arXiv subjects

Sezin Kircali Ata

Publications and source records attributed to Sezin Kircali Ata.

3 recordsLinked to original sources

arXiv2026

FAPlace: Joint Optimization of Chiplet Placement and Interposer Footprint for 2.5D Systems

The placement of chiplets on a silicon interposer is a pivotal step in 2.5D system integration, yet existing placement approaches typically assume a pre-defined interposer footprint. This creates a circular dependency: the optimal footprint cannot be known without first solving the placement, while the placement itself is constrained by the given dimensions. An undersized interposer may exclude feasible placements, while an oversized one yields unnecessarily sparse solutions. Moreover, even when the footprint area is minimized, few existing approaches explicitly control the interposer's aspect ratio. To jointly address these challenges, we propose FAPlace, a footprint aware mask guided sequential placement framework. FAPlace operates on a sufficiently large canvas, eliminating the circular dependency by allowing the optimal interposer footprint to emerge as an output of the optimization rather than a pre-specified input. At its core is a novel footprint mask that fuses area compactness with an aspect ratio penalty into a unified spatial cost map. Integrated with wirelength and thermal guidance masks, FAPlace delivers holistic multi-physics optimization in a deterministic, single pass process. Experimental results demonstrate that FAPlace reduces wirelength and footprint area while achieving near-unity aspect ratios, without compromising on thermal performance.

cs.AR↗

arXiv2020

Recent Advances in Network-based Methods for Disease Gene Prediction

Disease-gene association through Genome-wide association study (GWAS) is an arduous task for researchers. Investigating single nucleotide polymorphisms (SNPs) that correlate with specific diseases needs statistical analysis of associations. Considering the huge number of possible mutations, in addition to its high cost, another important drawback of GWAS analysis is the large number of false-positives. Thus, researchers search for more evidence to cross-check their results through different sources. To provide the researchers with alternative low-cost disease-gene association evidence, computational approaches come into play. Since molecular networks are able to capture complex interplay among molecules in diseases, they become one of the most extensively used data for disease-gene association prediction. In this survey, we aim to provide a comprehensive and an up-to-date review of network-based methods for disease gene prediction. We also conduct an empirical analysis on 14 state-of-the-art methods. To summarize, we first elucidate the task definition for disease gene prediction. Secondly, we categorize existing network-based efforts into network diffusion methods, traditional machine learning methods with handcrafted graph features and graph representation learning methods. Thirdly, an empirical analysis is conducted to evaluate the performance of the selected methods across seven diseases. We also provide distinguishing findings about the discussed methods based on our empirical analysis. Finally, we highlight potential research directions for future studies on disease gene prediction.

q-bio.QM↗

arXiv2020

Multi-View Collaborative Network Embedding

Real-world networks often exist with multiple views, where each view describes one type of interaction among a common set of nodes. For example, on a video-sharing network, while two user nodes are linked if they have common favorite videos in one view, they can also be linked in another view if they share common subscribers. Unlike traditional single-view networks, multiple views maintain different semantics to complement each other. In this paper, we propose MANE, a multi-view network embedding approach to learn low-dimensional representations. Similar to existing studies, MANE hinges on diversity and collaboration - while diversity enables views to maintain their individual semantics, collaboration enables views to work together. However, we also discover a novel form of second-order collaboration that has not been explored previously, and further unify it into our framework to attain superior node representations. Furthermore, as each view often has varying importance w.r.t. different nodes, we propose MANE+, an attention-based extension of MANE to model node-wise view importance. Finally, we conduct comprehensive experiments on three public, real-world multi-view networks, and the results demonstrate that our models consistently outperform state-of-the-art approaches.

cs.LG↗