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Ehsan Hajiramezanali

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14 papers

2 author rows

AAAI Conference 2026 Conference Paper

RAG-Enhanced Collaborative LLM Agents for Drug Discovery

Namkyeong Lee
Edward De Brouwer
Ehsan Hajiramezanali
Tommaso Biancalani
Chanyoung Park
Gabriele Scalia

Recent advances in large language models (LLMs) have shown great potential to accelerate drug discovery. However, the specialized nature of biochemical data often necessitates costly domain-specific fine-tuning, posing critical challenges. First, it hinders the application of more flexible general-purpose LLMs in cutting-edge drug discovery tasks. More importantly, it limits the rapid integration of the vast amounts of scientific data continuously generated through experiments and research. Compounding these challenges is the fact that real-world scientific questions are typically complex and open-ended, requiring reasoning beyond pattern matching or static knowledge retrieval. To address these challenges, we propose CLADD, a retrieval-augmented generation (RAG)-empowered agentic system tailored to drug discovery tasks. Through the collaboration of multiple LLM agents, CLADD dynamically retrieves information from biomedical knowledge bases, contextualizes query molecules, and integrates relevant evidence to generate responses - all without the need for domain-specific fine-tuning. Crucially, we tackle key obstacles in applying RAG workflows to biochemical data, including data heterogeneity, ambiguity, and multi-source integration. We demonstrate the flexibility and effectiveness of this framework across a variety of drug discovery tasks, showing that it outperforms general-purpose and domain-specific LLMs as well as traditional deep learning approaches.

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ICLR Conference 2025 Conference Paper

Adding Conditional Control to Diffusion Models with Reinforcement Learning

Yulai Zhao 0002
Masatoshi Uehara
Gabriele Scalia
Sun-Yuan Kung
Tommaso Biancalani
Sergey Levine
Ehsan Hajiramezanali

Diffusion models are powerful generative models that allow for precise control over the characteristics of the generated samples. While these diffusion models trained on large datasets have achieved success, there is often a need to introduce additional controls in downstream fine-tuning processes, treating these powerful models as pre-trained diffusion models. This work presents a novel method based on reinforcement learning (RL) to add such controls using an offline dataset comprising inputs and labels. We formulate this task as an RL problem, with the classifier learned from the offline dataset and the KL divergence against pre-trained models serving as the reward functions. Our method, **CTRL** (**C**onditioning pre-**T**rained diffusion models with **R**einforcement **L**earning), produces soft-optimal policies that maximize the abovementioned reward functions. We formally demonstrate that our method enables sampling from the conditional distribution with additional controls during inference. Our RL-based approach offers several advantages over existing methods. Compared to classifier-free guidance, it improves sample efficiency and can greatly simplify dataset construction by leveraging conditional independence between the inputs and additional controls. Additionally, unlike classifier guidance, it eliminates the need to train classifiers from intermediate states to additional controls. The code is available at https://github.com/zhaoyl18/CTRL.

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NeurIPS Conference 2024 Conference Paper

Bridging Model-Based Optimization and Generative Modeling via Conservative Fine-Tuning of Diffusion Models

Masatoshi Uehara
Yulai Zhao
Ehsan Hajiramezanali
Gabriele Scalia
Gokcen Eraslan
Avantika Lal
Sergey Levine
Tommaso Biancalani

AI-driven design problems, such as DNA/protein sequence design, are commonly tackled from two angles: generative modeling, which efficiently captures the feasible design space (e. g. , natural images or biological sequences), and model-based optimization, which utilizes reward models for extrapolation. To combine the strengths of both approaches, we adopt a hybrid method that fine-tunes cutting-edge diffusion models by optimizing reward models through RL. Although prior work has explored similar avenues, they primarily focus on scenarios where accurate reward models are accessible. In contrast, we concentrate on an offline setting where a reward model is unknown, and we must learn from static offline datasets, a common scenario in scientific domains. In offline scenarios, existing approaches tend to suffer from overoptimization, as they may be misled by the reward model in out-of-distribution regions. To address this, we introduce a conservative fine-tuning approach, BRAID, by optimizing a conservative reward model, which includes additional penalization outside of offline data distributions. Through empirical and theoretical analysis, we demonstrate the capability of our approach to outperform the best designs in offline data, leveraging the extrapolation capabilities of reward models while avoiding the generation of invalid designs through pre-trained diffusion models.

