, LLMs often struggle with long source codes that don't fit into the context window, which produces inaccurate translations. To address this, we propose a novel zero-shot code translation method that incorporates identifier replacement. By substituting user-given long identifiers with generalized placeholders during translation, our method allows the LLM to focus on the logical structure of the code, by reducing token count and memory usage, which improves the efficiency and cost-effectiveness of long code translation. Our empirical results demonstrate that our approach preserves syntactical and hierarchical information and produces translation results with reduced tokens.

Payel Santra, Madhusudan Ghosh, Debasis Ganguly et al.

Leveraging both labeled (input-output associations) and unlabeled data (wider contextual grounding) may provide complementary benefits in retrieval augmented generation (RAG). However, effectively combining evidence from these heterogeneous sources is challenging as the respective similarity scores are not inter-comparable. Additionally, aggregating beliefs from the outputs of multiple rankers can improve the effectiveness of RAG. Our proposed method first aggregates the top-documents from a number of IR models using a standard rank fusion technique for each source (labeled and unlabeled). Next, we standardize the retrieval score distributions within each source by applying z-score transformation before merging the top-retrieved documents from the two sources. We evaluate our approach on the fact verification task, demonstrating that it consistently improves over the best-performing individual ranker or source and also shows better out-of-domain generalization.

Rudrajit Dawn, Madhusudan Ghosh, Partha Basuchowdhuri et al.

Deep neural networks have enabled researchers to create powerful generalized frameworks, such as transformers, that can be used to solve well-studied problems in various application domains, such as text and image. However, such generalized frameworks are not available for solving graph problems. Graph structures are ubiquitous in many applications around us and many graph problems have been widely studied over years. In recent times, there has been a surge in deep neural network based approaches to solve graph problems, with growing availability of graph structured datasets across diverse domains. Nevertheless, existing methods are mostly tailored to solve a specific task and lack the capability to create a generalized model leading to solutions for different downstream tasks. In this work, we propose a novel, resource-efficient framework named \emph{U}nified \emph{G}raph \emph{N}etwork (UGN) by leveraging the feature extraction capability of graph convolutional neural networks (GCN) and 2-dimensional convolutional neural networks (Conv2D). UGN unifies various graph learning tasks, such as link prediction, node classification, community detection, graph-to-graph translation, knowledge graph completion, and more, within a cohesive framework, while exercising minimal task-specific extensions (e.g., formation of supernodes for coarsening massive networks to increase scalability, use of \textit{mean target connectivity matrix} (MTCM) representation for achieving scalability in graph translation task, etc.) to enhance the generalization capability of graph learning and analysis. We test the novel UGN framework for six uncorrelated graph problems, using twelve different datasets. Experimental results show that UGN outperforms the state-of-the-art baselines by a significant margin on ten datasets, while producing comparable results on the remaining dataset.

Shrimon Mukherjee, Madhusudan Ghosh, Partha Basuchowdhuri

Development of new drugs is an expensive and time-consuming process. Due to the world-wide SARS-CoV-2 outbreak, it is essential that new drugs for SARS-CoV-2 are developed as soon as possible. Drug repurposing techniques can reduce the time span needed to develop new drugs by probing the list of existing FDA-approved drugs and their properties to reuse them for combating the new disease. We propose a novel architecture DeepGLSTM, which is a Graph Convolutional network and LSTM based method that predicts binding affinity values between the FDA-approved drugs and the viral proteins of SARS-CoV-2. Our proposed model has been trained on Davis, KIBA (Kinase Inhibitor Bioactivity), DTC (Drug Target Commons), Metz, ToxCast and STITCH datasets. We use our novel architecture to predict a Combined Score (calculated using Davis and KIBA score) of 2,304 FDA-approved drugs against 5 viral proteins. On the basis of the Combined Score, we prepare a list of the top-18 drugs with the highest binding affinity for 5 viral proteins present in SARS-CoV-2. Subsequently, this list may be used for the creation of new useful drugs.