ECHO-PPI: Trustworthy AI for Evidence-Bundled Detection of Overlapping Protein Modules in Protein–Protein Interaction Networks 1. ECHO-PPI is an evidence-bundled framework for overlapping module detection in PPI networks that explicitly targets curator-facing interpretability: every protein–module assignment is exported with an auditable bundle of topology, semantic, and Gene Ontology (GO) evidence, plus a hierarchical confidence label (core/inner/outer/uncertain). 2. The key design shift is from “module lists” to “assignment-level decision support”: instead of only returning overlapping communities, ECHO-PPI records why a specific protein is placed into a specific module, and whether that membership should be treated as strong (core) or boundary/triage (inner/outer/uncertain). 3. The workflow integrates three evidence channels: (i) weighted PPI topology, (ii) semantic protein profiles (TF–IDF SVD embeddings of text/GO labels; Sentence-BERT is optional but not used in reported benchmarks), and (iii) GO evidence via module-specific GO TF–IDF “functional signatures,” while treating missing GO as missing evidence rather than biological absence. 4. For overlap-aware membership scoring, ECHO-PPI combines a boundary-sensitive topology metric (permanence) with functional dependency (alignment of a protein’s GO terms to a module’s GO TF–IDF signature) using a transparent mixture score M(p, C) = α Perm(p, C) (1−α) fd(p, C). Overlaps are added only if they improve the best existing assignment by a margin (gain threshold), with a conservative transfer rule for likely misplacements. 5. Candidate generation is broadened beyond a single clustering output: starting from MCL modules, ECHO-PPI adds nucleus-centered ego neighborhoods (1–2 hops), greedy topology–semantic expansions, semantic kNN sets that pass a graph-support filter, and hybrid unions when candidate Jaccard overlap is high; candidates are then scored with penalties for uncertainty and fragmentation. 6. A distinctive component is the deterministic “evidence-potential nucleus” score (BH), inspired by gravity-based representative selection, to prioritize high-support local nuclei using weighted degree, clustering coefficient, k-core, semantic neighborhood coherence, GO richness, and an annotation-sparsity penalty. Importantly, nuclei guide candidate construction and ranking rather than defining the final partition alone. 7. ECHO-PPI adds “recall-safe supplementation” to avoid the common failure mode of naive boundary expansion: it limits growth (≤15% relative size increase, at most two added proteins per module) and requires gated evidence gain, so expansions remain conservative and reviewable. 8. Confidence labeling is hierarchical and evidence-based: core requires both topology and semantic support above thresholds; inner/outer require weaker support; uncertain captures boundary cases. The paper emphasizes these labels as triage metadata (especially core vs non-core), not as calibrated probabilities, and reports how label distributions can shift with preprocessing and embedding normalization. 9. Benchmarking on yeast (Gavin socioaffinity network; plus a Krogan 2006 BioGRID-derived transfer benchmark) shows ECHO-PPI largely preserves the predictive behavior of the MCL overlap seed rather than outperforming the strongest baseline (ClusterONE). On Gavin full-gold, ClusterONE leads (F1 0.270) while ECHO-PPI matches MCL-scale performance (F1 0.162) but uniquely delivers complete required-field evidence-bundle coverage (1.00 vs 0.00 for baselines). 10. The paper’s central claim is therefore complementary to pure F1 optimization: ECHO-PPI makes overlapping module predictions inspectable, confidence-aware, and reproducible. Case studies (e.g., YKR018C, YIL161W) illustrate multi-membership outputs where semantic evidence can dominate topology in some assignments, explicitly signaling “hypotheses for manual review” rather than silently promoting all overlaps to equally strong complex memberships. 💻Code: github.com/MehrdadJalali-AI/… 📜Paper: arxiv.org/abs/2605.21216 #computationalbiology #bioinformatics #PPI #proteininteractions #networkscience #communitydetection #interpretableAI #trustworthyAI #GeneOntology #reproducibility

