Abhishek Pandey

Oscar Rivera, Ziqing Wang, Matthieu Dagommer et al.

Machine learning accelerates molecular property prediction, yet state-of-the-art Large Language Models and Graph Neural Networks operate as black boxes. In drug discovery, where safety is critical, this opacity risks masking false correlations and excluding human expertise. Existing interpretability methods suffer from the effectiveness-trustworthiness trade-off: explanations may fail to reflect a model's true reasoning, degrade performance, or lack domain grounding. Concept Bottleneck Models (CBMs) offer a solution by projecting inputs to human-interpretable concepts before readout, ensuring that explanations are inherently faithful to the decision process. However, adapting CBMs to chemistry faces three challenges: the Relevance Gap (selecting task-relevant concepts from a large descriptor space), the Annotation Gap (obtaining concept supervision for molecular data), and the Capacity Gap (degrading performance due to bottleneck constraints). We introduce GlassMol, a model-agnostic CBM that addresses these gaps through automated concept curation and LLM-guided concept selection. Experiments across thirteen benchmarks demonstrate that \method generally matches or exceeds black-box baselines, suggesting that interpretability does not sacrifice performance and challenging the commonly assumed trade-off. Code is available at https://github.com/walleio/GlassMol.

Xuefeng Liu, Songhao Jiang, Xiaotian Duan et al.

Protein-ligand binding is the process by which a small molecule (drug or inhibitor) attaches to a target protein. Binding affinity, which characterizes the strength of biomolecular interactions, is essential for tackling diverse challenges in life sciences, including therapeutic design, protein engineering, enzyme optimization, and elucidating biological mechanisms. Much work has been devoted to predicting binding affinity over the past decades. Here, we review recent significant works, with a focus on methods, evaluation strategies, and benchmark datasets. We note growing use of both traditional machine learning and deep learning models for predicting binding affinity, accompanied by an increasing amount of data on proteins and small drug-like molecules. With improved predictive performance and the FDA's phasing out of animal testing, AI-driven in silico models, such as AI virtual cells (AIVCs), are poised to advance binding affinity prediction; reciprocally, progress in building binding affinity predictors can refine AIVCs. Future efforts in binding affinity prediction and AI-driven in silico models can enhance the simulation of temporal dynamics, cell-type specificity, and multi-omics integration to support more accurate and personalized outcomes.

Ziqing Wang, Kexin Zhang, Zihan Zhao et al.

Large language models (LLMs) are introducing a paradigm shift in molecular discovery by enabling text-guided interaction with chemical spaces through natural language, symbolic notations, with emerging extensions to incorporate multi-modal inputs. To advance the new field of LLM for molecular discovery, this survey provides an up-to-date and forward-looking review of the emerging use of LLMs for two central tasks: molecule generation and molecule optimization. Based on our proposed taxonomy for both problems, we analyze representative techniques in each category, highlighting how LLM capabilities are leveraged across different learning settings. In addition, we include the commonly used datasets and evaluation protocols. We conclude by discussing key challenges and future directions, positioning this survey as a resource for researchers working at the intersection of LLMs and molecular science. A continuously updated reading list is available at https://github.com/REAL-Lab-NU/Awesome-LLM-Centric-Molecular-Discovery.

Shashi Kumar, Shakti P. Rath, Abhishek Pandey

Automatic Speech Recognition (ASR) systems suffer considerably when source speech is corrupted with noise or room impulse responses (RIR). Typically, speech enhancement is applied in both mismatched and matched scenario training and testing. In matched setting, acoustic model (AM) is trained on dereverberated far-field features while in mismatched setting, AM is fixed. In recent past, mapping speech features from far-field to close-talk using denoising autoencoder (DA) has been explored. In this paper, we focus on matched scenario training and show that the proposed joint VAE based mapping achieves a significant improvement over DA. Specifically, we observe an absolute improvement of 2.5% in word error rate (WER) compared to DA based enhancement and 3.96% compared to AM trained directly on far-field filterbank features.

Aditya Narayan Ravi, Snehal Vadvalkar, Abhishek Pandey et al.

