Protein-protein interactions (PPIs) govern nearly all cellular processes, yet computational methods for identifying binding partners typically produce ranked predictions without mechanistic justification. This creates a fundamental barrier to adoption because biologists cannot assess whether predictions reflect genuine biochemical insight or spurious correlations. We present \textbf{Protein Thoughts}, a framework that reformulates PPI discovery as an interpretable search problem with explicit reasoning. The system decomposes binding evidence into four biologically meaningful signals: sequence similarity reflecting evolutionary relationships, structural complementarity capturing geometric fit, interface balance, and chemical compatibility encoding residue-level interactions. Rather than collapsing these signals into an opaque score, we preserve their individual contributions through a transparent value function that enables both ranking and auditing. To navigate large candidate spaces efficiently, we introduce hypothesis-guided entropy-regularized Tree-of-Thoughts search. A fine-tuned language model generates search directives from embedding-derived features, classifying candidates as high-priority, exploratory, or skippable. These directives condition a Boltzmann policy that balances exploitation with entropy-driven exploration, while hypothesis-aware pruning prevents premature abandonment of promising candidates. For candidates exhibiting score disagreement, hypothesis-conditioned embedding-space flow matching transports protein embeddings toward the binder manifold. On the SHS148k benchmark, Protein Thoughts achieves mean best-binder rank of 11.2 versus 47.7 for an entropic tree search baseline, a 76% improvement, and for binding prediction the trained value function achieves $91.08 \pm 0.19$ Micro-F1, outperforming existing PPI methods on the same dataset.

Long-context inference is increasingly a memory-traffic problem. The culprit is the key--value (KV) cache: it grows with context length, batch size, layers, and heads, and it is read at every decoding step. Rotation-based scalar codecs meet this systems constraint by storing a norm, applying a shared random rotation, and quantizing one coordinate at a time. They are universal and random-access, but they discard the geometry created by the normalization step. After a Haar rotation, a block of $k$ consecutive coordinates is not a product source; it is a spherical-Beta source on the unit ball. We introduce \textsc{FibQuant}, a universal fixed-rate vector quantizer that keeps the same normalize--rotate--store interface while replacing scalar tables by a shared radial--angular codebook matched to this canonical source. The codebook combines Beta-quantile radii, Fibonacci\,/\,Roberts--Kronecker quasi-uniform directions, and multi-restart Lloyd--Max refinement. We prove that the resulting vector code strictly improves on its scalar product specialization at matched rate, with a high-rate gain that separates into a cell-shaping factor and a density-matching factor. The same construction gives a dense rate axis, including fractional-bit and sub-one-bit operating points, without calibration or variable-length addresses. On GPT-2 small KV caches, \textsc{FibQuant} traces a memory--fidelity frontier from $5\times$ compression at $0.99$ attention cosine similarity to $34\times$ at $0.95$. End-to-end on TinyLlama-1.1B, it is within $0.10$ perplexity of fp16 at $4\times$ compression and has $3.6\times$ lower perplexity than scalar \textsc{TurboQuant} at $b = 2$ ($8\times$ compression), where scalar random-access quantization begins to fail.

This paper studies the role of sinks and diagonal patterns as attention switch and anti-oversmoothing mechanisms. We analyze geometric conditions under which sinks can be represented, showing a necessary alignment between the embedding of the sink and all other embeddings. Next, we refine the current understanding of the role of sinks in oversmoothing prevention: we specify the conditions under which dense attention provably smooths more than sparse attention, and empirically verify that such conditions are often satisfied in practice. We further prove an equivalence between sinks and hard attention switch, in which the output of the attention is identically 0. Finally, we relax the hard attention switch by allowing token self-communication: we provide a quantitative comparison of the costs of representing sinks vs.\ diagonal patterns, showing why sinks are favored in pretrained transformers. The introduction and analysis of diagonal patterns and the generalization of the attention switch close the gap between what oversmoothing prevention requires and what sinks provide, while also establishing when and why attention layers act like MLPs if token communication is not necessary.

This paper introduces hyperspherical prototype networks, which unify classification and regression with prototypes on hyperspherical output spaces. For classification, a common approach is to define prototypes as the mean output vector over training examples per class. Here, we propose to use hyperspheres as output spaces, with class prototypes defined a priori with large margin separation. We position prototypes through data-independent optimization, with an extension to incorporate priors from class semantics. By doing so, we do not require any prototype updating, we can handle any training size, and the output dimensionality is no longer constrained to the number of classes. Furthermore, we generalize to regression, by optimizing outputs as an interpolation between two prototypes on the hypersphere. Since both tasks are now defined by the same loss function, they can be jointly trained for multi-task problems. Experimentally, we show the benefit of hyperspherical prototype networks for classification, regression, and their combination over other prototype methods, softmax cross-entropy, and mean squared error approaches.

Sparse Optimal Scoring (SOS) reformulates linear discriminant analysis to enable feature selection through elastic net regularization, making it well-suited for high-dimensional settings where the number of features exceeds observations. Most existing SOS methods use deflation-based strategies that compute discriminant vectors sequentially, which can propagate errors and produce suboptimal solutions. We propose a novel approach that estimates all discriminant vectors simultaneously under an explicit global orthogonality constraint, which we call Deflation-Free Sparse Optimal Scoring (DFSOS). DFSOS combines Bregman iteration with orthogonality-constrained optimization, decomposing the problem into tractable subproblems for scoring vectors, discriminant vectors, and orthogonality enforcement. We establish convergence to stationary points of the augmented Lagrangian under mild conditions. Extensive experiments using synthetic data and real-world time series data demonstrate that DFSOS achieves classification accuracy comparable to or better than existing deflation-based methods. These results indicate that deflation-free approaches offer a robust and effective framework for sparse discriminant analysis in high-dimensional problems.

Privacy Assessment on Reconstructed Images: Are Existing Evaluation Metrics Faithful to Human Perception? In Section 4.1, we briefly introduced how humans annotate the reconstructed images for different datasets. In the supplementary material, we have included a graphical user interface (GUI) that was utilized by the annotators. Figure 1 displays the GUI, where (A) and (B) were specifically designed for annotating different datasets. To minimize the influence of subjective bias, we use a relatively objective formulation: whether the reconstructed image can be correctly labeled.

We introduce Holographic Invariant Storage (HIS), a protocol that assembles known properties of bipolar Vector Symbolic Architectures into a design-time safety contract for LLM context-drift mitigation. The contract provides three closed-form guarantees evaluable before deployment: single-signal recovery fidelity converging to $1/\sqrt{2} \approx 0.707$ (regardless of noise depth or content), continuous-noise robustness $2Φ(1/σ) - 1$, and multi-signal capacity degradation $\approx\sqrt{1/(K+1)}$. These bounds, validated by Monte Carlo simulation ($n = 1{,}000$), enable a systems engineer to budget recovery fidelity and codebook capacity at design time -- a property no timer or embedding-distance metric provides. A pilot behavioral experiment (four LLMs, 2B--7B, 720 trials) confirms that safety re-injection improves adherence at the 2B scale; full results are in an appendix.

Neural Information Processing Systems http://nips.cc/