arXiv subjects

Milad Salem

Publications and source records attributed to Milad Salem.

4 recordsLinked to original sources

arXiv2026

Accurate structural modeling of chemically diverse molecular interfaces with Vilya-2

Structure-prediction networks built on co-evolutionary statistics have transformed protein-based drug discovery, yet their accuracy does not extend to peptide therapeutics--an increasingly important modality defined by non-canonical residues, macrocyclization, and complex topologies. We introduce Vilya-2, a diffusion transformer that extends the all-atom representation of Vilya-1 from modeling individual molecules to modeling their interactions with protein targets. This all-atom representation enables transfer learning between different molecular types, and delivers highly accurate structural modeling of peptides across sizes, classes, and compositions bound to therapeutically relevant targets. By generating diverse structural ensembles and ranking them with calibrated confidence, Vilya-2 recovers 59.1% of peptide interfaces to sub-2 {\AA} backbone RMSD, far exceeding the performance of a representative co-folding model even when that model is given the bound receptor as a template. In addition, Vilya-2 is state-of-the-art at small-molecule docking, and generalizes to novel protein-small molecule complexes unlike those seen in training. It also generalizes to modeling molecular conformations of diverse macrocycles and disulfide-stapled miniproteins several-fold larger than any molecule seen in training. Finally, Vilya-2 can be used as a foundation model, and fine-tuned to enrich for active compounds in hit-to-lead campaigns. By unifying predictive accuracy with broad generalizability across chemical space, Vilya-2 is the structure-prediction oracle that de novo peptide design pipelines require--establishing the all-atom approach as a general foundation for the design and evaluation of de novo peptide therapeutics.

cs.LG↗

arXiv2026

Vilya-1: An all-atom foundation model for macrocycle structure prediction and design

Macrocyclic peptides are an increasingly important therapeutic modality, but existing computational methods for modeling their structures and properties are limited in scope and do not generalize well across the synthetically accessible chemical space. In this work, we introduce Vilya-1, a deep learning model that addresses two central challenges in macrocycle design: sampling biologically relevant conformations across arbitrary chemistries and predicting key developability properties such as membrane permeability. Vilya-1 operates on a uniform all-atom representation and is trained on heterogeneous structural datasets spanning diverse topologies and chemical classes. Across a broad set of macrocycles composed of canonical and non-canonical residues, Vilya-1 substantially improves geometric accuracy relative to physics-based methods, co-folding networks, and deep-learning conformer generators, while maintaining broad chemical coverage that extends to small molecules. Vilya-1 also supports generative applications, enabling the design of novel macrocycles with tailored chemical, structural, and property profiles. Together, these capabilities establish Vilya-1 as a foundation model for accelerating the development of next-generation macrocycle therapeutics.

cs.LG↗

arXiv2018

ECG Arrhythmia Classification Using Transfer Learning from 2-Dimensional Deep CNN Features

Due to the recent advances in the area of deep learning, it has been demonstrated that a deep neural network, trained on a huge amount of data, can recognize cardiac arrhythmias better than cardiologists. Moreover, traditionally feature extraction was considered an integral part of ECG pattern recognition; however, recent findings have shown that deep neural networks can carry out the task of feature extraction directly from the data itself. In order to use deep neural networks for their accuracy and feature extraction, high volume of training data is required, which in the case of independent studies is not pragmatic. To arise to this challenge, in this work, the identification and classification of four ECG patterns are studied from a transfer learning perspective, transferring knowledge learned from the image classification domain to the ECG signal classification domain. It is demonstrated that feature maps learned in a deep neural network trained on great amounts of generic input images can be used as general descriptors for the ECG signal spectrograms and result in features that enable classification of arrhythmias. Overall, an accuracy of 97.23 percent is achieved in classifying near 7000 instances by ten-fold cross validation.

cs.LG↗

arXiv2018

Anomaly Generation using Generative Adversarial Networks in Host Based Intrusion Detection

Generative adversarial networks have been able to generate striking results in various domains. This generation capability can be general while the networks gain deep understanding regarding the data distribution. In many domains, this data distribution consists of anomalies and normal data, with the anomalies commonly occurring relatively less, creating datasets that are imbalanced. The capabilities that generative adversarial networks offer can be leveraged to examine these anomalies and help alleviate the challenge that imbalanced datasets propose via creating synthetic anomalies. This anomaly generation can be specifically beneficial in domains that have costly data creation processes as well as inherently imbalanced datasets. One of the domains that fits this description is the host-based intrusion detection domain. In this work, ADFA-LD dataset is chosen as the dataset of interest containing system calls of small foot-print next generation attacks. The data is first converted into images, and then a Cycle-GAN is used to create images of anomalous data from images of normal data. The generated data is combined with the original dataset and is used to train a model to detect anomalies. By doing so, it is shown that the classification results are improved, with the AUC rising from 0.55 to 0.71, and the anomaly detection rate rising from 17.07% to 80.49%. The results are also compared to SMOTE, showing the potential presented by generative adversarial networks in anomaly generation.

cs.LG↗