Cell Painting is a microscopy-based, high-content imaging assay that produces rich morphological profiles of cells and can support drug discovery by quantifying cellular responses to chemical perturbations. At scale, however, Cell Painting data is strongly affected by batch effects arising from differences in laboratories, instruments, and protocols, which can obscure biological signal. We present BALANS (Batch Alignment via Local Affinities and Subsampling), a scalable batch-correction method that aligns samples across batches by constructing a smoothed affinity matrix from pairwise distances. Given $n$ data points, BALANS builds a sparse affinity matrix $A \in \mathbb{R}^{n \times n}$ using two ideas. (i) For points $i$ and $j$, it sets a local scale using the distance from $i$ to its $k$-th nearest neighbor within the batch of $j$, then computes $A_{ij}$ via a Gaussian kernel calibrated by these batch-aware local scales. (ii) Rather than forming all $n^2$ entries, BALANS uses an adaptive sampling procedure that prioritizes rows with low cumulative neighbor coverage and retains only the strongest affinities per row, yielding a sparse but informative approximation of $A$. We prove that this sampling strategy is order-optimal in sample complexity and provides an approximation guarantee, and we show that BALANS runs in nearly linear time in $n$. Experiments on diverse real-world Cell Painting datasets and controlled large-scale synthetic benchmarks demonstrate that BALANS scales to large collections while improving runtime over native implementations of widely used batch-correction methods, without sacrificing correction quality.

Kevin Ta, Patrick Foley, Mattson Thieme et al.

Generating unique molecules with biochemically desired properties to serve as viable drug candidates is a difficult task that requires specialized domain expertise. In recent years, diffusion models have shown promising results in accelerating the drug design process through AI-driven molecular generation. However, training these models requires massive amounts of data, which are often isolated in proprietary silos. OpenFL is a federated learning framework that enables privacy-preserving collaborative training across these decentralized data sites. In this work, we present a federated discrete denoising diffusion model that was trained using OpenFL. The federated model achieves comparable performance with a model trained on centralized data when evaluating the uniqueness and validity of the generated molecules. This demonstrates the utility of federated learning in the drug design process. OpenFL is available at: https://github.com/securefederatedai/openfl

Peizhi Niu, Yu-Hsiang Wang, Vishal Rana et al.

We introduce a new graph diffusion model for small molecule generation, DMol, which outperforms the state-of-the-art DiGress model in terms of validity by roughly 1.5% across all benchmarking datasets while reducing the number of diffusion steps by at least 10-fold, and the running time to roughly one half. The performance improvements are a result of a careful change in the objective function and a graph noise scheduling approach which, at each diffusion step, allows one to only change a subset of nodes of varying size in the molecule graph. Another relevant property of the method is that it can be easily combined with junction-tree-like graph representations that arise by compressing a collection of relevant ring structures into supernodes. Unlike classical junction-tree techniques that involve VAEs and require complicated reconstruction steps, compressed DMol directly performs graph diffusion on a graph that compresses only a carefully selected set of frequent carbon rings into supernodes, which results in straightforward sample generation. This compressed DMol method offers additional validity improvements over generic DMol of roughly 2%, increases the novelty of the method, and further improves the running time due to reductions in the graph size.

Ziqing Wang, Yibo Wen, William Pattie et al.

Lead optimization in drug discovery requires efficiently navigating vast chemical space through iterative cycles to enhance molecular properties while preserving structural similarity to the original lead compound. Despite recent advances, traditional optimization methods struggle with sample efficiency-achieving good optimization performance with limited oracle evaluations. Large Language Models (LLMs) provide a promising approach through their in-context learning and instruction following capabilities, which align naturally with these iterative processes. However, existing LLM-based methods fail to leverage this strength, treating each optimization step independently. To address this, we present POLO (Preference-guided multi-turn Optimization for Lead Optimization), which enables LLMs to learn from complete optimization trajectories rather than isolated steps. At its core, POLO introduces Preference-Guided Policy Optimization (PGPO), a novel reinforcement learning algorithm that extracts learning signals at two complementary levels: trajectory-level optimization reinforces successful strategies, while turn-level preference learning provides dense comparative feedback by ranking intermediate molecules within each trajectory. Through this dual-level learning from intermediate evaluation, POLO achieves superior sample efficiency by fully exploiting each costly oracle call. Extensive experiments demonstrate that POLO achieves 84% average success rate on single-property tasks (2.3x better than baselines) and 50% on multi-property tasks using only 500 oracle evaluations, significantly advancing the state-of-the-art in sample-efficient molecular optimization.