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ICML Conference 2024 Conference Paper

Feedback Efficient Online Fine-Tuning of Diffusion Models

Masatoshi Uehara
Yulai Zhao 0002
Kevin Black
Ehsan Hajiramezanali
Gabriele Scalia
Nathaniel Lee Diamant
Alex M. Tseng
Sergey Levine

Diffusion models excel at modeling complex data distributions, including those of images, proteins, and small molecules. However, in many cases, our goal is to model parts of the distribution that maximize certain properties: for example, we may want to generate images with high aesthetic quality, or molecules with high bioactivity. It is natural to frame this as a reinforcement learning (RL) problem, in which the objective is to finetune a diffusion model to maximize a reward function that corresponds to some property. Even with access to online queries of the ground-truth reward function, efficiently discovering high-reward samples can be challenging: they might have a low probability in the initial distribution, and there might be many infeasible samples that do not even have a well-defined reward (e. g. , unnatural images or physically impossible molecules). In this work, we propose a novel reinforcement learning procedure that efficiently explores on the manifold of feasible samples. We present a theoretical analysis providing a regret guarantee, as well as empirical validation across three domains: images, biological sequences, and molecules.

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NeurIPS Conference 2024 Conference Paper

GFlowNet Assisted Biological Sequence Editing

Pouya M. Ghari
Alex M. Tseng
Gökcen Eraslan
Romain Lopez
Tommaso Biancalani
Gabriele Scalia
Ehsan Hajiramezanali

Editing biological sequences has extensive applications in synthetic biology and medicine, such as designing regulatory elements for nucleic-acid therapeutics and treating genetic disorders. The primary objective in biological-sequence editing is to determine the optimal modifications to a sequence which augment certain biological properties while adhering to a minimal number of alterations to ensure predictability and potentially support safety. In this paper, we propose GFNSeqEditor, a novel biological-sequence editing algorithm which builds on the recently proposed area of generative flow networks (GFlowNets). Our proposed GFNSeqEditor identifies elements within a starting seed sequence that may compromise a desired biological property. Then, using a learned stochastic policy, the algorithm makes edits at these identified locations, offering diverse modifications for each sequence to enhance the desired property. The number of edits can be regulated through specific hyperparameters. We conducted extensive experiments on a range of real-world datasets and biological applications, and our results underscore the superior performance of our proposed algorithm compared to existing state-of-the-art sequence editing methods.

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TMLR Journal 2024 Journal Article

Score-based Explainability for Graph Representations

Ehsan Hajiramezanali
Sepideh Maleki
Max W Shen
Kangway V. Chuang
Tommaso Biancalani
Gabriele Scalia

Despite the widespread use of unsupervised Graph Neural Networks (GNNs), their post-hoc explainability remains underexplored. Current graph explanation methods typically focus on explaining a single dimension of the final output. However, unsupervised and self-supervised GNNs produce d-dimensional representation vectors whose individual elements lack clear, disentangled semantic meaning. To tackle this issue, we draw inspiration from the success of score-based graph explainers in supervised GNNs and propose a novel framework, grXAI, for graph representation explainability. grXAI generalizes existing score-based graph explainers to identify the subgraph most responsible for constructing the latent representation of the input graph. This framework can be easily and efficiently implemented as a wrapper around existing methods, enabling the explanation of graph representations through connected subgraphs, which are more human-intelligible. Extensive qualitative and quantitative experiments demonstrate grXAI's strong ability to identify subgraphs that effectively explain learned graph representations across various unsupervised tasks and learning algorithms.

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ICML Conference 2023 Conference Paper

Towards Understanding and Improving GFlowNet Training

Max W. Shen
Emmanuel Bengio
Ehsan Hajiramezanali
Andreas Loukas
Kyunghyun Cho
Tommaso Biancalani

Generative flow networks (GFlowNets) are a family of algorithms that learn a generative policy to sample discrete objects $x$ with non-negative reward $R(x)$. Learning objectives guarantee the GFlowNet samples $x$ from the target distribution $p^*(x) \propto R(x)$ when loss is globally minimized over all states or trajectories, but it is unclear how well they perform with practical limits on training resources. We introduce an efficient evaluation strategy to compare the learned sampling distribution to the target reward distribution. As flows can be underdetermined given training data, we clarify the importance of learned flows to generalization and matching $p^*(x)$ in practice. We investigate how to learn better flows, and propose (i) prioritized replay training of high-reward $x$, (ii) relative edge flow policy parametrization, and (iii) a novel guided trajectory balance objective, and show how it can solve a substructure credit assignment problem. We substantially improve sample efficiency on biochemical design tasks.

