arXiv subjects

Vadim Ratner

Publications and source records attributed to Vadim Ratner.

6 recordsLinked to original sources

arXiv2024

MAMMAL -- Molecular Aligned Multi-Modal Architecture and Language

Large language models applied to vast biological datasets have the potential to transform biology by uncovering disease mechanisms and accelerating drug development. However, current models are often siloed, trained separately on small-molecules, proteins, or transcriptomic data, limiting their ability to capture complex, multi-modal interactions. Effective drug discovery requires computational tools that integrate multiple biological entities while supporting prediction and generation, a challenge existing models struggle to address. For this purpose, we present MAMMAL - Molecular Aligned Multi-Modal Architecture and Language - a versatile method applied to create a multi-task foundation model that learns from large-scale biological datasets across diverse modalities, including proteins, small-molecules, and omics. MAMMAL's structured prompt syntax supports classification, regression, and generation tasks while handling token and scalar inputs and outputs. Evaluated on eleven diverse downstream tasks, it reaches a new state of the art (SOTA) in nine tasks and is comparable to SOTA in two tasks, all within a unified architecture, unlike prior task-specific models. Additionally, we explored Alphafold 3 binding prediction capabilities on antibody-antigen and nanobody-antigen complexes showing significantly better classification performance of MAMMAL in 3 out of 4 targets. The model code and pretrained weights are publicly available at https://github.com/BiomedSciAI/biomed-multi-alignment and https://huggingface.co/ibm/biomed.omics.bl.sm.ma-ted-458m

q-bio.QM↗

arXiv2024

A large dataset curation and benchmark for drug target interaction

Bioactivity data plays a key role in drug discovery and repurposing. The resource-demanding nature of \textit{in vitro} and \textit{in vivo} experiments, as well as the recent advances in data-driven computational biochemistry research, highlight the importance of \textit{in silico} drug target interaction (DTI) prediction approaches. While numerous large public bioactivity data sources exist, research in the field could benefit from better standardization of existing data resources. At present, different research works that share similar goals are often difficult to compare properly because of different choices of data sources and train/validation/test split strategies. Additionally, many works are based on small data subsets, leading to results and insights of possible limited validity. In this paper we propose a way to standardize and represent efficiently a very large dataset curated from multiple public sources, split the data into train, validation and test sets based on different meaningful strategies, and provide a concrete evaluation protocol to accomplish a benchmark. We analyze the proposed data curation, prove its usefulness and validate the proposed benchmark through experimental studies based on an existing neural network model.

q-bio.BM↗

arXiv2018

Learning multiple non-mutually-exclusive tasks for improved classification of inherently ordered labels

Medical image classification involves thresholding of labels that represent malignancy risk levels. Usually, a task defines a single threshold, and when developing computer-aided diagnosis tools, a single network is trained per such threshold, e.g. as screening out healthy (very low risk) patients to leave possibly sick ones for further analysis (low threshold), or trying to find malignant cases among those marked as non-risk by the radiologist ("second reading", high threshold). We propose a way to rephrase the classification problem in a manner that yields several problems (corresponding to different thresholds) to be solved simultaneously. This allows the use of Multiple Task Learning (MTL) methods, significantly improving the performance of the original classifier, by facilitating effective extraction of information from existing data.

cs.CV↗

arXiv2018

Regularized adversarial examples for model interpretability

As machine learning algorithms continue to improve, there is an increasing need for explaining why a model produces a certain prediction for a certain input. In recent years, several methods for model interpretability have been developed, aiming to provide explanation of which subset regions of the model input is the main reason for the model prediction. In parallel, a significant research community effort is occurring in recent years for developing adversarial example generation methods for fooling models, while not altering the true label of the input,as it would have been classified by a human annotator. In this paper, we bridge the gap between adversarial example generation and model interpretability, and introduce a modification to the adversarial example generation process which encourages better interpretability. We analyze the proposed method on a public medical imaging dataset, both quantitatively and qualitatively, and show that it significantly outperforms the leading known alternative method. Our suggested method is simple to implement, and can be easily plugged into most common adversarial example generation frameworks. Additionally, we propose an explanation quality metric - $APE$ - "Adversarial Perturbative Explanation", which measures how well an explanation describes model decisions.

cs.LG↗

arXiv2018

AdapterNet - learning input transformation for domain adaptation

Deep neural networks have demonstrated impressive performance in various machine learning tasks. However, they are notoriously sensitive to changes in data distribution. Often, even a slight change in the distribution can lead to drastic performance reduction. Artificially augmenting the data may help to some extent, but in most cases, fails to achieve model invariance to the data distribution. Some examples where this sub-class of domain adaptation can be valuable are various imaging modalities such as thermal imaging, X-ray, ultrasound, and MRI, where changes in acquisition parameters or acquisition device manufacturer will result in a different representation of the same input. Our work shows that standard fine-tuning fails to adapt the model in certain important cases. We propose a novel method of adapting to a new data source, and demonstrate near perfect adaptation on a customized ImageNet benchmark. Moreover, our method does not require any samples from the original data set, it is completely explainable and can be tailored to the task.

cs.CV↗

arXiv2015

Multiple Liquid Bridges with Non-Smooth Interfaces

We consider a coexistence of two axisymmetric liquid bridges LB_i and LB_m of two immiscible liquids i and m which are immersed in a third liquid (or gas) e and trapped between two smooth solid bodies with axisymmetric surfaces S_1,S_2 and free contact lines. Evolution of liquid bridges allows two different configurations of LB_i and LB_m with multiple (five or three) interfaces of non-smooth shape. We formulate a variational problem with volume constraints and present its governing equations supplemented by boundary conditions. We find a universal relationship between curvature of the interfaces and discuss the Young relation at the singular curve where all liquids meet together.

physics.flu-dyn↗