Vishwanath Pratap Singh, Shakti P. Rath, Abhishek Pandey

This paper presents a novel deep learning architecture for acoustic model in the context of Automatic Speech Recognition (ASR), termed as MixNet. Besides the conventional layers, such as fully connected layers in DNN-HMM and memory cells in LSTM-HMM, the model uses two additional layers based on Mixture of Experts (MoE). The first MoE layer operating at the input is based on pre-defined broad phonetic classes and the second layer operating at the penultimate layer is based on automatically learned acoustic classes. In natural speech, overlap in distribution across different acoustic classes is inevitable, which leads to inter-class mis-classification. The ASR accuracy is expected to improve if the conventional architecture of acoustic model is modified to make them more suitable to account for such overlaps. MixNet is developed keeping this in mind. Analysis conducted by means of scatter diagram verifies that MoE indeed improves the separation between classes that translates to better ASR accuracy. Experiments are conducted on a large vocabulary ASR task which show that the proposed architecture provides 13.6% and 10.0% relative reduction in word error rates compared to the conventional models, namely, DNN and LSTM respectively, trained using sMBR criteria. In comparison to an existing method developed for phone-classification (by Eigen et al), our proposed method yields a significant improvement.

Vishwanath Pratap Singh, Shakti P. Rath, Abhishek Pandey

Conventional automatic speech recognition (ASR) system uses second-order minkowski loss during inference time which is suboptimal as it incorporates only first order statistics in posterior estimation [2]. In this paper we have proposed higher order minkowski loss (4th Order and 6th Order) during inference time, without any changes during training time. The main contribution of the paper is to show that higher order loss uses higher order statistics in posterior estimation, which improves the prediction ability of acoustic model in ASR system. We have shown mathematically that posterior probability obtained due to higher order loss is function of second order posterior and thus the method can be incorporated in standard ASR system in an easy manner. It is to be noted that all changes are proposed during test(inference) time, we do not make any change in any training pipeline. Multiple baseline systems namely, TDNN1, TDNN2, DNN and LSTM are developed to verify the improvement incurred due to higher order minkowski loss. All experiments are conducted on LibriSpeech dataset and performance metrics are word error rate (WER) on "dev-clean", "test-clean", "dev-other" and "test-other" datasets.

Vishwanath Pratap Singh, Shashi Kumar, Ravi Shekhar Jha et al.

The COVID-19 pandemic has resulted in more than 125 million infections and more than 2.7 million casualties. In this paper, we attempt to classify covid vs non-covid cough sounds using signal processing and deep learning methods. Air turbulence, the vibration of tissues, movement of fluid through airways, opening, and closure of glottis are some of the causes for the production of the acoustic sound signals during cough. Does the COVID-19 alter the acoustic characteristics of breath, cough, and speech sounds produced through the respiratory system? This is an open question waiting for answers. In this paper, we incorporated novel data augmentation methods for cough sound augmentation and multiple deep neural network architectures and methods along with handcrafted features. Our proposed system gives 14% absolute improvement in area under the curve (AUC). The proposed system is developed as part of Interspeech 2021 special sessions and challenges viz. diagnosing of COVID-19 using acoustics (DiCOVA). Our proposed method secured the 5th position on the leaderboard among 29 participants.

Abhishek Pandey, Anjna Jayant Deen, Rajeev Pandey

The improvement of the accuracy of image query retrieval used image classification technique. Image classification is well known technique of supervised learning. The improved method of image classification increases the working efficiency of image query retrieval. For the improvements of classification technique we used RBF neural network function for better prediction of feature used in image retrieval.Colour content is represented by pixel values in image classification using radial base function(RBF) technique. This approach provides better result compare to SVM technique in image representation.Image is represented by matrix though RBF using pixel values of colour intensity of image. Firstly we using RGB colour model. In this colour model we use red, green and blue colour intensity values in matrix.SVM with partical swarm optimization for image classification is implemented in content of images which provide better Results based on the proposed approach are found encouraging in terms of color image classification accuracy.