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ICLR Conference 2022 Conference Paper

MoReL: Multi-omics Relational Learning

Arman Hasanzadeh
Ehsan Hajiramezanali
Nick G. Duffield
Xiaoning Qian

Multi-omics data analysis has the potential to discover hidden molecular interactions, revealing potential regulatory and/or signal transduction pathways for cellular processes of interest when studying life and disease systems. One of critical challenges when dealing with real-world multi-omics data is that they may manifest heterogeneous structures and data quality as often existing data may be collected from different subjects under different conditions for each type of omics data. We propose a novel deep Bayesian generative model to efficiently infer a multi-partite graph encoding molecular interactions across such heterogeneous views, using a fused Gromov-Wasserstein (FGW) regularization between latent representations of corresponding views for integrative analysis. With such an optimal transport regularization in the deep Bayesian generative model, it not only allows incorporating view-specific side information, either with graph-structured or unstructured data in different views, but also increases the model flexibility with the distribution-based regularization. This allows efficient alignment of heterogeneous latent variable distributions to derive reliable interaction predictions compared to the existing point-based graph embedding methods. Our experiments on several real-world datasets demonstrate enhanced performance of MoReL in inferring meaningful interactions compared to existing baselines.

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NeurIPS Conference 2021 Conference Paper

SubTab: Subsetting Features of Tabular Data for Self-Supervised Representation Learning

Talip Ucar
Ehsan Hajiramezanali
Lindsay Edwards

Self-supervised learning has been shown to be very effective in learning useful representations, and yet much of the success is achieved in data types such as images, audio, and text. The success is mainly enabled by taking advantage of spatial, temporal, or semantic structure in the data through augmentation. However, such structure may not exist in tabular datasets commonly used in fields such as healthcare, making it difficult to design an effective augmentation method, and hindering a similar progress in tabular data setting. In this paper, we introduce a new framework, Subsetting features of Tabular data (SubTab), that turns the task of learning from tabular data into a multi-view representation learning problem by dividing the input features to multiple subsets. We argue that reconstructing the data from the subset of its features rather than its corrupted version in an autoencoder setting can better capture its underlying latent representation. In this framework, the joint representation can be expressed as the aggregate of latent variables of the subsets at test time, which we refer to as collaborative inference. Our experiments show that the SubTab achieves the state of the art (SOTA) performance of 98. 31% on MNIST in tabular setting, on par with CNN-based SOTA models, and surpasses existing baselines on three other real-world datasets by a significant margin.

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ICML Conference 2020 Conference Paper

Bayesian Graph Neural Networks with Adaptive Connection Sampling

Arman Hasanzadeh
Ehsan Hajiramezanali
Shahin Boluki
Mingyuan Zhou
Nick G. Duffield
Krishna Narayanan 0001
Xiaoning Qian

We propose a unified framework for adaptive connection sampling in graph neural networks (GNNs) that generalizes existing stochastic regularization methods for training GNNs. The proposed framework not only alleviates over-smoothing and over-fitting tendencies of deep GNNs, but also enables learning with uncertainty in graph analytic tasks with GNNs. Instead of using fixed sampling rates or hand-tuning themas model hyperparameters in existing stochastic regularization methods, our adaptive connection sampling can be trained jointly with GNN model parameters in both global and local fashions. GNN training with adaptive connection sampling is shown to be mathematically equivalent to an efficient approximation of training BayesianGNNs. Experimental results with ablation studies on benchmark datasets validate that adaptively learning the sampling rate given graph training data is the key to boost the performance of GNNs in semi-supervised node classification, less prone to over-smoothing and over-fitting with more robust prediction.