音圧はそう大した事はないけど、ピンポイントの周波数帯でしっかりと音を出す事が出来ると思うんよ。ピンクフロイドの　ClusterOneのピアノに代表されるような暗くてスムーズなザ・ドリーム-ハウスピアノがいい！　 youtu.be/hz9lusYH6Ag

ClusterOne designed by Studio MM, pllc features Stûv 16-in fireplace boasting a new innovative combustion system offering a panoramic view of flames buff.ly/LhQBDUB

Studio MM’s ClusterOne in upstate New York is defined by dual stucco-clad volumes, Castor and Pollux, joined by a floating glass hallway. buff.ly/w7UYUot #TimberAndGlass #StuccoDesign #MaterialExpression

ClusterOne Residence by Studio MM Architect #building #architects #design #architecture #illustrarch

I had a courtesy meeting with Mr. Niko Peleshi in his new capacity as Chair of SP parliamentary group. Opening of negotiations ClusterOne is a momentum for all actors in AL to engage & contribute in strengthening democracy & prepare for free and fair elections in 2025. 🇳🇱🤝🇦🇱

Fight against corruption & org. crime needs politics, institutions & civil society to contribute. Our MATRA project - ClusterOne Platform held an open discussion on SPAK and Special Court, Albania’s invaluable game-changers.

We are so so so excited to share the long-awaited final photos of ClusterOne! bit.ly/3yW71wx #ClusterOne #studiommarchitect

#nowplaying Pink Floyd - Cluster One (360 Reality Audio / Official Audio) via @YOUTUBE youtube.com/watch?v=r5qKD_JI… #PinkFloyd #ClusterOne #TheDivisionBell #360RealityAudio #OfficialAudio #progrock #instrumental #warble #なうぷりべか

Happy to see students so interested &willing to share thoughts, insights, speaking up on matters of EU integration process. Is there light at the end of the tunnel? Undoubtably so! 👏@AlbaniaCluster @ISP_Institute @CSDGALBANIA @IKomiteti #ClusterOne #MATRA #NLstrictfairengaged

28.03.1994 Há 30 anos,Pink Floyd lançava The Division Bell,e provava que era possível continuar sem Roger Waters. #divisionbell #thedivisionbell #pinkfloyd #davidgilmour #sydbarrett #rogerwaters #marooned #clusterone #music #30thbirthday #30th #30anos #1994

深夜のインライ ありがとうございました😭 明日はclusterONE MAN LIVE 21:00〜です！！ 是非お待ちしてます☺️ おやすみ😴

2023.12.20 MASA #cluster ONE MAN LIVE 今日はいつもと違う内容で お送りしました✨ -2023ラストセトリ- 🎄クリスマスソング ・ベテルギウス ・メリクリ ・Last Christmas 🍊オリジナルソング ・ハピネス ・MAGIC TIME ・ありのまま 遅い時間にも関わらずお越し頂き ありがとうございました！！ clusterONE MAN史上 1番長い時間MCしました🥹 想い伝わったら嬉しいです。 ✅12月23日の たりほんChristmas LIVE が最後の大舞台🔥 是非見にきてください！！ 🎫:tarihonn.stores.jp #まさいずむ #MASA #ありのまま #ハピネス #クリスマス #cluster #メタバース

年内ラストのclusterONE MAN！！！ SMBリーダーのLIVE 是非観にいこー！！

He deffo is a

Sometimes it’s for the best m8 🤣

thinks he banned an account that is still there and i have to switch to an account that he got banned and is not there. fecking hun logic or drugs😂😂😂

so you want me to switch to an account that you reported for sectarian tweets but you can't show the sectarian tweets and i can't switch to the account as it is banned now? is this some kind of hun logic thing? thanks for the screengrabs as this is hilarious😂😂

what cluster account did you get banned? i can only find one and he posted today. Did you get him banned today?

so the cluster account that has been posting for years you got banned is not the cluster account you got banned? what account did you get banned?