Moshiko Raboh

Yoel Shoshan, Moshiko Raboh, Michal Ozery-Flato et al.

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

Bum Chul Kwon, Ben Shapira, Moshiko Raboh et al.

The chemical space of drug-like molecules is vast, motivating the development of generative models that must learn broad chemical distributions, enable conditional generation by capturing structure-property representations, and provide fast molecular generation. Meeting the objectives depends on modeling choices, including the probabilistic modeling approach, the conditional generative formulation, the architecture, and the molecular input representation. To address the challenges, we present STAR-VAE (Selfies-encoded, Transformer-based, AutoRegressive Variational Auto Encoder), a scalable latent-variable framework with a Transformer encoder and an autoregressive Transformer decoder. It is trained on 79 million drug-like molecules from PubChem, using SELFIES to guarantee syntactic validity. The latent-variable formulation enables conditional generation: a property predictor supplies a conditioning signal that is applied consistently to the latent prior, the inference network, and the decoder. Our contributions are: (i) a Transformer-based latent-variable encoder-decoder model trained on SELFIES representations; (ii) a principled conditional latent-variable formulation for property-guided generation; and (iii) efficient finetuning with low-rank adapters (LoRA) in both encoder and decoder, enabling fast adaptation with limited property and activity data. On the GuacaMol and MOSES benchmarks, our approach matches or exceeds baselines, and latent-space analyses reveal smooth, semantically structured representations that support both unconditional exploration and property-aware generation. On the Tartarus benchmarks, the conditional model shifts docking-score distributions toward stronger predicted binding. These results suggest that a modernized, scale-appropriate VAE remains competitive for molecular generation when paired with principled conditioning and parameter-efficient finetuning.

Moshiko Raboh, Roei Herzig, Gal Chechik et al.

Reasoning about complex visual scenes involves perception of entities and their relations. Scene graphs provide a natural representation for reasoning tasks, by assigning labels to both entities (nodes) and relations (edges). Unfortunately, reasoning systems based on SGs are typically trained in a two-step procedure: First, training a model to predict SGs from images; Then, a separate model is created to reason based on predicted SGs. In many domains, it is preferable to train systems jointly in an end-to-end manner, but SGs are not commonly used as intermediate components in visual reasoning systems because being discrete and sparse, scene-graph representations are non-differentiable and difficult to optimize. Here we propose Differentiable Scene Graphs (DSGs), an image representation that is amenable to differentiable end-to-end optimization, and requires supervision only from the downstream tasks. DSGs provide a dense representation for all regions and pairs of regions, and do not spend modelling capacity on areas of the images that do not contain objects or relations of interest. We evaluate our model on the challenging task of identifying referring relationships (RR) in three benchmark datasets, Visual Genome, VRD and CLEVR. We describe a multi-task objective, and train in an end-to-end manner supervised by the downstream RR task. Using DSGs as an intermediate representation leads to new state-of-the-art performance.

Roei Herzig, Moshiko Raboh, Gal Chechik et al.

Machine understanding of complex images is a key goal of artificial intelligence. One challenge underlying this task is that visual scenes contain multiple inter-related objects, and that global context plays an important role in interpreting the scene. A natural modeling framework for capturing such effects is structured prediction, which optimizes over complex labels, while modeling within-label interactions. However, it is unclear what principles should guide the design of a structured prediction model that utilizes the power of deep learning components. Here we propose a design principle for such architectures that follows from a natural requirement of permutation invariance. We prove a necessary and sufficient characterization for architectures that follow this invariance, and discuss its implication on model design. Finally, we show that the resulting model achieves new state of the art results on the Visual Genome scene graph labeling benchmark, outperforming all recent approaches.