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NeurIPS Conference 2020 Conference Paper

BayReL: Bayesian Relational Learning for Multi-omics Data Integration

Ehsan Hajiramezanali
Arman Hasanzadeh
Nick Duffield
Krishna Narayanan
Xiaoning Qian

High-throughput molecular profiling technologies have produced high-dimensional multi-omics data, enabling systematic understanding of living systems at the genome scale. Studying molecular interactions across different data types helps reveal signal transduction mechanisms across different classes of molecules. In this paper, we develop a novel Bayesian representation learning method that infers the relational interactions across multi-omics data types. Our method, Bayesian Relational Learning (BayReL) for multi-omics data integration, takes advantage of a priori known relationships among the same class of molecules, modeled as a graph at each corresponding view, to learn view-specific latent variables as well as a multi-partite graph that encodes the interactions across views. Our experiments on several real-world datasets demonstrate enhanced performance of BayReL in inferring meaningful interactions compared to existing baselines.

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NeurIPS Conference 2019 Conference Paper

Semi-Implicit Graph Variational Auto-Encoders

Arman Hasanzadeh
Ehsan Hajiramezanali
Krishna Narayanan
Nick Duffield
Mingyuan Zhou
Xiaoning Qian

Semi-implicit graph variational auto-encoder (SIG-VAE) is proposed to expand the flexibility of variational graph auto-encoders (VGAE) to model graph data. SIG-VAE employs a hierarchical variational framework to enable neighboring node sharing for better generative modeling of graph dependency structure, together with a Bernoulli-Poisson link decoder. Not only does this hierarchical construction provide a more flexible generative graph model to better capture real-world graph properties, but also does SIG-VAE naturally lead to semi-implicit hierarchical variational inference that allows faithful modeling of implicit posteriors of given graph data, which may exhibit heavy tails, multiple modes, skewness, and rich dependency structures. SIG-VAE integrates a carefully designed generative model, well suited to model real-world sparse graphs, and a sophisticated variational inference network, which propagates the graph structural information and distribution uncertainty to capture complex posteriors. SIG-VAE clearly outperforms a simple combination of VGAE with variational inference, including semi-implicit variational inference~(SIVI) or normalizing flow (NF), which does not propagate uncertainty in its inference network, and provides more interpretable latent representations than VGAE does. Extensive experiments with a variety of graph data show that SIG-VAE significantly outperforms state-of-the-art methods on several different graph analytic tasks.

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NeurIPS Conference 2019 Conference Paper

Variational Graph Recurrent Neural Networks

Ehsan Hajiramezanali
Arman Hasanzadeh
Krishna Narayanan
Nick Duffield
Mingyuan Zhou
Xiaoning Qian

Representation learning over graph structured data has been mostly studied in static graph settings while efforts for modeling dynamic graphs are still scant. In this paper, we develop a novel hierarchical variational model that introduces additional latent random variables to jointly model the hidden states of a graph recurrent neural network (GRNN) to capture both topology and node attribute changes in dynamic graphs. We argue that the use of high-level latent random variables in this variational GRNN (VGRNN) can better capture potential variability observed in dynamic graphs as well as the uncertainty of node latent representation. With semi-implicit variational inference developed for this new VGRNN architecture (SI-VGRNN), we show that flexible non-Gaussian latent representations can further help dynamic graph analytic tasks. Our experiments with multiple real-world dynamic graph datasets demonstrate that SI-VGRNN and VGRNN consistently outperform the existing baseline and state-of-the-art methods by a significant margin in dynamic link prediction.

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NeurIPS Conference 2018 Conference Paper

Bayesian multi-domain learning for cancer subtype discovery from next-generation sequencing count data

Ehsan Hajiramezanali
Siamak Zamani Dadaneh
Alireza Karbalayghareh
Mingyuan Zhou
Xiaoning Qian

Precision medicine aims for personalized prognosis and therapeutics by utilizing recent genome-scale high-throughput profiling techniques, including next-generation sequencing (NGS). However, translating NGS data faces several challenges. First, NGS count data are often overdispersed, requiring appropriate modeling. Second, compared to the number of involved molecules and system complexity, the number of available samples for studying complex disease, such as cancer, is often limited, especially considering disease heterogeneity. The key question is whether we may integrate available data from all different sources or domains to achieve reproducible disease prognosis based on NGS count data. In this paper, we develop a Bayesian Multi-Domain Learning (BMDL) model that derives domain-dependent latent representations of overdispersed count data based on hierarchical negative binomial factorization for accurate cancer subtyping even if the number of samples for a specific cancer type is small. Experimental results from both our simulated and NGS datasets from The Cancer Genome Atlas (TCGA) demonstrate the promising potential of BMDL for effective multi-domain learning without ``negative transfer'' effects often seen in existing multi-task learning and transfer learning methods.

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